Last edit: 05-08-29 Graham Wideman
| Last edit: 05-08-29 Graham Wideman |
FreeSurfer |
| FreeSurfer Program and File Survey Article created: 2003-01-20 |
The following is a survey of programs and files provided with: Harvard MGH FreeSurfer, "current" version (2001-10).
This survey omits several directories, notably the AFNI and MNI tools which are surveyed separately.
For an explanation of the Program and File Survey, see here.
2003-01-27 Notes: Some FreeSurfer program files are particularly tricky to survey, because of the multiple conventions (which flags, or possibly no flags) used to elicit help info, and in whether that info is delivered to stdout or stderr. The current listing below is a worthwhile start, but could be improved. I've also since noticed that several programs generate more than one help/usage output, with the two variants actually conflicting with each other. In some cases, one of the outputs is clearly a left over message from code that was stolen from some other exectable. In other cases, which output is correct is more ambiguous. Sooner or later I may revisit the surveyor program and make it more persistent in eliciting all help variants for closer scrutiny, and flagging inconsistencies.
| /binfs/freesurfer_alpha/ | |||
|
#SOURCE_ME_TO_RECONSTRUCT# /binfs/freesurfer_alpha/ |
#: 1 Sz: 396 |
6/20/2001 2:06:25 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
#tkmeditColorsCMA# /binfs/freesurfer_alpha/ |
#: 2 Sz: 5293 |
8/2/2001 7:29:50 AM | ASCII text |
|
christophe_parc.txt /binfs/freesurfer_alpha/ |
#: 3 Sz: 3702 |
3/15/2001 11:43:15 AM | ASCII text, with CRLF line terminators |
|
FreeSurferDefs.csh /binfs/freesurfer_alpha/ |
#: 4 Sz: 1591 |
8/14/2001 8:33:21 AM | C shell script text executable |
#! /bin/csh ############################################################################ # $CSURF_DIR/FreeSurferDefs.csh: setup environment for FreeSurfer (csh,tsch) ############################################################################ ### need these 3 to run FreeSurfer programs (user .cshrc setenv's override) |
|||
|
FreeSurferEnv.csh /binfs/freesurfer_alpha/ |
#: 5 Sz: 6343 |
5/31/2001 4:31:38 PM | ASCII English text |
|
ic8.tri /binfs/freesurfer_alpha/ |
#: 6 Sz: 56441176 |
3/14/2001 3:21:59 PM | ASCII text |
|
INSTALL /binfs/freesurfer_alpha/ |
#: 7 Sz: 3457 |
8/2/2001 1:54:03 PM | ASCII English text |
|
InverseDefs.csh /binfs/freesurfer_alpha/ |
#: 8 Sz: 1285 |
10/5/2000 7:42:45 AM | ASCII text |
|
IRIX /binfs/freesurfer_alpha/ |
#: 9 Sz: 2521264 |
9/1/2001 10:06:15 AM | ELF 32-bit MSB MIPS-I executable, MIPS, version 1 |
|
Linux /binfs/freesurfer_alpha/ |
#: 10 Sz: 2173652 |
9/1/2001 10:05:14 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <subject name> <hemisphere> This program positions the tessellation of the cortical surface at the white matter surface, then the gray matter surface and generate surface files for these surfaces as well as a 'curvature' file for the cortical thickness, and a surface file which approximates layer IV of the cortical sheet. valid options are: -q omit self-intersection and only generate gray/white surface. -c create curvature and area files from white matter surface -a <avgs> average curvature values <avgs> times (default=10) -whiteonly only generate white matter surface |
|||
|
nmr-std-env /binfs/freesurfer_alpha/ |
#: 11 Sz: 2750 |
5/31/2001 4:18:57 PM | ASCII English text |
|
nmr-std-env~ /binfs/freesurfer_alpha/ |
#: 12 Sz: 2765 |
10/24/2000 10:26:40 AM | ASCII English text |
|
noarch /binfs/freesurfer_alpha/ |
#: 13 Sz: 76954 |
5/25/2001 8:15:08 AM | a /usr/bin/wish script text executable |
#!/usr/bin/wish # this script looks at the headers of ima files in a predetermined archive direc tory. The default archive directory is over-ridden by the environment variable A RCHIVE_DIR. the user selcets a session and the path to that session is proveded to the script that copies the relevant files via nfs to the local machine and un packs them locally into b shorts. #--------------------------------------------------------------------------------------# #Structure of this script: #global variables #subroutines # dialogs # functions #widgets #bindings #main #--------------------------------------------------------------------------------------# #export ALPHA_BIN=/space/annecy/5/users/inverse/freesurfer_alpha/bin #cp unpack_ima.tcl $ALPHA_BIN/noarch #export PATH=$PATH:$ALPHA_BIN/noarch #export PATH=$PATH:$ALPHA_BIN/Linux #----------------------------------------------------------------------------------------# # global variable defined elsewhere # sessionNumber: integer 0-N, numerical order of sessions read # # session(sessionNumber, fieldValue) A 2-D array containing all that is known about the sessions. # The field Keys are: # 0 patient_name # 1 patient_ID # 2 study_date # 3 registration_date # 4 registration_time # 5 experimenter # 6 experiment_name # 7 path to first file in session directory # # displayedSessions A list containing the "session" indices which are currently displayed # in the list box #-----------------------------------------------------------------------------------------# #define needed variables |
|||
|
README /binfs/freesurfer_alpha/ |
#: 14 Sz: 887 |
4/5/2000 12:14:23 PM | ASCII English text |
|
scanseq.unpackinfo /binfs/freesurfer_alpha/ |
#: 15 Sz: 4015 |
5/14/2001 10:20:23 AM | ASCII text |
|
Solaris /binfs/freesurfer_alpha/ |
#: 16 Sz: 2152532 |
9/1/2001 10:05:42 AM | ELF 32-bit MSB executable, SPARC, version 1 (SYSV) |
|
tar-exclude-more /binfs/freesurfer_alpha/ |
#: 17 Sz: 1406 |
5/31/2001 3:37:05 PM | ASCII text |
|
tkmeditColorsCMA /binfs/freesurfer_alpha/ |
#: 18 Sz: 5292 |
6/28/2001 11:42:22 AM | ASCII text |
|
tkmeditColorsCMA~ /binfs/freesurfer_alpha/ |
#: 19 Sz: 5161 |
6/28/2001 8:16:39 AM | ASCII text |
| /binfs/freesurfer_alpha/afni/ | |||
| /binfs/freesurfer_alpha/afni/ Skipped directory per survey instructions | |||
|
AVW2COR.m /binfs/freesurfer_alpha/afni/ |
#: 20 Sz: 1626 |
9/7/2000 3:28:04 PM | MatLab script |
function AVW2COR(fname,pathlocation)
% Converts an AVW volume to COR-* files
% AVW2COR function to translate an 8-bit
% uchar AVW file to a series of MGH-style
% COR files that also have an 8-bit uchar
% datatype.
% Example: AVW2COR('Registered3Mean.img','/data9/tim/Surfaces/spgr_one')
% will read in the volume RegisteredVol.img
% and output files named /data9/tim/Surfaces/COR-[0-256]*
% Written 1/21/99: Timothy M. Ellmore, LBC/NIMH
% an afni BRIK may be formed from the resulting COR files with the command
%to3d -anat -prefix raw -session $SUBJECTS_DIR/$subjname/afni \
% -view orig -datum byte -orient LSP $SUBJECTS_DIR/$subjname/mri/orig/COR-\[0-256]\*
% for MGH flattening COR files have these dimensions
|
|||
|
BRIK2MGH.m /binfs/freesurfer_alpha/afni/ |
#: 21 Sz: 1797 |
9/7/2000 3:28:04 PM | MatLab script |
function BRIK2MGH(fname,xdim,ydim,zdim,timepoints,type,foutstem)
% BRIK2MGH function to read 3D+time AFNI BRIK
% of any type and dimensionality and convert
% to MGH-style bshort of bfloat files and
% accompanying MGH header files
%
% Example: this writes out 16 .bshort and .hdr files
% BRIK2MGH('/data9/mike/AS/afni/ASt3avvr+orig.BRIK',64,64,16,100,'short','test_')
%
% Written December 11, 1998 by Timothy M. Ellmore
% Laboratory of Brain and Cognition, NIMH
|
|||
|
COR2AVW.m /binfs/freesurfer_alpha/afni/ |
#: 22 Sz: 2440 |
9/7/2000 3:28:04 PM | MatLab script |
function COR2AVW(fname,volfname,hdrflag)
% Converts a list of COR-* files to an AVW volume
% COR2AVW function to translate MGH-style COR
% files produces with the Dale flattening
% software to an AVW volume. COR files are
% always have 8-bit unsigned char datatype,
% so the output volume will have that here
% as well.
% Example: COR2AVW('images.txt','TestVol','y')
% will read in COR files listed in images.txt
% and output files TestVol.hdr and TestVol.img
% Written 1/21/99: Timothy M. Ellmore, LBC/NIMH
% Converts a list of COR-* files to an AVW volume
% for MGH flattening COR files have these dimensions
|
|||
|
MakeSurf.tcl /binfs/freesurfer_alpha/afni/ |
#: 23 Sz: 6545 |
9/7/2000 3:28:04 PM | a /usr/local/bin/tclsh |
#!/usr/local/bin/tclsh # MakeSurf.tcl: Menu-Driven Surface Based Processing # # Written by: # Timothy M. Ellmore, LBC/NIMH/NIH, Started October 1998 # # With lots of help, suggestions and encouragement from: # Michael S. Beauchamp, Ph.D, LBC/NIMH/NIH # John D. Van Horn, Ph.D, LBC/NIMH/NIH # # MakeSurf.tcl Implements and further automates the surface-based # analysis programs designed and written by Anders Dale, Martin # Sereno and Bruce Fischl at Massachusetts General Hospital. # This scheme is described in more detail in: # # Dale AM, Fischl B, Sereno MI. Cortical Surface-Based Analysis I: # Segmentation and Surface Reconstruction. (to be published) # # Fischl B, Sereno MI, Dale AM. Cortical Surface-Based Analysis II: # Surface-Based Coordinate System. (to be published) # # MakeSurf.tcl was last modified on: March 4, 1999 # # Beginning of Menu-Driven Surface Processing Script # # platform dependent definitions |
|||
|
MakeSurfTools.tcl /binfs/freesurfer_alpha/afni/ |
#: 24 Sz: 139846 |
9/7/2000 3:28:04 PM | ASCII English text, with CRLF line terminators |
|
README.afni /binfs/freesurfer_alpha/afni/ |
#: 25 Sz: 156 |
9/7/2000 3:31:11 PM | ASCII English text |
| /binfs/freesurfer_alpha/afni/IRIX/ Skipped directory per survey instructions | |||
| /binfs/freesurfer_alpha/afni/Linux/ | |||
|
1dplot /binfs/freesurfer_alpha/afni/Linux/ |
#: 26 Sz: 906648 |
9/7/2000 3:28:06 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 1dplot [options] tsfile
Graphs the columns of a *.1D type time series file to the screen.
Options:
-sep = Plot each column in a separate sub-graph.
-one = Plot all columns together in one big graph.
[default = -sep]
-dx xx = Spacing between points on the x-axis is 'xx'
[default = 1]
-ignore nn = Skip first 'nn' rows in the input file
[default = 0]
-xlabel aa = Put string 'aa' below the x-axis
[default = no axis label]
-ylabel aa = Put string 'aa' to the left of the y-axis
[default = no axis label]
-ynames aa bb ... = Use the strings 'aa', 'bb', etc., as
labels to the right of the graphs,
corresponding to each input column.
These strings CANNOT start with the
'-' character.
-volreg = Makes the 'ynames' be the same as the
6 labels used in plug_volreg for
Roll, Pitch, Yaw, I-S, R-L, and A-P
movements, in that order.
You may also select a subset of columns to display using
a tsfile specification like 'fred.1D[0,3,5]', indicating
that columns #0, #3, and #5 will be the only ones plotted.
For more details on this selection scheme, see the output
of '3dcalc -help'.
Example: graphing a 'dfile' output by 3dvolreg, when TR=5:
1dplot -volreg -dx 5 -xlabel Time 'dfile[1..6]'
|
|||
|
24swap /binfs/freesurfer_alpha/afni/Linux/ |
#: 27 Sz: 18148 |
9/7/2000 3:28:06 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 24swap [options] file ...
Swaps bytes pairs and/or quadruples on the files listed.
Options:
-q Operate quietly
-pattern pat 'pat' determines the pattern of 2 and 4
byte swaps. Each element is of the form
2xN or 4xN, where N is the number of
bytes to swap as pairs (for 2x) or
as quadruples (for 4x). For 2x, N must
be divisible by 2; for 4x, N must be
divisible by 4. The whole pattern is
made up of elements separated by colons,
as in '-pattern 4x39984:2x0'. If bytes
are left over after the pattern is used
up, the pattern starts over. However,
if a byte count N is zero, as in the
example, then it means to continue until
the end of file.
N.B.: A default pattern can be stored in the Unix
environment variable AFNI_24SWAP_PATTERN.
If no -pattern option is given, the default
will be used. If there is no default, then
nothing will be done.
N.B.: If there are bytes 'left over' at the end of the file,
they are written out unswapped. This will happen
if the file is an odd number of bytes long.
N.B.: If you just want to swap pairs, see program 2swap.
For quadruples only, see program 4swap.
N.B.: This program will overwrite the input file!
You might want to test it first.
Example: 24swap -pat 4x8:2x0 fred
If fred contains 'abcdabcdabcdabcdabcd' on input,
then fred has 'dcbadcbabadcbadcbadc' on output.
|
|||
|
2dImReg /binfs/freesurfer_alpha/afni/Linux/ |
#: 28 Sz: 408484 |
9/7/2000 3:28:07 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 2dImReg
Date: 10 September 1999
entered initialize_program
This program performs 2d image registration. Image alignment is
performed on a slice-by-slice basis for the input 3d+time dataset,
relative to a user specified base image.
Usage:
2dImReg
-input fname Filename of input 3d+time dataset to process
-basefile fname Filename of 3d+time dataset for base image
(default = current input dataset)
-base num Time index for base image (0 <= num)
(default: num = 3)
-nofine Deactivate fine fit phase of image registration
(default: fine fit is active)
-fine blur dxy dphi Set fine fit parameters
where:
blur = FWHM of blurring prior to registration (in pixels)
(default: blur = 1.0)
dxy = Convergence tolerance for translations (in pixels)
(default: dxy = 0.07)
dphi = Convergence tolerance for rotations (in degrees)
(default: dphi = 0.21)
-prefix pname Prefix name for output 3d+time dataset
-dprefix dname Write files 'dname'.dx, 'dname'.dy, 'dname'.psi
containing the registration parameters for each
slice in chronological order.
File formats:
'dname'.dx: time(sec) dx(pixels)
'dname'.dy: time(sec) dy(pixels)
'dname'.psi: time(sec) psi(degrees)
-dmm Change dx and dy output format from pixels to mm
-rprefix rname Write files 'rname'.oldrms and 'rname'.newrms
containing the volume RMS error for the original
and the registered datasets, respectively.
File formats:
'rname'.oldrms: volume(number) rms_error
'rname'.newrms: volume(number) rms_error
-debug Lots of additional output to screen
|
|||
|
2swap /binfs/freesurfer_alpha/afni/Linux/ |
#: 29 Sz: 5268 |
9/7/2000 3:28:07 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 2swap [-q] file ... -- Swaps byte pairs on the files listed. The -q option means to work quietly. |
|||
|
3dANOVA /binfs/freesurfer_alpha/afni/Linux/ |
#: 30 Sz: 268120 |
9/7/2000 3:28:07 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dANOVA
Author: B. Douglas Ward
Date: 08 September 1999
This program performs single factor ANOVA on 3D data sets
Usage:
3dANOVA
-levels r r = number of factor levels
-dset 1 filename data set for factor level 1
. . . . . .
-dset 1 filename data set for factor level 1
. . . . . .
-dset r filename data set for factor level r
. . . . . .
-dset r filename data set for factor level r
[-voxel num] screen output for voxel # num
[-diskspace] print out disk space required for
program execution
The following commands generate individual AFNI 2 sub-brick datasets:
(In each case, output is written to the file with the specified
prefix file name.)
[-ftr prefix] F-statistic for treatment effect
[-mean i prefix] estimate of factor level i mean
[-diff i j prefix] difference between factor levels
[-contr c1...cr prefix] contrast in factor levels
The following command generates one AFNI 'bucket' type dataset:
[-bucket prefix] create one AFNI 'bucket' dataset whose
sub-bricks are obtained by concatenating
the above output files; the output 'bucket'
is written to file with prefix file name
|
|||
|
3dANOVA2 /binfs/freesurfer_alpha/afni/Linux/ |
#: 31 Sz: 287640 |
9/7/2000 3:28:08 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dANOVA2
Author: B. Douglas Ward
Date: 09 September 1999
This program performs two-factor ANOVA on 3D data sets
Usage:
3dANOVA2
-type k type of ANOVA model to be used:
k=1 fixed effects model (A and B fixed)
k=2 random effects model (A and B random)
k=3 mixed effects model (A fixed, B random)
-alevels a a = number of levels of factor A
-blevels b b = number of levels of factor B
-dset 1 1 filename data set for level 1 of factor A
and level 1 of factor B
. . . . . .
-dset i j filename data set for level i of factor A
and level j of factor B
. . . . . .
-dset a b filename data set for level a of factor A
and level b of factor B
[-voxel num] screen output for voxel # num
[-diskspace] print out disk space required for
program execution
The following commands generate individual AFNI 2 sub-brick datasets:
(In each case, output is written to the file with the specified
prefix file name.)
[-ftr prefix] F-statistic for treatment effect
[-fa prefix] F-statistic for factor A effect
[-fb prefix] F-statistic for factor B effect
[-fab prefix] F-statistic for interaction
[-amean i prefix] estimate mean of factor A level i
[-bmean j prefix] estimate mean of factor B level j
[-xmean i j prefix] estimate mean of cell at level i of
factor A, level j of factor B
[-adiff i j prefix] difference between levels i and j of
factor A
[-bdiff i j prefix] difference between levels i and j of
factor B
[-xdiff i j k l prefix] difference between cell mean at A=i,B=j
and cell mean at A=k,B=l
[-acontr c1 ... ca prefix] contrast in factor A levels
[-bcontr c1 ... cb prefix] contrast in factor B levels
[-xcontr c11 ... c1b c21 ... c2b ... ca1 ... cab prefix]
contrast in cell means
The following command generates one AFNI 'bucket' type dataset:
[-bucket prefix] create one AFNI 'bucket' dataset whose
sub-bricks are obtained by concatenating
the above output files; the output 'bucket'
is written to file with prefix file name
|
|||
|
3dANOVA3 /binfs/freesurfer_alpha/afni/Linux/ |
#: 32 Sz: 303928 |
9/7/2000 3:28:08 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dANOVA3
Author: B. Douglas Ward
Date: 09 September 1999
This program performs three-factor ANOVA on 3D data sets.
Usage:
3dANOVA3
-type k type of ANOVA model to be used:
k = 1 A,B,C fixed; AxBxC
k = 2 A,B,C random; AxBxC
k = 3 A fixed; B,C random; AxBxC
k = 4 A,B fixed; C random; AxBxC
k = 5 A,B fixed; C random; AxB,BxC,C(A)
-alevels a a = number of levels of factor A
-blevels b b = number of levels of factor B
-clevels c c = number of levels of factor C
-dset 1 1 1 filename data set for level 1 of factor A
and level 1 of factor B
and level 1 of factor C
. . . . . .
-dset i j k filename data set for level i of factor A
and level j of factor B
and level k of factor C
. . . . . .
-dset a b c filename data set for level a of factor A
and level b of factor B
and level c of factor C
[-voxel num] screen output for voxel # num
[-diskspace] print out disk space required for
program execution
The following commands generate individual AFNI 2 sub-brick datasets:
(In each case, output is written to the file with the specified
prefix file name.)
[-fa prefix] F-statistic for factor A effect
[-fb prefix] F-statistic for factor B effect
[-fc prefix] F-statistic for factor C effect
[-fab prefix] F-statistic for A*B interaction
[-fac prefix] F-statistic for A*C interaction
[-fbc prefix] F-statistic for B*C interaction
[-fabc prefix] F-statistic for A*B*C interaction
[-amean i prefix] estimate of factor A level i mean
[-bmean i prefix] estimate of factor B level i mean
[-cmean i prefix] estimate of factor C level i mean
[-xmean i j k prefix] estimate mean of cell at factor A level i,
factor B level j, factor C level k
[-adiff i j prefix] difference between factor A levels i and j
[-bdiff i j prefix] difference between factor B levels i and j
[-cdiff i j prefix] difference between factor C levels i and j
[-xdiff i j k l m n prefix] difference between cell mean at A=i,B=j,
C=k, and cell mean at A=l,B=m,C=n
[-acontr c1...ca prefix] contrast in factor A levels
[-bcontr c1...cb prefix] contrast in factor B levels
[-ccontr c1...cc prefix] contrast in factor C levels
The following command generates one AFNI 'bucket' type dataset:
[-bucket prefix] create one AFNI 'bucket' dataset whose
sub-bricks are obtained by concatenating
the above output files; the output 'bucket'
is written to file with prefix file name
|
|||
|
3daxialize /binfs/freesurfer_alpha/afni/Linux/ |
#: 33 Sz: 460128 |
9/7/2000 3:28:17 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 3daxialize [options] dataset
Purpose: Read in a dataset and write it out as a new dataset
with the data brick oriented as axial slices.
The input dataset must have a .BRIK file.
One application is to create a dataset that can
be used with the AFNI volume rendering plugin.
Options:
-prefix ppp = Use 'ppp' as the prefix for the new dataset.
[default = 'axialize']
-verbose = Print out a progress pacifier.
|
|||
|
3dbuc2fim /binfs/freesurfer_alpha/afni/Linux/ |
#: 34 Sz: 245028 |
9/7/2000 3:28:18 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program 3dbuc2fim
Last revision: 18 March 1998
This program converts bucket sub-bricks to fim (fico, fitt, fift, ...)
type dataset.
Usage:
3dbuc2fim -prefix pname d1+orig[index]
This produces a fim dataset.
-or-
3dbuc2fim -prefix pname d1+orig[index1] d2+orig[index2]
This produces a fico (fitt, fift, ...) dataset,
depending on the statistic type of the 2nd subbrick,
with d1+orig[index1] -> intensity sub-brick of pname
d2+orig[index2] -> threshold sub-brick of pname
-or-
3dbuc2fim -prefix pname d1+orig[index1,index2]
This produces a fico (fitt, fift, ...) dataset,
depending on the statistic type of the 2nd subbrick,
with d1+orig[index1] -> intensity sub-brick of pname
d1+orig[index2] -> threshold sub-brick of pname
where the options are:
-prefix pname = Use 'pname' for the output dataset prefix name.
OR -output pname [default='buc2fim']
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
-verb = Print out some verbose output as the program
proceeds
Command line arguments after the above are taken as input datasets.
A dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
Sub-brick indexes start at 0.
N.B.: The sub-bricks are output in the order specified, which may
not be the order in the original datasets. For example, using
fred+orig[5,3]
will cause the sub-brick #5 in fred+orig to be output as the intensity
sub-brick, and sub-brick #3 to be output as the threshold sub-brick
in the new dataset.
N.B.: The '$', '(', ')', '[', and ']' characters are special to
the shell, so you will have to escape them. This is most easily
done by putting the entire dataset plus selection list inside
single quotes, as in 'fred+orig[5,9]'.
|
|||
|
3dbucket /binfs/freesurfer_alpha/afni/Linux/ |
#: 35 Sz: 247428 |
9/7/2000 3:28:19 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program 3dbucket
Last revision: 04 February 1998
Concatenate sub-bricks from input datasets into one big
'bucket' dataset.
Usage: 3dbucket options
where the options are:
-prefix pname = Use 'pname' for the output dataset prefix name.
OR -output pname [default='buck']
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
-glueto fname = Append bricks to the end of the 'fname' dataset.
This command is an alternative to the -prefix
and -session commands.
-dry = Execute a 'dry run'; that is, only print out
what would be done. This is useful when
combining sub-bricks from multiple inputs.
-verb = Print out some verbose output as the program
proceeds (-dry implies -verb).
-fbuc = Create a functional bucket.
-abuc = Create an anatomical bucket. If neither of
these options is given, the output type is
determined from the first input type.
Command line arguments after the above are taken as input datasets.
A dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
You can also add a sub-brick selection list after the end of the
dataset name. This allows only a subset of the sub-bricks to be
included into the output (by default, all of the input dataset
is copied into the output). A sub-brick selection list looks like
one of the following forms:
fred+orig[5] ==> use only sub-brick #5
fred+orig[5,9,17] ==> use #5, #9, and #12
fred+orig[5..8] or [5-8] ==> use #5, #6, #7, and #8
fred+orig[5..13(2)] or [5-13(2)] ==> use #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
fred+orig[0..$(3)]
N.B.: The sub-bricks are output in the order specified, which may
not be the order in the original datasets. For example, using
fred+orig[0..$(2),1..$(2)]
will cause the sub-bricks in fred+orig to be output into the
new dataset in an interleaved fashion. Using
fred+orig[$..0]
will reverse the order of the sub-bricks in the output.
N.B.: Bucket datasets have multiple sub-bricks, but do NOT have
a time dimension. You can input sub-bricks from a 3D+time dataset
into a bucket dataset. You can use the '3dinfo' program to see
how many sub-bricks a 3D+time or a bucket dataset contains.
N.B.: The '$', '(', ')', '[', and ']' characters are special to
the shell, so you will have to escape them. This is most easily
done by putting the entire dataset plus selection list inside
single quotes, as in 'fred+orig[5..7,9]'.
N.B.: In non-bucket functional datasets (like the 'fico' datasets
output by FIM, or the 'fitt' datasets output by 3dttest), sub-brick
[0] is the 'intensity' and sub-brick [1] is the statistical parameter
used as a threshold. Thus, to create a bucket dataset using the
intensity from dataset A and the threshold from dataset B, and
calling the output dataset C, you would type
3dbucket -prefix C -fbuc 'A+orig[0]' -fbuc 'B+orig[1]'
|
|||
|
3dcalc /binfs/freesurfer_alpha/afni/Linux/ |
#: 36 Sz: 438708 |
9/7/2000 3:28:19 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Do arithmetic on 3D datasets, voxel-by-voxel [no inter-voxel computation].
Usage: 3dcalc [options]
where the options are:
-verbose = Makes the program print out various information as
it progresses.
-datum type = Coerce the output data to be stored as the given type,
which may be byte, short, or float.
[default = datum of first input dataset]
-fscale = Force scaling of the output to the maximum integer
range. This only has effect if the output datum
is byte or short (either forced or defaulted).
This option is often necessary to eliminate unpleasant
truncation artifacts.
[The default is to scale only if the computed values
seem to need it -- are all less than 1 or there is
at least one value beyond the integer upper limit.]
** In earlier versions of 3dcalc, scaling (if used) was
applied to all sub-bricks equally -- a common scale
factor was used. This would cause trouble if the values
in different sub-bricks were in vastly different scales.
In this version, each sub-brick gets its own scale factor.
To override this behaviour, use the '-gscale' option.
-gscale = Same as '-fscale', but also forces each output sub-brick to
get the same scaling factor. This may be desirable
for 3D+time datasets, for example.
-a dname = Read dataset 'dname' and call the voxel values 'a'
in the expression that is input below. 'a' may be any
single letter from 'a' to 'z'.
** If some letter name is used in the expression, but not
present in one of the dataset options here, then that
variable is set to 0.
** If the letter is followed by a number, then that number
is used to select the sub-brick of the dataset which
will be used in the calculations. For example,
'-b3 dname' specifies that the variable 'b' refers to
sub-brick 3 of the dataset (indexes start at 0).
N.B.: Another way to achieve the effect of '-b3' is described
below in the 'INPUT DATASET SPECIFICATION' section.
-expr "expression"
Apply the expression within quotes to the input datasets,
one voxel at a time, to produce the output dataset.
("sqrt(a*b)" to compute the geometric mean, for example).
-prefix pname = Use 'pname' for the output dataset prefix name.
[default='calc']
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
3D+TIME DATASETS:
This version of 3dcalc can operate on 3D+time datasets. Each input dataset
will be in one of these conditions:
(A) Is a regular 3D (no time) dataset; or
(B) Is a 3D+time dataset with a sub-brick index specified ('-b3'); or
(C) Is a 3D+time dataset with no sub-brick index specified ('-b').
If there is at least one case (C) dataset, then the output dataset will
also be 3D+time; otherwise it will be a 3D dataset with one sub-brick.
When producing a 3D+time dataset, datasets in case (A) or (B) will be
treated as if the particular brick being used has the same value at each
point in time.
Multi-brick 'bucket' datasets may also be used. Note that if multi-brick
(bucket or 3D+time) datasets are used, the lowest letter dataset will
serve as the template for the output; that is, '-b fred+tlrc' takes
precedence over '-c wilma+tlrc'. (The program 3drefit can be used to
alter the .HEAD parameters of the output dataset, if desired.)
INPUT DATASET SPECIFICATION:
An input dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
You can also add a sub-brick selection list after the end of the
dataset name. This allows only a subset of the sub-bricks to be
read in (by default, all of a dataset's sub-bricks are input).
A sub-brick selection list looks like one of the following forms:
fred+orig[5] ==> use only sub-brick #5
fred+orig[5,9,17] ==> use #5, #9, and #12
fred+orig[5..8] or [5-8] ==> use #5, #6, #7, and #8
fred+orig[5..13(2)] or [5-13(2)] ==> use #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
fred+orig[0..$(3)]
N.B.: The sub-bricks are read in the order specified, which may
not be the order in the original dataset. For example, using
fred+orig[0..$(2),1..$(2)]
will cause the sub-bricks in fred+orig to be input into memory
in an interleaved fashion. Using
fred+orig[$..0]
will reverse the order of the sub-bricks.
N.B.: The '$', '(', ')', '[', and ']' characters are special to
the shell, so you will have to escape them. This is most easily
done by putting the entire dataset plus selection list inside
forward single quotes, as in 'fred+orig[5..7,9]'.
1D TIME SERIES:
You can also input a '*.1D' time series file in place of a dataset.
In this case, the value at each spatial voxel at time index n will be
the same, and will be the n-th value from the time series file.
At least one true dataset must be input. If all the input datasets
are 3D (single sub-brick) or are single sub-bricks from multi-brick
datasets, then the output will be a 'manufactured' 3D+time dataset
For example, suppose that 'a3D+orig' is a 3D dataset:
3dcalc -a a3D+orig -b b.1D -expr "a*b"
The output dataset will 3D+time with the value at (x,y,z,t) being
computed by a3D(x,y,z)*b(t). The TR for this dataset will be set
to 1 second -- this could be altered later with program 3drefit.
Another method to set up the correct timing would be to input an
unused 3D+time dataset -- 3dcalc will then copy that dataset's time
information, but simply do not use that dataset's letter in -expr.
COORDINATES and DEFAULT VALUES:
If you don't use '-x', '-y', or '-z' for a dataset, then the voxel
spatial coordinates will be loaded into those variables. For example,
the expression 'a*step(x*x+y*y+z*z-100)' will zero out all the voxels
inside a 10 mm radius of the origin.
Similarly, the '-i', '-j', and '-k' values, if not otherwise used,
will be loaded with the voxel index coordinates.
Otherwise undefined letters will be set to zero. In the future,
new default values for other letters may be added.
PROBLEMS:
** Complex-valued datasets cannot be processed.
** This program is not very efficient (but is faster than it used to be).
EXPRESSIONS:
Arithmetic expressions are allowed, using + - * / ** and parentheses.
As noted above, datasets are referred to by single letter variable names.
At this time, C relational, boolean, and conditional expressions are
NOT implemented. Built in functions include:
sin , cos , tan , asin , acos , atan , atan2,
sinh , cosh , tanh , asinh , acosh , atanh , exp ,
log , log10, abs , int , sqrt , max , min ,
J0 , J1 , Y0 , Y1 , erf , erfc , qginv, qg ,
rect , step , astep, bool , and , or , mofn ,
sind , cosd , tand , median,
where qg(x) = reversed cdf of a standard normal distribution
qginv(x) = inverse function to qg,
min, max, atan2 each take 2 arguments,
J0, J1, Y0, Y1 are Bessel functions (see Watson),
erf, erfc are the error and complementary error functions,
sind, cosd, tand take arguments in degrees (vs. radians),
median(a,b,c,...) computes the median of its arguments
[median takes a variable number of arguments].
The following functions are designed to help implement logical
functions, such as masking of 3D volumes against some criterion:
step(x) = {1 if x>0 , 0 if x<=0},
astep(x,y) = {1 if abs(x) > y , 0 otherwise} = step(abs(x)-y)
rect(x) = {1 if abs(x)<=0.5, 0 if abs(x)>0.5},
bool(x) = {1 if x != 0.0 , 0 if x == 0.0},
and(a,b,...,c) = {1 if all arguments are nonzero, 0 if any are zero}
or(a,b,...,c) = {1 if any arguments are nonzero, 0 if all are zero}
mofn(m,a,...,c) = {1 if at least 'm' arguments are nonzero, 0 otherwise}
These last 3 functions take a variable number of arguments.
The following 27 new [Mar 1999] functions are used for statistical
conversions, as in the program 'cdf':
fico_t2p(t,a,b,c), fico_p2t(p,a,b,c), fico_t2z(t,a,b,c),
fitt_t2p(t,a) , fitt_p2t(p,a) , fitt_t2z(t,a) ,
fift_t2p(t,a,b) , fift_p2t(p,a,b) , fift_t2z(t,a,b) ,
fizt_t2p(t) , fizt_p2t(p) , fizt_t2z(t) ,
fict_t2p(t,a) , fict_p2t(p,a) , fict_t2z(t,a) ,
fibt_t2p(t,a,b) , fibt_p2t(p,a,b) , fibt_t2z(t,a,b) ,
fibn_t2p(t,a,b) , fibn_p2t(p,a,b) , fibn_t2z(t,a,b) ,
figt_t2p(t,a,b) , figt_p2t(p,a,b) , figt_t2z(t,a,b) ,
fipt_t2p(t,a) , fipt_p2t(p,a) , fipt_t2z(t,a) .
See the output of 'cdf -help' for documentation on the meanings of
and arguments to these functions. (After using one of these, you
may wish to use program '3drefit' to modify the dataset statistical
auxiliary parameters.)
Computations are carried out in double precision before being
truncated to the final output 'datum'.
Note that the quotes around the expression are needed so the shell
doesn't try to expand * characters, or interpret parentheses.
(Try the 'ccalc' program to see how the expression evaluator works.
The arithmetic parser and evaluator is written in Fortran-77 and
is derived from a program written long ago by RW Cox to facilitate
compiling on an array processor hooked up to a VAX. It's a mess,
but it works - somewhat slowly.)
|
|||
|
3dclust /binfs/freesurfer_alpha/afni/Linux/ |
#: 37 Sz: 444224 |
9/7/2000 3:28:20 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dclust
Author: R. W. Cox et al.
Date: 26 March 1999
Copyright 1994-9 Medical College of Wisconsin
Simple-minded Cluster Detection in 3D Datasets
Usage: 3dclust [editing options] [-summarize] rmm vmul dset ...
where rmm = cluster connection radius (mm);
vmul = minimum cluster volume (micro-liters)
(both rmm and vmul must be positive);
dset = input dataset (more than one allowed).
The report is sent to stdout.
The -noabs option uses the signed voxel intensities (not the
abs. value) for calculation of the mean and SEM
The -summarize option will write out only the total
nonzero voxel count and volume for each dataset.
The editing options are as in 3dmerge
(including use of the -1dindex and -1tindex options).
The program does not work on complex-valued datasets!
Using the -1noneg option is strongly recommended!
SEM values are not realistic for interpolated data sets!
A ROUGH correction is to multiply the SEM of the interpolated
data set by the square root of the number of interpolated
voxels per original voxel.
|
|||
|
3ddata.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 38 Sz: 88465 |
9/7/2000 3:28:20 PM | ASCII C program text |
|
3dDeconvolve /binfs/freesurfer_alpha/afni/Linux/ |
#: 39 Sz: 303852 |
9/7/2000 3:28:09 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dDeconvolve
Author: B. Douglas Ward
Date: 09 September 1999
Program to calculate the deconvolution of a measured 3d+time dataset
with a specified input stimulus time series. This program will also
perform multiple linear regression using multiple input stimulus time
series. Output consists of an AFNI 'bucket' type dataset containing the
least squares estimates of the linear regression coefficients, t-statistics
for significance of the coefficients, partial F-statistics for significance
of the individual input stimuli, and the F-statistic for significance of
the overall regression. Additional output consists of a 3d+time dataset
containing the estimated system impulse response function.
Usage:
3dDeconvolve
-input fname fname = filename of 3d+time input dataset
[-nodata] Evaluate experimental design only (no input data)
[-nfirst fnum] fnum = number of first dataset image to use in
the deconvolution procedure. (default = 0)
[-nlast lnum] lnum = number of last dataset image to use in
the deconvolution procedure. (default = last)
[-polort pnum] pnum = degree of polynomial corresponding to the
null hypothesis (pnum = 0, 1, or 2)
(default pnum = 1)
[-rmsmin r] r = minimum rms error to reject reduced model
[-fdisp fval] Write (to screen) results for those voxels
whose F-statistic is > fval
-num_stimts num num = number of input stimulus time series
(0 <= num <= 20)
-stim_file k sname sname = filename of kth time series input stimulus
-stim_label k slabel slabel = label for kth time series input stimulus
[-stim_minlag k m] m = minimum time lag for kth input stimulus
(default m = 0)
[-stim_maxlag k n] n = maximum time lag for kth input stimulus
(default n = 0)
[-glt s gltname] Perform s simultaneous linear tests, as specified
by the matrix contained in file gltname
[-iresp k iprefix] iprefix = prefix of 3d+time output dataset which
will contain the kth estimated impulse response
[-sresp k sprefix] sprefix = prefix of 3d+time output dataset which
will contain the standard deviations of the
kth impulse response function parameters
[-bucket bprefix] Create one AFNI 'bucket' dataset containing various
parameters of interest, such as the F-statistic for
significance of the estimated impulse response.
Output 'bucket' dataset is written to prefixname.
|
|||
|
3ddup /binfs/freesurfer_alpha/afni/Linux/ |
#: 40 Sz: 219616 |
9/7/2000 3:28:21 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 3ddup [options] dataset
'Duplicates' a 3D dataset by making a warp-on-demand copy.
Applications:
- allows AFNI to resample a dataset to a new grid without
destroying an existing data .BRIK
- change a functional dataset to anatomical, or vice-versa
OPTIONS:
-type = Convert to the given 'type', which must be
chosen from the same list as in to3d
-session dirname = Write output into given directory (default=./)
-prefix pname = Use 'pname' for the output directory prefix
(default=dup)
N.B.: Even if the new dataset is anatomical, it will not contain
any markers, duplicated from the original, or otherwise.
|
|||
|
3dfim /binfs/freesurfer_alpha/afni/Linux/ |
#: 41 Sz: 265592 |
9/7/2000 3:28:21 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dfim
Date: 10 September 1999
Copyright 1996 Medical College of Wisconsin
Program: 3dfim
Purpose: Calculate functional image from 3d+time data file.
Usage: 3dfim [-im1 num] -input fname -prefix name
-ideal fname [-ideal fname] [-ort fname]
options are:
-im1 num num = index of first image to be used in time series
correlation; default is 1
-input fname fname = filename of 3d + time data file for input
-prefix name name = prefix of filename for saving functional data
-ideal fname fname = filename of a time series to which the image data
is to be correlated.
-percent p Calculate percentage change due to the ideal time series
p = maximum allowed percentage change from baseline
Note: values greater than p are set equal to p.
-ort fname fname = filename of a time series to which the image data
is to be orthogonalized
N.B.: It is possible to specify more than
one ideal time series file. Each one is separately correlated
with the image time series and the one most highly correlated
is selected for each pixel. Multiple ideals are specified
using more than one '-ideal fname' option, or by using the
form '-ideal [ fname1 fname2 ... ]' -- this latter method
allows the use of wildcarded ideal filenames.
The '[' character that indicates the start of a group of
ideals can actually be any ONE of these: [{/%
and the ']' that ends the group can be: ]}/%
[Format of ideal time series files:
ASCII; one number per line;
Same number of lines as images in the time series;
Value over 33333 --> don't use this image in the analysis]
N.B.: It is also possible to specify more than
one ort time series file. The image time series is
orthogonalized to each ort time series. Multiple orts are
specified by using more than one '-ort fname' option,
or by using the form '-ort [ fname1 fname2 ... ]'. This
latter method allows the use of wildcarded ort filenames.
The '[' character that indicates the start of a group of
ideals can actually be any ONE of these: [{/%
and the ']' that ends the group can be: ]}/%
[Format of ort time series files:
ASCII; one number per line;
At least same number of lines as images in the time series]
|
|||
|
3dFourier /binfs/freesurfer_alpha/afni/Linux/ |
#: 42 Sz: 283080 |
9/7/2000 3:28:10 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
3dFourier (c) 1999 Medical College of Wisconsin by T. Ross and K. Heimerl Version 0.8 last modified 8-17-99 Usage: 3dFourier [options] dataset The paramters and options are: dataset an afni compatible 3d+time dataset to be operated upon -prefix name output name for new 3d+time dataset [default = fourier] -lowpass f low pass filter with a cutoff of f Hz -highpass f high pass filter with a cutoff of f Hz -ignore n ignore the first n images [default = 1] -retrend Any mean and linear trend are removed before filtering. This will restore the trend after filtering. Note that by combining the lowpass and highpass options, one can construct bandpass and notch filters |
|||
|
3dfractionize /binfs/freesurfer_alpha/afni/Linux/ |
#: 43 Sz: 263832 |
9/7/2000 3:28:22 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 3dfractionize [options]
* For each voxel in the output dataset, computes the fraction
of it that is occupied by nonzero voxels from the input.
* The fraction is stored as a short in the range 0..10000,
indicating fractions running from 0..1.
* The template dataset is used only to define the output grid;
its brick(s) will not be read into memory.
* The actual values stored in the input dataset are irrelevant,
except in that they are zero or nonzero.
The purpose of this program is to allow the resampling of a mask
dataset (the input) from a fine grid to a coarse grid (defined by
the template). When you are using the output, you will probably
want to threshold the mask so that voxels with a tiny occupancy
fraction aren't used. This can be done in 3dmaskave, by using
3calc, or with the '-clip' option below.
Options are:
-template tset = Use dataset 'tset' as a template for the output.
-input iset = Use dataset 'iset' for the input.
Only the sub-brick #0 of the input is used.
You can use the sub-brick selection technique
described in '3dcalc -help' to choose the
desired sub-brick from a multi-brick dataset.
-prefix ppp = Use 'ppp' for the prefix of the output.
[default = 'fractionize']
-clip fff = Clip off voxels that are less than 'fff' occupied.
'fff' can be a number between 0.0 and 1.0, meaning
the fraction occupied, can be a number between 1.0
and 100.0, meaning the percent occupied, or can be
a number between 100.0 and 10000.0, meaning the
direct output value to use as a clip level.
[default = 0.0]
This program will also work in going from a coarse grid to a fine grid,
but it isn't clear that this capability has any purpose.
-- RWCox - February 1999
|
|||
|
3dFriedman /binfs/freesurfer_alpha/afni/Linux/ |
#: 44 Sz: 258808 |
9/7/2000 3:28:10 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dFriedman
Author: B. Douglas Ward
Date: 08 September 1999
This program performs nonparametric Friedman test for
randomized complete block design experiments.
Usage:
3dFriedman
-levels s s = number of treatments
-dset 1 filename data set for treatment #1
. . . . . .
-dset 1 filename data set for treatment #1
. . . . . .
-dset s filename data set for treatment #s
. . . . . .
-dset s filename data set for treatment #s
[-workmem mega] number of megabytes of RAM to use
for statistical workspace
[-voxel num] screen output for voxel # num
-out prefixname Friedman statistics are written
to file prefixname
|
|||
|
3dFWHM /binfs/freesurfer_alpha/afni/Linux/ |
#: 45 Sz: 209600 |
9/7/2000 3:28:09 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
This program estimates the Filter Width Half Maximum (FWHM). Usage: 3dFWHM -dset file file = name of input AFNI 3d dataset [-quiet] suppress screen output [-out file] file = name of output file |
|||
|
3dhistog /binfs/freesurfer_alpha/afni/Linux/ |
#: 46 Sz: 454368 |
9/7/2000 3:28:23 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Compute histogram of 3D Dataset
Usage: 3dhistog [editing options] [histogram options] dataset
The editing options are the same as in 3dmerge.
The histogram options are:
-nbin # Means to use '#' bins (default = 100)
Special Case: for short or byte dataset bricks,
set '#' to zero to have the number
of bins set by the brick range.
-thr r Means to count only voxels with the statistics threshold above 'r'
-dind i Means to take data from sub-brick 'i'
-tind j Means to take threshold from sub-brick 'j'
-omit x Means to omit the value 'x' from the count.
-notit Means to leave the title line off the output.
The histogram is written to stdout.
|
|||
|
3dinfo /binfs/freesurfer_alpha/afni/Linux/ |
#: 47 Sz: 224820 |
9/7/2000 3:28:23 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Prints out sort-of-useful information from a 3D dataset's header
Usage: 3dinfo [-v] dataset [dataset ...]
The -v option means print out verbose information:
* All the statistics for each time in a time-dependent dataset.
* All the Notes in a dataset header
(without -v, only the first 5 Notes will be printed).
|
|||
|
3dIntracranial /binfs/freesurfer_alpha/afni/Linux/ |
#: 48 Sz: 255412 |
9/7/2000 3:28:11 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dIntracranial
Author: B. D. Ward
Date: 09 September 1999
This program performs automatic segmentation of intracranial region.
Usage:
3dIntracranial
-anat filename Filename of anat dataset to be segmented
[-min_val a] Minimum voxel intensity limit
Default: Internal PDF estimate for lower bound
[-max_val b] Maximum voxel intensity limit
Default: Internal PDF estimate for upper bound
[-min_conn m] Minimum voxel connectivity to enter
Default: m=4
[-max_conn n] Maximum voxel connectivity to leave
Default: n=2
[-mask] Generate functional image mask (complement)
Default: Generate anatomical image
[-quiet] Suppress output to screen
-prefix pname Prefix name for file to contain segmented image
|
|||
|
3dKruskalWallis /binfs/freesurfer_alpha/afni/Linux/ |
#: 49 Sz: 258776 |
9/7/2000 3:28:11 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dKruskalWallis
Author: B. Douglas Ward
Date: 08 September 1999
This program performs nonparametric Kruskal-Wallis test for
comparison of multiple treatments.
Usage:
3dKruskalWallis
-levels s s = number of treatments
-dset 1 filename data set for treatment #1
. . . . . .
-dset 1 filename data set for treatment #1
. . . . . .
-dset s filename data set for treatment #s
. . . . . .
-dset s filename data set for treatment #s
[-workmem mega] number of megabytes of RAM to use
for statistical workspace
[-voxel num] screen output for voxel # num
-out prefixnamename Kruskal-Wallis statistics are written
to file prefixname
|
|||
|
3dMannWhitney /binfs/freesurfer_alpha/afni/Linux/ |
#: 50 Sz: 258424 |
9/7/2000 3:28:12 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dMannWhitney
Author: B. Douglas Ward
Date: 08 September 1999
This program performs nonparametric Mann-Whitney two-sample test.
Usage:
3dMannWhitney
-dset 1 filename data set for X observations
. . . . . .
-dset 1 filename data set for X observations
-dset 2 filename data set for Y observations
. . . . . .
-dset 2 filename data set for Y observations
[-workmem mega] number of megabytes of RAM to use
for statistical workspace
[-voxel num] screen output for voxel # num
-out prefixname estimated population delta and
Wilcoxon-Mann-Whitney statistics
written to file prefixname
|
|||
|
3dmaskave /binfs/freesurfer_alpha/afni/Linux/ |
#: 51 Sz: 214976 |
9/7/2000 3:28:24 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 3dmaskave [options] dataset
Computes average of all voxels in the input dataset
which satisfy the criterion in the options list.
If no options are given, then all voxels are included.
Options:
-mask mset Means to use the dataset 'mset' as a mask:
Only voxels with nonzero values in 'mset'
will be averaged from 'dataset'. Note
that the mask dataset and the input dataset
must have the same number of voxels.
-mindex miv Means to use sub-brick #'miv' from the mask
dataset. If not given, miv=0.
-mrange a b Means to further restrict the voxels from
'mset' so that only those mask values
between 'a' and 'b' (inclusive) will
be used. If this option is not given,
all nonzero values from 'mset' are used.
Note that if a voxel is zero in 'mset', then
it won't be included, even if a < 0 < b.
-dindex div Means to use sub-brick #'div' from the dataset.
If not given, all sub-bricks will be processed.
-drange a b Means to only include voxels from the dataset whose
values fall in the range 'a' to 'b' (inclusive).
Otherwise, all voxel values are included.
-slices p q Means to only included voxels from the dataset
whose slice numbers are in the range 'p' to 'q'
(inclusive). Slice numbers range from 0 to
NZ-1, where NZ can be determined from the output
of program 3dinfo. The default is to include
data from all slices.
[There is no provision for geometrical voxel]
[selection except in the slice (z) direction]
-sigma Means to compute the standard deviation as well
as the mean.
-dump Means to print out all the voxel values that
go into the average.
-udump Means to print out all the voxel values that
go into the average, UNSCALED by any internal
factors.
N.B.: the scale factors for a sub-brick
can be found using program 3dinfo.
-indump Means to print out the voxel indexes (i,j,k) for
each dumped voxel. Has no effect if -dump
or -udump is not also used.
N.B.: if nx,ny,nz are the number of voxels in
each direction, then the array offset
in the brick corresponding to (i,j,k)
is i+j*nx+k*nx*ny.
The output is printed to stdout (the terminal), and can be
saved to a file using the usual redirection operation '>'.
|
|||
|
3dmerge /binfs/freesurfer_alpha/afni/Linux/ |
#: 52 Sz: 500468 |
9/7/2000 3:28:25 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program 3dmerge
Last revision: 04 February 1998
Edit and/or merge 3D datasets
Usage: 3dmerge [options] datasets ...
where the options are:
EDITING OPTIONS APPLIED TO EACH INPUT DATASET:
-1thtoin = Copy threshold data over intensity data.
This is only valid for datasets with some
thresholding statistic attached. All
subsequent operations apply to this
substituted data.
-2thtoin = The same as -1thtoin, but do NOT scale the
threshold values from shorts to floats when
processing. This option is only provided
for compatibility with the earlier versions
of the AFNI package '3d*' programs.
-1noneg = Zero out voxels with negative intensities
-1abs = Take absolute values of intensities
-1clip val = Clip intensities in range (-val,val) to zero
-2clip v1 v2 = Clip intensities in range (v1,v2) to zero
-1uclip val = These options are like the above, but do not apply
-2uclip v1 v2 any automatic scaling factor that may be attached
to the data. These are for use only in special
circumstances. (The 'u' means 'unscaled'. Program
'3dinfo' can be used to find the scaling factors.)
N.B.: Only one of these 'clip' options can be used; you cannot
combine them to have multiple clipping executed.
-1thresh thr = Use the threshold data to censor the intensities
(only valid for 'fith', 'fico', or 'fitt' datasets).
N.B.: The value 'thr' is floating point, in the range
0.0 < thr < 1.0 for 'fith' and 'fico' datasets,
and 0.0 < thr < 32.7 for 'fitt' datasets.
-1blur_sigma bmm = Gaussian blur with sigma = bmm (in mm)
-1blur_rms bmm = Gaussian blur with rms deviation = bmm
-1blur_fwhm bmm = Gaussian blur with FWHM = bmm
-t1blur_sigma bmm= Gaussian blur of threshold with sigma = bmm(in mm)
-t1blur_rms bmm = Gaussian blur of threshold with rms deviation = bmm
-t1blur_fwhm bmm = Gaussian blur of threshold with FWHM = bmm
-1zvol x1 x2 y1 y2 z1 z2
= Zero out entries inside the 3D volume defined
by x1 <= x <= x2, y1 <= y <= y2, z1 <= z <= z2 ;
N.B.: The ranges of x,y,z in a dataset can be found
using the '3dinfo' program. Dimensions are in mm.
N.B.: This option may not work correctly at this time, but
I've not figured out why!
The following cluster options are mutually exclusive:
-1clust rmm vmul = Form clusters with connection distance rmm
and clip off data not in clusters of
volume at least vmul microliters
-1clust_mean rmm vmul = Same as -1clust, but all voxel intensities
within a cluster are replaced by the average
intensity of the cluster.
-1clust_max rmm vmul = Same as -1clust, but all voxel intensities
within a cluster are replaced by the maximum
intensity of the cluster.
-1clust_amax rmm vmul = Same as -1clust, but all voxel intensities
within a cluster are replaced by the maximum
absolute intensity of the cluster.
-1clust_smax rmm vmul = Same as -1clust, but all voxel intensities
within a cluster are replaced by the maximum
signed intensity of the cluster.
-1clust_size rmm vmul = Same as -1clust, but all voxel intensities
within a cluster are replaced by the size
of the cluster (in multiples of vmul).
-1clust_order rmm vmul= Same as -1clust, but all voxel intensities
within a cluster are replaced by the cluster
size index (largest cluster=1, next=2, ...).
The following commands produce erosion and dilation of 3D clusters.
These commands assume that one of the -1clust commands has been used.
The purpose is to avoid forming strange clusters with 2 (or more)
main bodies connected by thin 'necks'. Erosion can cut off the neck.
Dilation will minimize erosion of the main bodies.
Note: Manipulation of values inside a cluster (-1clust commands)
occurs AFTER the following two commands have been executed.
-1erode pv For each voxel, set the intensity to zero unless pv %
of the voxels within radius rmm are nonzero.
-1dilate Restore voxels that were removed by the previous
command if there remains a nonzero voxel within rmm.
The following filter options are mutually exclusive:
-1filter_mean rmm = Set each voxel to the average intensity of the
voxels within a radius of rmm.
-1filter_nzmean rmm = Set each voxel to the average intensity of the
non-zero voxels within a radius of rmm.
-1filter_max rmm = Set each voxel to the maximum intensity of the
voxels within a radius of rmm.
-1filter_amax rmm = Set each voxel to the maximum absolute intensity
of the voxels within a radius of rmm.
-1filter_smax rmm = Set each voxel to the maximum signed intensity
of the voxels within a radius of rmm.
-1filter_aver rmm = Same idea as '_mean', but implemented using a
new code that should be faster.
The following threshold filter options are mutually exclusive:
-t1filter_mean rmm = Set each correlation or threshold voxel to the
average of the voxels within a radius of rmm.
-t1filter_nzmean rmm = Set each correlation or threshold voxel to the
average of the non-zero voxels within
a radius of rmm.
-t1filter_max rmm = Set each correlation or threshold voxel to the
maximum of the voxels within a radius of rmm.
-t1filter_amax rmm = Set each correlation or threshold voxel to the
maximum absolute intensity of the voxels
within a radius of rmm.
-t1filter_smax rmm = Set each correlation or threshold voxel to the
maximum signed intensity of the voxels
within a radius of rmm.
-t1filter_aver rmm = Same idea as '_mean', but implemented using a
new code that should be faster.
-1mult factor = Multiply intensities by the given factor
-1zscore = If the sub-brick is labeled as a statistic from
a known distribution, it will be converted to
an equivalent N(0,1) deviate (or 'z score').
If the sub-brick is not so labeled, nothing will
be done.
The above '-1' options are carried out in the order given above,
regardless of the order in which they are entered on the command line.
N.B.: The 3 '-1blur' options just provide different ways of
specifying the radius used for the blurring function.
The relationships among these specifications are
sigma = 0.57735027 * rms = 0.42466090 * fwhm
The requisite convolutions are done using FFTs; this is by
far the slowest operation among the editing options.
OTHER OPTIONS:
-datum type = Coerce the output data to be stored as the given type,
which may be byte, short, or float.
N.B.: Byte data cannot be negative. If this datum type is chosen,
any negative values in the edited and/or merged dataset
will be set to zero.
-keepthr = When using 3dmerge to edit exactly one dataset of a
functional type with a threshold statistic attached,
normally the resulting dataset is of the 'fim'
(intensity only) type. This option tells 3dmerge to
copy the threshold data (unedited in any way) into
the output dataset.
N.B.: This option is ignored if 3dmerge is being used to
combine 2 or more datasets.
N.B.: The -datum option has no effect on the storage of the
threshold data. Instead use '-thdatum type'.
-doall = Apply editing and merging options to ALL sub-bricks
uniformly in a dataset.
N.B.: All datasets must have the same number of sub-bricks
when using the -doall option.
N.B.: The threshold specific options (such as -1thresh,
-keepthr, -tgfisher, etc.) are not compatible with
the -doall command. Neither are the -1dindex or
the -1tindex options.
N.B.: All labels and statistical parameters for individual
sub-bricks are copied from the first dataset. It is
the responsibility of the user to verify that these
are appropriate. Note that sub-brick auxiliary data
can be modified using program 3drefit.
-1dindex j = Uses sub-brick #j as the data source , and uses sub-brick
-1tindex k = #k as the threshold source. With these, you can operate
on any given sub-brick of the inputs dataset(s) to produce
as output a 1 brick dataset. If desired, a collection
of 1 brick datasets can later be assembled into a
multi-brick bucket dataset using program '3dbucket'
or into a 3D+time dataset using program '3dTcat'.
N.B.: If these options aren't used, j=0 and k=1 are the defaults.
MERGING OPTIONS APPLIED TO FORM THE OUTPUT DATASET:
[That is, different ways to combine results. The]
[following '-g' options are mutually exclusive! ]
-gmean = Combine datasets by averaging intensities
(including zeros) -- this is the default
-gnzmean = Combine datasets by averaging intensities
(not counting zeros)
-gmax = Combine datasets by taking max intensity
(e.g., -7 and 2 combine to 2)
-gamax = Combine datasets by taking max absolute intensity
(e.g., -7 and 2 combine to 7)
-gsmax = Combine datasets by taking max signed intensity
(e.g., -7 and 2 combine to -7)
-gcount = Combine datasets by counting number of 'hits' in
each voxel (see below for defintion of 'hit')
-gorder = Combine datasets in order of input:
* If a voxel is nonzero in dataset #1, then
that value goes into the voxel.
* If a voxel is zero in dataset #1 but nonzero
in dataset #2, then the value from #2 is used.
* And so forth: the first dataset with a nonzero
entry in a given voxel 'wins'
-gfisher = Takes the arctanh of each input, averages these,
and outputs the tanh of the average. If the input
datum is 'short', then input values are scaled by
0.0001 and output values by 10000. This option
is for merging bricks of correlation coefficients.
MERGING OPERATIONS APPLIED TO THE THRESHOLD DATA:
[That is, different ways to combine the thresholds. If none of these ]
[are given, the thresholds will not be merged and the output dataset ]
[will not have threshold data attached. Note that the following '-tg']
[command line options are mutually exclusive, but are independent of ]
[the '-g' options given above for merging the intensity data values. ]
-tgfisher = This option is only applicable if each input dataset
is of the 'fico' or 'fith' types -- functional
intensity plus correlation or plus threshold.
(In the latter case, the threshold values are
interpreted as correlation coefficients.)
The correlation coefficients are averaged as
described by -gfisher above, and the output
dataset will be of the fico type if all inputs
are fico type; otherwise, the output datasets
will be of the fith type.
N.B.: The difference between the -tgfisher and -gfisher
methods is that -tgfisher applies to the threshold
data stored with a dataset, while -gfisher
applies to the intensity data. Thus, -gfisher
would normally be applied to a dataset created
from correlation coefficients directly, or from
the application of the -1thtoin option to a fico
or fith dataset.
OPTIONAL WAYS TO POSTPROCESS THE COMBINED RESULTS:
[May be combined with the above methods.]
[Any combination of these options may be used.]
-ghits count = Delete voxels that aren't !=0 in at least
count datasets (!=0 is a 'hit')
-gclust rmm vmul = Form clusters with connection distance rmm
and clip off data not in clusters of
volume at least vmul microliters
The '-g' and '-tg' options apply to the entire group of input datasets.
OPTIONS THAT CONTROL THE NAMES OF THE OUTPUT DATASET:
-session dirname = write output into given directory (default=./)
-prefix pname = use 'pname' for the output directory prefix
(default=mrg)
NOTES:
** If only one dataset is read into this program, then the '-g'
options do not apply, and the output dataset is simply the
'-1' options applied to the input dataset (i.e., edited).
** A merged output dataset is ALWAYS of the intensity-only variety.
** You can combine the outputs of 3dmerge with other sub-bricks
using the program 3dbucket.
** Complex-valued datasets cannot be merged.
** This program cannot handle time-dependent datasets.
** Note that the input datasets are specified by their .HEAD files,
but that their .BRIK files must exist also!
|
|||
|
3dnewid /binfs/freesurfer_alpha/afni/Linux/ |
#: 53 Sz: 183004 |
9/7/2000 3:28:25 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Copyright 1994-6 Medical College of Wisconsin Assigns a new ID code to a dataset; this is useful when making a copy of a dataset, so that the internal ID codes remain unique. Usage: 3dnewid dataset [dataset ...] |
|||
|
3dNLfim /binfs/freesurfer_alpha/afni/Linux/ |
#: 54 Sz: 358380 |
9/7/2000 3:28:12 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dNLfim
Author: B. Douglas Ward
Date: 09 September 1999
This program calculates a nonlinear regression for each voxel of the
input AFNI 3d+time data set. The nonlinear regression is calculated
by means of a least squares fit to the signal plus noise models which
are specified by the user.
Usage:
3dNLfim
-input fname fname = filename of 3d + time data file for input
[-inTR] set the TR of the created timeseries to be the TR
of the prototype dataset
[The default is to compute with TR = 1.]
[The model functions are called for a ]
[time grid of 0, TR, 2*TR, 3*TR, .... ]
-ignore num num = skip this number of initial images in the
time series for regresion analysis; default = 3
[-time fname] fname = ASCII file containing each time point
in the time series. Defaults to even spacing
given by TR (this option overrides -inTR).
-signal slabel slabel = name of (non-linear) signal model
-noise nlabel nlabel = name of (linear) noise model
-sconstr k c d constraints for kth signal parameter:
c <= gs[k] <= d
-nconstr k c d constraints for kth noise parameter:
c+b[k] <= gn[k] <= d+b[k]
[-nabs] use absolute constraints for noise parameters:
c <= gn[k] <= d
[-nrand n] n = number of random test points
[-nbest b] b = find opt. soln. for b best test points
[-rmsmin r] r = minimum rms error to reject reduced model
[-fdisp fval] display (to screen) results for those voxels
whose f-statistic is > fval
The following commands generate individual AFNI 2 sub-brick datasets:
[-freg fname] perform f-test for significance of the regression;
output 'fift' is written to prefix filename fname
[-fsmax fname] estimate signed maximum of signal; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-ftmax fname] estimate time of signed maximum; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-fpsmax fname] calculate (signed) maximum percentage change of
signal from baseline; output 'fift' is
written to prefix filename fname
[-farea fname] calculate area between signal and baseline; store
with f-test for regression; output 'fift' is
written to prefix filename fname
[-fparea fname] percentage area of signal relative to baseline;
store with f-test for regression; output 'fift'
is written to prefix filename fname
[-fscoef k fname] estimate kth signal parameter gs[k]; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-fncoef k fname] estimate kth noise parameter gn[k]; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-tscoef k fname] perform t-test for significance of the kth signal
parameter gs[k]; output 'fitt' is written
to prefix filename fname
[-tncoef k fname] perform t-test for significance of the kth noise
parameter gn[k]; output 'fitt' is written
to prefix filename fname
The following commands generate one AFNI 'bucket' type dataset:
[-bucket n prefixname] create one AFNI 'bucket' dataset containing
n sub-bricks; n=0 creates default output;
output 'bucket' is written to prefixname
The mth sub-brick will contain:
[-brick m scoef k label] kth signal parameter regression coefficient
[-brick m ncoef k label] kth noise parameter regression coefficient
[-brick m tmax label] time at max. abs. value of signal
[-brick m smax label] signed max. value of signal
[-brick m psmax label] signed max. value of signal as percent
above baseline level
[-brick m area label] area between signal and baseline
[-brick m parea label] signed area between signal and baseline
as percent of baseline area
[-brick m fstat label] F-stat for significance of the regression
[-brick m tscoef k label] t-stat for kth signal parameter coefficient
[-brick m tncoef k label] t-stat for kth noise parameter coefficient
The following commands write the time series fit for each voxel
to an AFNI 3d+time dataset:
[-sfit fname] fname = prefix for output 3d+time signal model fit
[-snfit fname] fname = prefix for output 3d+time signal+noise fit
|
|||
|
3dnoise /binfs/freesurfer_alpha/afni/Linux/ |
#: 55 Sz: 217300 |
9/7/2000 3:28:25 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 3dnoise [-blast] [-snr fac] [-nl x ] datasets ...
Estimates noise level in 3D datasets, and optionally
set voxels below the noise threshold to zero.
This only works on datasets that are stored as shorts,
and whose elements are all nonnegative.
-blast = Set values at or below the cutoff to zero.
In 3D+time datasets, a spatial location
is set to zero only if a majority of time
points fall below the cutoff; in that case
all the values at that location are zeroed.
-snr fac = Set cutoff to 'fac' times the estimated
noise level. Default fac = 2.5. What to
use for this depends strongly on your MRI
system -- I often use 5, but our true SNR
is about 100 for EPI.
-nl x = Set the noise level to 'x', skipping the
estimation procedure.
Author -- RW Cox
|
|||
|
3dNotes /binfs/freesurfer_alpha/afni/Linux/ |
#: 56 Sz: 195056 |
9/7/2000 3:28:13 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Skipped per survey instructions. Probably a program that expects console input |
|||
|
3dnvals /binfs/freesurfer_alpha/afni/Linux/ |
#: 57 Sz: 194912 |
9/7/2000 3:28:26 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Prints out the number of sub-bricks in a 3D dataset Usage: 3dnvals dataset |
|||
|
3dpc /binfs/freesurfer_alpha/afni/Linux/ |
#: 58 Sz: 296068 |
9/7/2000 3:28:26 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Principal Component Analysis of 3D Datasets
Usage: 3dpc [options] dataset dataset ...
Each input dataset may have a sub-brick selector list.
Otherwise, all sub-bricks from a dataset will be used.
OPTIONS:
-dmean = remove the mean from each input brick (across space)
-vmean = remove the mean from each input voxel (across bricks)
[N.B.: -dmean and -vmean are mutually exclusive]
[default: don't remove either mean]
-vnorm = L2 normalize each input voxel time series
[occurs after the de-mean operations above,]
[and before the brick normalization below. ]
-normalize = L2 normalize each input brick (after mean subtraction)
[default: don't normalize]
-pcsave sss = 'sss' is the number of components to save in the output;
it can't be more than the number of input bricks
[default = all of them = number of input bricks]
-prefix pname = Name for output dataset (will be a bucket type);
also, the eigen-timeseries will be in 'pname'.1D
(all of them) and in 'pnameNN.1D' for eigenvalue
#NN individually (NN=00 .. 'sss'-1, corresponding
to the brick index in the output dataset)
[default value of pname = 'pc']
-1ddum ddd = Add 'ddd' dummy lines to the top of each *.1D file.
These lines will have the value 999999, and can
be used to align the files appropriately.
[default value of ddd = 0]
-verbose = Print progress reports during the computations
-float = Save eigen-bricks as floats
[default = shorts, scaled so that |max|=10000]
-mask mset = Use the 0 sub-brick of dataset 'mset' as a mask
to indicate which voxels to analyze (a sub-brick
selector is allowed) [default = use all voxels]
|
|||
|
3dproject /binfs/freesurfer_alpha/afni/Linux/ |
#: 59 Sz: 550140 |
9/7/2000 3:28:27 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Projection along cardinal axes from a 3D dataset
Usage: 3dproject [editing options]
[-sum|-max|-amax|-smax] [-output root] [-nsize] [-mirror]
[-RL {all | x1 x2}] [-AP {all | y1 y2}] [-IS {all | z1 z2}]
[-ALL] dataset
Program to produce orthogonal projections from a 3D dataset.
-sum ==> Add the dataset voxels along the projection direction
-max ==> Take the maximum of the voxels [the default is -sum]
-amax ==> Take the absolute maximum of the voxels
-smax ==> Take the signed maximum of the voxels; for example,
-max ==> -7 and 2 go to 2 as the projected value
-amax ==> -7 and 2 go to 7 as the projected value
-smax ==> -7 and 2 go to -7 as the projected value
-nsize ==> Scale the output images up to 'normal' sizes
(e.g., 64x64, 128x128, or 256x256)
This option only applies to byte or short datasets.
-mirror ==> The radiologists' and AFNI convention is to display
axial and coronal images with the subject's left on
the right of the image; the use of this option will
mirror the axial and coronal projections so that
left is left and right is right.
-output root ==> Output projections will named
root.sag, root.cor, and root.axi
[the default root is 'proj']
-RL all ==> Project in the Right-to-Left direction along
all the data (produces root.sag)
-RL x1 x2 ==> Project in the Right-to-Left direction from
x-coordinate x1 to x2 (mm)
[negative x is Right, positive x is Left]
[OR, you may use something like -RL 10R 20L
to project from x=-10 mm to x=+20 mm ]
-AP all ==> Project in the Anterior-to-Posterior direction along
all the data (produces root.cor)
-AP y1 y2 ==> Project in the Anterior-to-Posterior direction from
y-coordinate y1 to y2 (mm)
[negative y is Anterior, positive y is Posterior]
[OR, you may use something like -AP 10A 20P
to project from y=-10 mm to y=+20 mm ]
-IS all ==> Project in the Inferior-to-Superior direction along
all the data (produces root.axi)
-IS y1 y2 ==> Project in the Inferior-to-Superior direction from
z-coordinate z1 to z2 (mm)
[negative z is Inferior, positive z is Superior]
[OR, you may use something like -IS 10I 20S
to project from z=-10 mm to z=+20 mm ]
-ALL ==> Equivalent to '-RL all -AP all -IS all'
* NOTE that a projection direction will not be used if the bounds aren't
given for that direction; thus, at least one of -RL, -AP, or -IS must
be used, or nothing will be computed!
* NOTE that in the directions transverse to the projection direction,
all the data is used; that is, '-RL -5 5' will produce a full sagittal
image summed over a 10 mm slice, irrespective of the -IS or -AP extents.
* NOTE that the [editing options] are the same as in 3dmerge.
In particular, the '-1thtoin' option can be used to project the
threshold data (if available).
|
|||
|
3drefit /binfs/freesurfer_alpha/afni/Linux/ |
#: 60 Sz: 227280 |
9/7/2000 3:28:28 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Changes some of the information inside a 3D dataset's header.
Note that this program does NOT change the .BRIK file at all;
the main purpose of 3drefit is to fix up errors made when
using to3d.
To see the current values stored in a .HEAD file, use the command
'3dinfo dataset'. Using 3dinfo both before and after 3drefit is
a good idea to make sure the changes have been made correctly!
Usage: 3drefit [options] dataset ...
where the options are
-orient code Sets the orientation of the 3D volume(s) in the .BRIK.
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
** WARNING: when changing the orientation, you must be sure
to check the origins as well, to make sure that the volume
is positioned correctly in space.
-xorigin distx Puts the center of the edge voxel off at the given
-yorigin disty distance, for the given axis (x,y,z); distances in mm.
-zorigin distz (x=first axis, y=second axis, z=third axis).
Usually, only -zorigin makes sense. Note that this
distance is in the direction given by the corresponding
letter in the -orient code. For example, '-orient RAI'
would mean that '-zorigin 30' sets the center of the
first slice at 30 mm Inferior. See the to3d manual
for more explanations of axes origins.
** SPECIAL CASE: you can use the string 'cen' in place of
a distance to force that axis to be re-centered.
-xdel dimx Makes the size of the voxel the given dimension,
-ydel dimy for the given axis (x,y,z); dimensions in mm.
-zdel dimz ** WARNING: if you change a voxel dimension, you will
probably have to change the origin as well.
-TR time Changes the TR time to a new value (see 'to3d -help').
** WARNING: this only applies to 3D+time datasets.
-newid Changes the ID code of this dataset as well.
-nowarp Removes all warping information from dataset.
-statpar v ... Changes the statistical parameters stored in this
dataset. See 'to3d -help' for more details.
-markers Adds an empty set of AC-PC markers to the dataset,
if it can handle them (is anatomical, is in the +orig
view, and isn't 3D+time).
** WARNING: this will erase any markers that already exist!
-view code Changes the 'view' to be 'code', where the string 'code'
is one of 'orig', 'acpc', or 'tlrc'.
** WARNING: The program will also change the .HEAD and .BRIK
filenames to match. If the dataset filenames already
exist in the '+code' view, then this option will fail.
You will have to rename the dataset files before trying
to use '-view'. If you copy the files and then use
'-view', don't forget to use '-newid' as well!
-byteorder bbb Sets the byte order string in the header.
Allowable values for 'bbb' are:
LSB_FIRST MSB_FIRST NATIVE_ORDER
Note that this does not change the .BRIK file!
This is done by programs 2swap and 4swap.
-appkey ll Appends the string 'll' to the keyword list for the
whole dataset.
-repkey ll Replaces the keyword list for the dataset with the
string 'll'.
-empkey Destroys the keyword list for the dataset.
-type Changes the type of data that is declared for this
dataset, where 'type' is chosen from the following:
ANATOMICAL TYPES
spgr == Spoiled GRASS fse == Fast Spin Echo
epan == Echo Planar anat == MRI Anatomy
ct == CT Scan spct == SPECT Anatomy
pet == PET Anatomy mra == MR Angiography
bmap == B-field Map diff == Diffusion Map
omri == Other MRI abuc == Anat Bucket
FUNCTIONAL TYPES
fim == Intensity fith == Inten+Thr
fico == Inten+Cor fitt == Inten+Ttest
fift == Inten+Ftest fizt == Inten+Ztest
fict == Inten+ChiSq fibt == Inten+Beta
fibn == Inten+Binom figt == Inten+Gamma
fipt == Inten+Poisson fbuc == Func-Bucket
The options below allow you to attach auxiliary data to sub-bricks
in the dataset. Each option may be used more than once so that
multiple sub-bricks can be modified in a single run of 3drefit.
-sublabel n ll Attach to sub-brick #n the label string 'll'.
-subappkey n ll Add to sub-brick #n the keyword string 'll'.
-subrepkey n ll Replace sub-brick #n's keyword string with 'll'.
-subempkey n Empty out sub-brick #n' keyword string
-substatpar n type v ...
Attach to sub-brick #n the statistical type and
the auxiliary parameters given by values 'v ...',
where 'type' is one of the following:
type Description PARAMETERS
---- ----------- ----------------------------------------
fico Cor SAMPLES FIT-PARAMETERS ORT-PARAMETERS
fitt Ttest DEGREES-of-FREEDOM
fift Ftest NUMERATOR and DENOMINATOR DEGREES-of-FREEDOM
fizt Ztest N/A
fict ChiSq DEGREES-of-FREEDOM
fibt Beta A (numerator) and B (denominator)
fibn Binom NUMBER-of-TRIALS and PROBABILITY-per-TRIAL
figt Gamma SHAPE and SCALE
fipt Poisson MEAN
|
|||
|
3dRegAna /binfs/freesurfer_alpha/afni/Linux/ |
#: 61 Sz: 324208 |
9/7/2000 3:28:14 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dRegAna
Author: B. Douglas Ward
Date: 09 September 1999
This program performs multiple linear regression analysis.
Usage:
3dRegAna
-rows n number of input datasets
-cols m number of X variables
-xydata X11 X12 ... X1m filename X variables and Y observations
. .
. .
. .
-xydata Xn1 Xn2 ... Xnm filename X variables and Y observations
-model i1 ... iq : j1 ... jr definition of linear regression model;
reduced model:
Y = f(Xj1,...,Xjr)
full model:
Y = f(Xj1,...,Xjr,Xi1,...,Xiq)
[-diskspace] print out disk space required for program execution
[-workmem mega] number of megabytes of RAM to use for statistical
workspace (default = 12)
[-rmsmin r] r = minimum rms error to reject constant model
[-fdisp fval] display (to screen) results for those voxels
whose F-statistic is > fval
[-flof alpha] alpha = minimum p value for F due to lack of fit
The following commands generate individual AFNI 2 sub-brick datasets:
[-fcoef k prefixname] estimate of kth regression coefficient
along with F-test for the regression
is written to AFNI `fift' dataset
[-rcoef k prefixname] estimate of kth regression coefficient
along with coef. of mult. deter. R^2
is written to AFNI `fith' dataset
[-tcoef k prefixname] estimate of kth regression coefficient
along with t-test for the coefficient
is written to AFNI `fitt' dataset
The following commands generate one AFNI 'bucket' type dataset:
[-bucket n prefixname] create one AFNI 'bucket' dataset having
n sub-bricks; n=0 creates default output;
output 'bucket' is written to prefixname
The mth sub-brick will contain:
[-brick m coef k label] kth parameter regression coefficient
[-brick m fstat label] F-stat for significance of regression
[-brick m rstat label] coefficient of multiple determination R^2
[-brick m tstat k label] t-stat for kth regression coefficient
|
|||
|
3dROIstats /binfs/freesurfer_alpha/afni/Linux/ |
#: 62 Sz: 208960 |
9/7/2000 3:28:13 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 3dROIstats -mask[n] mset [options] datasets
Options:
-mask[n] mset Means to use the dataset 'mset' as a mask:
If n is present, it specifies which sub-brick
in mset to use a la 3dcalc. Note: do not include
the brackets if specifing a sub-brick, they are
there to indicate that they are optional. If not
present, 0 is assumed
Voxels with the same nonzero values in 'mset'
will be statisticized from 'dataset'. This will
be repeated for all the different values in mset.
I.e. all of the 1s in mset are one ROI, as are all
of the 2s, etc.
Note that the mask dataset and the input dataset
must have the same number of voxels and that mset
must be BYTE or SHORT.
-debug Print out debugging information
The following options specify what stats are computed. By default
the mean is always computed.
-nzmean Compute the mean using only non_zero voxels. Implies
the oppisite for the normal mean computed
-nzvoxels Compute the number of non_zero voxels
-sigma Means to compute the standard deviation as well
as the mean.
The output is printed to stdout (the terminal), and can be
saved to a file using the usual redirection operation '>'.
|
|||
|
3drotate /binfs/freesurfer_alpha/afni/Linux/ |
#: 63 Sz: 339420 |
9/7/2000 3:28:28 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 3drotate [options] dataset
Rotates and/or translates all bricks from an AFNI dataset.
'dataset' may contain a sub-brick selector list.
The options are:
-prefix fname = Sets the output dataset prefix name to be 'fname'
-verbose = Prints out progress reports
At most one of these shift options can be used:
-ashift dx dy dz = Shifts the dataset 'dx' mm in the x-direction, etc.,
AFTER rotation.
-bshift dx dy dz = Shifts the dataset 'dx' mm in the x-direction, etc.,
BEFORE rotation.
The shift distances by default are along the (x,y,z) axes of the dataset
storage directions (see the output of '3dinfo dataset'). To specify them
anatomically, you can suffix a distance with one of the symbols
'R', 'L', 'A', 'P', 'I', and 'S', meaning 'Right', 'Left', 'Anterior',
'Posterior', 'Inferior', and 'Superior', respectively.
-rotate th1 th2 th3
Specifies the 3D rotation to be composed of 3 planar rotations:
1) 'th1' degrees about the 1st axis, followed by
2) 'th2' degrees about the (rotated) 2nd axis, followed by
3) 'th3' degrees about the (doubly rotated) 3rd axis.
Which axes are used for these rotations is specified by placing
one of the symbols 'R', 'L', 'A', 'P', 'I', and 'S' at the end
of each angle (e.g., '10.7A'). These symbols denote rotation
about the 'Right-to-Left', 'Left-to-Right', 'Anterior-to-Posterior',
'Posterior-to-Anterior', 'Inferior-to-Superior', and
'Superior-to-Inferior' axes, respectively. A positive rotation is
defined by the right-hand rule.
Example: 3drotate -prefix Elvis -bshift 10S 0 0 -rotate 30R 0 0 Sinatra+orig
This will shift the input 10 mm in the superior direction, followed by a 30
degree rotation about the Right-to-Left axis (i.e., nod the head forward).
Algorithm: The rotation+shift is decomposed into 4 1D shearing operations
(the 3D generalization of Paeth's algorithm). The interpolation
(i.e., resampling) method used for these shears can be controlled
by the following options:
-Fourier = Use a Fourier method (the default: most accurate; slowest).
-linear = Use linear (1st order polynomial) interpolation (least accurate).
-cubic = Use the cubic (3rd order) Lagrange polynomial method.
-quintic = Use the quintic (5th order) Lagrange polynomial method.
-heptic = Use the heptic (7th order) Lagrange polynomial method.
|
|||
|
3dTcat /binfs/freesurfer_alpha/afni/Linux/ |
#: 64 Sz: 252804 |
9/7/2000 3:28:15 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Concatenate sub-bricks from input datasets into one big 3D+time dataset.
Usage: 3dTcat options
where the options are:
-prefix pname = Use 'pname' for the output dataset prefix name.
OR -output pname [default='tcat']
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
-glueto fname = Append bricks to the end of the 'fname' dataset.
This command is an alternative to the -prefix
and -session commands.
-dry = Execute a 'dry run'; that is, only print out
what would be done. This is useful when
combining sub-bricks from multiple inputs.
-verb = Print out some verbose output as the program
proceeds (-dry implies -verb).
Using -verb twice results in quite lengthy output.
-rlt = Remove linear trends in each voxel time series loaded
from each input dataset, SEPARATELY. That is, the
data from each dataset is detrended separately.
At least 3 sub-bricks from a dataset must be input
for this option to apply.
Notes: (1) -rlt removes the least squares fit of 'a+b*t'
to each voxel time series; this means that
the mean is removed as well as the trend.
This effect makes it impractical to compute
the % Change using AFNI's internal FIM.
(2) To have the mean of each dataset time series added
back in, use this option in the form '-rlt+'.
In this case, only the slope 'b*t' is removed.
(3) To have the overall mean of all dataset time
series added back in, use this option in the
form '-rlt++'. In this case, 'a+b*t' is removed
from each input dataset separately, and the
mean of all input datasets is added back in at
the end. (This option will work properly only
if all input datasets use at least 3 sub-bricks!)
(4) -rlt can be used on datasets that contain shorts
or floats, but not on complex- or byte-valued
datasets.
Command line arguments after the above are taken as input datasets.
A dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
SUB-BRICK SELECTION:
You can also add a sub-brick selection list after the end of the
dataset name. This allows only a subset of the sub-bricks to be
included into the output (by default, all of the input dataset
is copied into the output). A sub-brick selection list looks like
one of the following forms:
fred+orig[5] ==> use only sub-brick #5
fred+orig[5,9,17] ==> use #5, #9, and #12
fred+orig[5..8] or [5-8] ==> use #5, #6, #7, and #8
fred+orig[5..13(2)] or [5-13(2)] ==> use #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
fred+orig[0..$(3)]
NOTES:
* The TR and other time-axis properties are taken from the
first input dataset that is itself 3D+time. If no input
datasets contain such information, then TR is set to 1.0.
This can be altered using the 3drefit program.
* The sub-bricks are output in the order specified, which may
not be the order in the original datasets. For example, using
fred+orig[0..$(2),1..$(2)]
will cause the sub-bricks in fred+orig to be output into the
new dataset in an interleaved fashion. Using
fred+orig[$..0]
will reverse the order of the sub-bricks in the output.
If the -rlt option is used, the sub-bricks selected from each
input dataset will be re-ordered into the output dataset, and
then this sequence will be detrended.
* You can use the '3dinfo' program to see how many sub-bricks
a 3D+time or a bucket dataset contains.
* The '$', '(', ')', '[', and ']' characters are special to
the shell, so you will have to escape them. This is most easily
done by putting the entire dataset plus selection list inside
single quotes, as in 'fred+orig[5..7,9]'.
* You may wish to use the 3drefit program on the output dataset
to modify some of the .HEAD file parameters.
|
|||
|
3dTSgen /binfs/freesurfer_alpha/afni/Linux/ |
#: 65 Sz: 329100 |
9/7/2000 3:28:15 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dTSgen
Author: B. Douglas Ward
Date: 09 September 1999
This program generates an AFNI 3d+time data set. The time series for
each voxel is generated according to a user specified signal + noise
model.
Usage:
3dTSgen
-input fname fname = filename of prototype 3d + time data file
[-inTR] set the TR of the created timeseries to be the TR
of the prototype dataset
[The default is to compute with TR = 1.]
[The model functions are called for a ]
[time grid of 0, TR, 2*TR, 3*TR, .... ]
-signal slabel slabel = name of (non-linear) signal model
-noise nlabel nlabel = name of (linear) noise model
-sconstr k c d constraints for kth signal parameter:
c <= gs[k] <= d
-nconstr k c d constraints for kth noise parameter:
c+b[k] <= gn[k] <= d+b[k]
-sigma s s = std. dev. of additive Gaussian noise
[-voxel num] screen output for voxel #num
-output fname fname = filename of output 3d + time data file
The following commands generate individual AFNI 1 sub-brick datasets:
[-scoef k fname] write kth signal parameter gs[k];
output 'fim' is written to prefix filename fname
[-ncoef k fname] write kth noise parameter gn[k];
output 'fim' is written to prefix filename fname
The following commands generate one AFNI 'bucket' type dataset:
[-bucket n prefixname] create one AFNI 'bucket' dataset containing
n sub-bricks; n=0 creates default output;
output 'bucket' is written to prefixname
The mth sub-brick will contain:
[-brick m scoef k label] kth signal parameter regression coefficient
[-brick m ncoef k label] kth noise parameter regression coefficient
|
|||
|
3dTsmooth /binfs/freesurfer_alpha/afni/Linux/ |
#: 66 Sz: 254920 |
9/7/2000 3:28:16 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 3dTsmooth [options] dataset
Smooths each voxel time series in a 3D+time dataset and produces as
output a new 3D+time dataset.
General Options:
-prefix ppp = Sets the prefix of the output dataset to be 'ppp'.
[default = 'smooth']
-datum type = Coerce the output data to be stored as the given type.
[default = input data type]
The following options define the smoothing filter to be used.
All filters in this program use 3 input points to compute one
output point: a = input value before the current point
b = input value at the current point
c = input value after the current point
[at the left end, a=b; at the right end, c=b]
-lin = 3 point linear filter: 0.15*a + 0.70*b + 0.15*c
[This is the default smoother]
-med = 3 point median filter: median(a,b,c)
-osf = 3 point order statistics filter:
0.15*min(a,b,c) + 0.70*median(a,b,c) + 0.15*max(a,b,c)
-3lin m = 3 point linear filter: 0.5*(1-m)*a + m*b + 0.5*(1-m)*c
Here, 'm' is a number strictly between 0 and 1.
|
|||
|
3dttest /binfs/freesurfer_alpha/afni/Linux/ |
#: 67 Sz: 488404 |
9/7/2000 3:28:29 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Gosset (Student) t-test sets of 3D datasets
Usage 1: 3dttest [options] -set1 datasets ... -set2 datasets ...
for comparing the means of 2 sets of datasets (voxel by voxel).
Usage 2: 3dttest [options] -base1 bval -set2 datasets ...
for comparing the mean of 1 set of datasets against a constant.
OUTPUTS:
A single dataset is created that is the voxel-by-voxel difference
of the mean of set2 minus the mean of set1 (or minus 'bval').
The output dataset will be of the intensity+Ttest ('fitt') type.
The t-statistic at each voxel can be used as an interactive
thresholding tool in AFNI.
t-TESTING OPTIONS:
-set1 datasets ... = Specifies the collection of datasets to put into
the first set. The mean of set1 will be tested
with a 2-sample t-test against the mean of set2.
N.B.: -set1 and -base1 are mutually exclusive!
-base1 bval = 'bval' is a numerical value that the mean of set2
will be tested against with a 1-sample t-test.
-set2 datasets ... = Specifies the collection of datasets to put into
the second set. There must be at least 2 datasets
in each of set1 (if used) and set2.
-paired = Specifies the use of a paired-sample t-test to
compare set1 and set2. If this option is used,
set1 and set2 must have the same cardinality.
N.B.: A paired test is intended for use when the set1 and set2
dataset function values may be pairwise correlated.
If they are in fact uncorrelated, this test has less
statistical 'power' than the unpaired (default) t-test.
This loss of power is the price that is paid for
insurance against pairwise correlations.
-unpooled = Specifies that the variance estimates for set1 and
set2 be computed separately (not pooled together).
This only makes sense if -paired is NOT given.
N.B.: If this option is used, the number of degrees
of freedom per voxel is a variable, rather
than a constant. NOT RECOMMENDED.
-workmem mega = 'mega' specifies the number of megabytes of RAM
to use for statistical workspace. It defaults
to 12. The program will run faster if this is
larger (see the NOTES section below).
The -base1 or -set1 command line switches must follow all other options
(including those described below) except for the -set2 switch.
INPUT EDITING OPTIONS: The same as are available in 3dmerge.
OUTPUT OPTIONS: these options control the output files.
-session dirname = Write output into given directory (default=./)
-prefix pname = Use 'pname' for the output directory prefix
(default=tdif)
-datum type = Use 'type' to store the output difference
in the means; 'type' may be short or float.
How the default is determined is described
in the notes below.
NOTES:
** To economize on memory, 3dttest makes multiple passes through
the input datasets. On each pass, the entire editing process
will be carried out again. For efficiency's sake, it is
better to carry out the editing using 3dmerge to produce
temporary datasets, and then run 3dttest on them. This applies
with particular force if a 'blurring' option is used.
Note also that editing a dataset requires that it be read into
memory in its entirety (so that the disk file is not altered).
This will increase the memory needs of the program far beyond
the level set by the -workmem option.
** The input datasets are specified by their .HEAD files,
but their .BRIK files must exist also! This program cannot
'warp-on-demand' from other datasets.
** This program cannot deal with time-dependent or complex-valued datasets!
By default, the output dataset function values will be shorts if the
first input dataset is byte- or short-valued; otherwise they will be
floats. This behavior may be overridden using the -datum option.
However, the t-statistic at each voxel will be always be
stored as a short integer that is 1000 times the actual t-value.
|
|||
|
3dvolreg /binfs/freesurfer_alpha/afni/Linux/ |
#: 68 Sz: 420436 |
9/7/2000 3:28:30 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 3dvolreg [options] dataset
Registers each 3D sub-brick from the input dataset to the base brick.
'dataset' may contain a sub-brick selector list.
OPTIONS:
-verbose Print progress reports. Use twice for LOTS of output.
-Fourier Perform the alignments using Fourier interpolation.
-heptic Use heptic polynomial interpolation.
-quintic Use quintic polynomical interpolation.
-cubic Use cubic polynomial interpolation.
Default = Fourier [slowest and most accurate interpolator]
-clipit Clips the values in each output sub-brick to be in the same
range as the corresponding input volume.
The interpolation schemes can produce values outside
the input range, which is sometimes annoying.
-prefix fname Use 'fname' for the output dataset prefix.
The program tries not to overwrite an existing dataset.
Default = 'volreg'.
-base n Sets the base brick to be the 'n'th sub-brick
from the input dataset (indexing starts at 0).
Default = 0 (first sub-brick).
-base 'bset[n]' Sets the base brick to be the 'n'th sub-brick
from the dataset specified by 'bset', as in
-base 'elvis+orig[4]'
The quotes are needed because the '[]' characters
are special to the shell.
-dfile dname Save the motion parameters in file 'dname'.
The output is in 9 ASCII formatted columns:
n roll pitch yaw dS dL dP rmsold rmsnew
where: n = sub-brick index
roll = rotation about the I-S axis }
pitch = rotation about the R-L axis } degrees CCW
yaw = rotation about the A-P axis }
dS = displacement in the Superior direction }
dL = displacement in the Left direction } mm
dP = displacement in the Posterior direction }
rmsold = RMS difference between input brick and base brick
rmsnew = RMS difference between output brick and base brick
N.B.: If the '-dfile' option is not given, the parameters aren't saved.
N.B.: The motion parameters are those needed to bring the sub-brick
back into alignment with the base. In 3drotate, it is as if
the following options were applied to each input sub-brick:
-rotate <roll>I <pitch>R <yaw>A -ashift <dS>S <dL]>L <dP]>P
Algorithm: Iterated linearized weighted least squares to make each
sub-brick as like as possible to the base brick.
This method is useful for finding SMALL MOTIONS ONLY.
See program 3drotate for the volume shift/rotate algorithm.
The following options can be used to control the iterations:
-maxite m = allow up to 'm' iterations for convergence
[default = 9].
-x_thresh x = iterations converge when maximum movement
is less than 'x' voxels [default=0.050000],
-rot_thresh r = and when maximum rotation is less than
'r' degrees [default=0.070000].
-delta d = distance, in voxel size, used to compute
image derivatives using finite differences
[default=0.700000].
-final mode = do the final interpolation using the method
defined by 'mode', which is one of the
strings 'cubic', 'quintic', 'heptic', or
'Fourier'
[default=mode used to estimate parameters].
-weight 'wset[n]' = set the weighting applyed to each voxel
proportional to the brick specified here
[default=smoothed base brick].
Warning: This program can consume large very quantities of memory.
Use of '-verbose -verbose' will show the amount of workspace,
and the steps used in each iteration.
|
|||
|
3dWilcoxon /binfs/freesurfer_alpha/afni/Linux/ |
#: 69 Sz: 258712 |
9/7/2000 3:28:16 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: 3dWilcoxon
Author: B. Douglas Ward
Date: 08 September 1999
This program performs the nonparametric Wilcoxon signed-rank test
for paired comparisons of two samples.
Usage:
3dWilcoxon
-dset 1 filename data set for X observations
. . . . . .
-dset 1 filename data set for X observations
-dset 2 filename data set for Y observations
. . . . . .
-dset 2 filename data set for Y observations
[-workmem mega] number of megabytes of RAM to use
for statistical workspace
[-voxel num] screen output for voxel # num
-out prefixname estimated population delta and
Wilcoxon signed-rank statistics are
written to file prefixname
|
|||
|
3T_toafni /binfs/freesurfer_alpha/afni/Linux/ |
#: 70 Sz: 8736 |
9/7/2000 3:28:07 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
|
4swap /binfs/freesurfer_alpha/afni/Linux/ |
#: 71 Sz: 5300 |
9/7/2000 3:28:30 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: 4swap [-q] file ... -- Swaps byte quadruples on the files listed. The -q option means to work quietly. |
|||
|
abut /binfs/freesurfer_alpha/afni/Linux/ |
#: 72 Sz: 87200 |
9/7/2000 3:28:31 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
ABUT: put noncontiguous FMRI slices together [for to3d]
Copyright 1994,1995 Medical College of Wisconsin
method: put zero valued slices in the gaps, then
replicate images to simulate thinner slices
Usage:
abut [-dzin thickness] [-dzout thickness] [-root name]
[-linear | -blocky] [-verbose] [-skip n+gap] ... images ...
-dzin the thickness value in mm; if not given,
taken to be 1.0 (in which case, the output
thickness and gap sizes are simply relative
to the slice thickness, rather than absolute)
-dzout the output slice thickness, usually smaller than
the input thickness; if not given, the program
will compute a value (the smaller the ratio
dzout/dzin is, the more slices will be output)
-root 'name' is the root (or prefix) for the output
slice filename; for example, '-root fred.'
will result in files fred.0001, fred.0002, ...
-linear if present, this flag indicates that subdivided slices
will be linearly interpolated rather than simply
replicated -- this will make the results smoother
in the through-slice direction (if dzout < dzin)
-blocky similar to -linear, but uses AFNI's 'blocky' interpolation
when possible to put out intermediate slices.
Both interpolation options only apply when dzout < dzin
and when an output slice has a non-gappy neighbor.
-skip 'n+gap' indicates that a gap is to be inserted
between input slices #n and #n+1, where n=1,2,...;
for example, -skip 6+5.5 means put a gap of 5.5 mm
between slices 6 and 7.
More than one -skip option is allowed. They must all occur
before the list of input image filenames.
|
|||
|
adwarp /binfs/freesurfer_alpha/afni/Linux/ |
#: 73 Sz: 443436 |
9/7/2000 3:28:31 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: adwarp.c
Author: B. Douglas Ward
Date: 10 September 1999
Usage: adwarp [options]
Resamples a 'data parent' dataset to the grid defined by an
'anat parent' dataset. The anat parent dataset must contain
in its .HEAD file the coordinate transformation (warp) needed
to bring the data parent dataset to the output grid. This
program provides a batch implementation of the interactive
AFNI 'Write' buttons, one dataset at a time.
Example: adwarp -apar anat+tlrc -dpar func+orig
N.B.: If func+tlrc already exists, it will be overwritten!
Options (so to speak):
----------------------
-apar aset = Set the anat parent dataset to 'aset'. This
is a nonoptional option (must be present).
-dpar dset = Set the data parent dataset to 'dset'. This
is a nonoptional option (must be present).
-prefix ppp = Set the prefix for the output dataset to 'ppp'.
The default is the prefix of 'dset'.
-dxyz ddd = Set the grid spacing in the output datset to
'ddd' mm. The default is 1 mm.
-verbose = Print out progress reports.
-resam rrr = Set the resampling mode to 'rrr', which must be
one of the following [default is Li]:
NN = Nearest Neighbor
Li = Linear Interpolation
Cu = Cubic Interpolation
Bk = Blocky Interpolation
|
|||
|
afni /binfs/freesurfer_alpha/afni/Linux/ |
#: 74 Sz: 3476104 |
9/7/2000 3:28:38 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
MCW AFNI: Analysis of Functional NeuroImages, by R.W. Cox (rwcox@mcw.edu)
version 2.24a: Copyright Medical College of Wisconsin: 28 September 1999
Development supported by MCW funds and by NIH grants MH51358 & NS34798.
Clinical uses are not recommended, and have not been evaluated by the FDA.
Usage 1: read in sessions of 3D datasets (created by to3d)
afni [options] [session_directory ...]
-purge Conserve memory by purging data to disk.
[Use this if you run out of memory when running AFNI.]
[This will slow the code down, so use only if needed.]
-posfunc Set up the color 'pbar' to use only positive function values.
-R Recursively search each session_directory for more session
subdirectories.
WARNING: This will descend the entire filesystem hierarchy from
each session_directory given on the command line. On a
large disk, this may take a long time. To limit the
recursion to 5 levels (for example), use -R5.
-ignore N Tells the program to 'ignore' the first N points in
time series for graphs and FIM calculations.
-im1 N Tells the program to use image N as the first one for
graphs and FIM calculations (same as '-ignore N-1')
-tlrc_small These options set whether to use the 'small' or 'big'
-tlrc_big Talairach brick size. The compiled in default for
the program is now 'big', unlike AFNI 1.0x.
-noqual Tells AFNI not to enforce the 'quality' checks when
making the transformations to +acpc and +tlrc.
-unique Tells the program to create a unique set of colors
for each AFNI controller window. This allows
different datasets to be viewed with different
grayscales or colorscales. Note that -unique
will only work on displays that support 12 bit
PseudoColor (e.g., SGI workstations) or TrueColor.
-orient code Tells afni the orientation in which to display
x-y-z coordinates (upper left of control window).
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
The default code is RAI ==> DICOM order. This can
be set with the environment variable AFNI_ORIENT.
As a special case, using the code 'flipped' is
equivalent to 'LPI' (this is for Steve Rao).
-noplugins Tells the program not to load plugins.
(Plugins can also be disabled by setting the
environment variable AFNI_NOPLUGINS.)
-yesplugouts Tells the program to listen for plugouts.
(Plugouts can also be enabled by setting the
environment variable AFNI_YESPLUGOUTS.)
-YESplugouts Makes the plugout code print out lots of messages
(useful for debugging a new plugout).
-noplugouts Tells the program NOT to listen for plugouts.
(This option is available to override
the AFNI_YESPLUGOUTS environment variable.)
-skip_afnirc Tells the program NOT to read the file .afnirc
in the home directory. See README.setup for
details on the use of .afnirc for initialization.
If no session_directories are given, then the program will use
the current working directory (i.e., './').
The maximum number of sessions is now set to 64.
The maximum number of anatomies per session is 192.
The maximum number of functions per session is 192.
A session must have at least one anatomical dataset in it.
Usage 2: read in images for 'quick and dirty' viewing
afni -im [options] im1 im2 im3 ...
-im Flag to read in images instead of 3D datasets
(Talaraich and functional stuff won't work)
-dy yratio Tells afni the downscreen pixel size is 'yratio' times
the across-screen (x) pixel dimension (default=1.0)
-dz zratio Tells afni the slice thickness is 'zratio' times
the x pixel dimension (default=1.0)
-orient code Tells afni the orientation of the input images.
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
(the default code is ASL ==> sagittal images).
Note that this use of '-orient' is different from
the use when viewing datasets.
-resize Tells afni that all images should be resized to fit
the size of the first one, if they don't already fit
(by default, images must all 'fit' or afni will stop)
-datum type Tells afni to convert input images into the type given:
byte, short, float, complex are the legal types.
The image files (im1 ...) are the same formats as accepted by to3d.
General options (for either Usage):
-gamma gg Tells afni that the gamma correction factor for the
monitor is 'gg' (default gg is 1.0; greater than
1.0 makes the image contrast larger -- this may
also be adjusted interactively)
-install Tells afni to install a new X11 Colormap. This only
means something for PseudoColor displays. Also, it
usually cause the notorious 'technicolor' effect.
-ncolors nn Tells afni to use 'nn' gray levels for the image
displays (default is 80)
-xtwarns Tells afni to show any Xt warning messages that may
occur; the default is to suppress these messages.
-tbar name Uses 'name' instead of 'AFNI' in window titlebars.
-flipim and The '-flipim' option tells afni to display images in the
-noflipim 'flipped' radiology convention (left on the right).
The '-noflipim' option tells afni to display left on
the left, as neuroscientists generally prefer. This
latter mode can also be set by the Unix environment
variable 'AFNI_LEFT_IS_LEFT'. The '-flipim' mode is
the default.
-trace Turns routine call tracing on, for debugging purposes.
-TRACE Turns even more verbose tracing on, for more debugging.
-nomall Disables use of the mcw_malloc() library routines.
N.B.: Many of these options, as well as the initial color set up,
can be controlled by appropriate X11 resources. See the
file AFNI.Xdefaults for instructions and examples.
|
|||
|
afni_environ.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 75 Sz: 219 |
9/7/2000 3:28:38 PM | ASCII C program text |
|
afni_warp.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 76 Sz: 5639 |
9/7/2000 3:28:38 PM | ASCII C program text |
|
AlphaSim /binfs/freesurfer_alpha/afni/Linux/ |
#: 77 Sz: 110212 |
9/7/2000 3:28:30 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: AlphaSim Author: B. Douglas Ward Date: 30 July 1999 This program performs alpha probability simulations. Usage: AlphaSim -nx n1 n1 = number of voxels along x-axis -ny n2 n2 = number of voxels along y-axis -nz n3 n3 = number of voxels along z-axis -dx d1 d1 = voxel size (mm) along x-axis -dy d2 d2 = voxel size (mm) along y-axis -dz d3 d3 = voxel size (mm) along z-axis [-fwhm s] s = Gaussian filter width (FWHM) [-fwhmx sx] sx = Gaussian filter width, x-axis (FWHM) [-fwhmy sy] sy = Gaussian filter width, y-axis (FWHM) [-fwhmz sz] sz = Gaussian filter width, z-axis (FWHM) [-sigma s] s = Gaussian filter width (1 sigma) [-sigmax sx] sx = Gaussian filter width, x-axis (1 sigma) [-sigmay sy] sy = Gaussian filter width, y-axis (1 sigma) [-sigmaz sz] sz = Gaussian filter width, z-axis (1 sigma) [-power] perform statistical power calculations [-ax n1] n1 = extent of active region (in voxels) along x-axis [-ay n2] n2 = extent of active region (in voxels) along y-axis [-az n3] n3 = extent of active region (in voxels) along z-axis [-zsep z] z = z-score separation between signal and noise -rmm r r = cluster connection radius (mm) -pthr p p = individual voxel threshold probability -iter n n = number of Monte Carlo simulations [-quiet] suppress screen output [-out file] file = name of output file |
|||
|
byteorder /binfs/freesurfer_alpha/afni/Linux/ |
#: 78 Sz: 13396 |
9/7/2000 3:28:38 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
CPU byte order = LSB_FIRST |
|||
|
ccalc /binfs/freesurfer_alpha/afni/Linux/ |
#: 79 Sz: 154448 |
9/7/2000 3:28:38 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Skipped per survey instructions. Probably a program that expects console input |
|||
|
cdf /binfs/freesurfer_alpha/afni/Linux/ |
#: 80 Sz: 95460 |
9/7/2000 3:28:39 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage 1: cdf [-v] -t2p statname t params
Usage 2: cdf [-v] -p2t statname p params
Usage 3: cdf [-v] -t2z statname t params
This program does various conversions using the cumulative distribution
function (cdf) of certain canonical probability functions. The optional
'-v' indicates to be verbose -- this is for debugging purposes, mostly.
Usage 1: Converts a statistic 't' to a tail probability.
Usage 2: Converts a tail probability 'p' to a statistic.
Usage 3: Converts a statistic 't' to a N(0,1) value (or z-score)
that has the same tail probability.
The parameter 'statname' refers to the type of distribution to be used.
The numbers in the params list are the auxiliary parameters for the
particular distribution. The following table shows the available
distribution functions and their parameters:
statname Description PARAMETERS
-------- ----------- ----------------------------------------
fico Cor SAMPLES FIT-PARAMETERS ORT-PARAMETERS
fitt Ttest DEGREES-of-FREEDOM
fift Ftest NUMERATOR and DENOMINATOR DEGREES-of-FREEDOM
fizt Ztest N/A
fict ChiSq DEGREES-of-FREEDOM
fibt Beta A (numerator) and B (denominator)
fibn Binom NUMBER-of-TRIALS and PROBABILITY-per-TRIAL
figt Gamma SHAPE and SCALE
fipt Poisson MEAN
|
|||
|
cdflib.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 81 Sz: 4540 |
9/7/2000 3:28:39 PM | ASCII C program text |
|
count /binfs/freesurfer_alpha/afni/Linux/ |
#: 82 Sz: 6644 |
9/7/2000 3:28:39 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: count [options] bot top [step]
* Produces many numbered copies of the root and/or suffix,
counting from 'bot' to 'top' with stride 'step'.
* If 'bot' > 'top', counts backwards with stride '-step'.
* If step is of the form 'R#', then '#' random counts are produced
in the range 'bot..top' (inclusive).
* 'bot' and 'top' must not be negative; step must be positive.
Options:
-digits n prints numbers with 'n' digits [default=4]
-root rrr prints string 'rrr' before the number [default=empty]
-suffix sss prints string 'sss' after the number [default=empty]
-scale fff multiplies each number by the factor 'fff';
if this option is used, -digits is ignored and
the floating point format '%g' is used for output.
('fff' can be a floating point number.)
The main application of this program is for use in C shell programming:
foreach fred ( `count 1 20` )
mv wilma.${fred} barney.${fred}
end
The backward quote operator in the foreach statement executes the
count program, captures its output, and puts it on the command line.
The loop body renames each file wilma.0001 to wilma.0020 to barney.0001
to barney.0020. Read the man page for csh to get more information. In
particular, the csh built-in command '@' can be useful.
|
|||
|
coxplot.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 83 Sz: 15978 |
9/7/2000 3:28:39 PM | ASCII C program text |
|
cs.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 84 Sz: 1017 |
9/7/2000 3:28:39 PM | ASCII English text |
|
editvol.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 85 Sz: 15556 |
9/7/2000 3:28:39 PM | ASCII C program text |
|
eispack.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 86 Sz: 10908 |
9/7/2000 3:28:39 PM | ASCII C program text, with very long lines |
|
f2c.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 87 Sz: 4747 |
9/7/2000 3:28:39 PM | ASCII C program text |
|
FD2 /binfs/freesurfer_alpha/afni/Linux/ |
#: 88 Sz: 253080 |
9/7/2000 3:28:18 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Functional EPIs (64x64, 128x128, 256x256) in any X11 window.
EPI images in 256x256 Signa format are accepted too.
It displays EPI time or frequency course window.
Usage: [options] image1, [image2, ..., image10000]
Where options are:
-d display - X11 display
-geom geometry - initial geometry
-nc #_of_colors - initial number of colors [2-410] (def 80)
-sp #_of_degree - range of color spectrum [0-360] degree (def 240)
-gam gamma - gamma correction (1 for no correction)
-num #_of_images - # of images in time course [2-10000].
-im1 image_# - first image in time course. Previous images will be
filled with this one for proper timing of others.
-ideal ref_file - use ref_file for fim-like calculations
-pcthresh # - use # as threshold for correlation
-extra - files after this are not used in time course
(used instead of -num option)
-fim_colors L thr1 pos1 neg2 ... thrL posL negL
- set up L thresholds and colors for FIM overlay
-gsize x y - set graph window size to x by y pixels
Events:
Program quit : <q> or <Q>
Change to colors : <C>
Change to B & W : <B>
Swap colors : <s>
Restore colors : Button_3 at image center
Squeeze colors : #2 or #3 button - right side of image
Expand colors : left side of image
Circ. color bar : #2 or #3 button at the color bar
Color saturation : #2 or #3 button - the top or bottom
Exact image number: press <I>, enter_number, <CR>
First image : 1
Last image : l
Next image : >
Previous image : <
dragging red pointer works too
Scale Plot up : +
Scale Plot down : -
Increase Grid Spacing : G
Decrease Grid Spacing : g
Toggle Grid and Colors: r
Toggle Frame colors : R
Increase matrix size : M
Decrease matrix size : m
Exact matrix size : N #of_size <CR> (1 to 25 only)
Save minigraph in ASCII file : press <p>
[with xxx_yyy.suffix filename] press <w>
Save current image to a file : press <S>
Position frame in the image : press Button_1 in the image area,
drag cursor, and release button.
Center frame on desired pixel : press Button_1 over desired minigraph.
Rotate image 90 deg. clockwise : press Button_3 in [Rot] window.
counterclockwise : press Button_1 in [Rot] window.
Change to differential display : press [Diff] window. Set first and
last image for averaged reference.
Average of set of images : press [AvIm] (can be used in Diff mode).
Compute FIM overlay : press [FIM], choose ref file,threshold,
then press [GO]
Last image in time course : L
Toggle autoscale of images : A
Hide FIM overlay : H
Hide frame in image : h
Toggle overlay checkerboard : O
Read image into program : F (for file)
Remove image from program : K (for kill)
Move to image 1..9 : 1,2,...9
Toggle common graph baselines : b
|
|||
|
fim2 /binfs/freesurfer_alpha/afni/Linux/ |
#: 89 Sz: 226424 |
9/7/2000 3:28:39 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: fim2 [options] image_files ...
where 'image_files ...' is a sequence of MRI filenames,
options are:
-pcnt # correlation coeff. threshold will be 1 - 0.01 * #
-pcthresh # correlation coeff. threshold will be #
-im1 # index of image file to use as first in time series;
default is 1; previous images are filled with this
image to synchronize with the reference time series
-num # number of images to actually use, if more than this
many are specified on the command line; default is
to use all images
-non this option turns off the default normalization of
the output activation image; the user should provide
a scaling factor via '-coef #', or '1' will be used
-coef # the scaling factor used to convert the activation output
from floats to short ints (if -non is also present)
-ort fname fname = filename of a time series to which the image data
will be orthogonalized before correlations are computed;
any number of -ort options (from 0 on up) may be used
-ideal fname fname = filename of a time series to which the image data
is to be correlated; exactly one such time series is
required; if the -ideal option is not used, then the
first filename after all the options will be used
N.B.: This version of fim2 allows the specification of more than
one ideal time series file. Each one is separately correlated
with the image time series and the one most highly correlated
is selected for each pixel. Multiple ideals are specified
using more than one '-ideal fname' option, or by using the
form '-ideal [ fname1 fname2 ... ]' -- this latter method
allows the use of wildcarded ideal filenames.
The '[' character that indicates the start of a group of
ideals can actually be any ONE of these: [{/%
and the ']' that ends the group can be: ]}/%
[Format of ort and ideal time series files:
ASCII; one number per line;
Same number of lines as images in the time series;
Value over 33333 --> don't use this image in the analysis]
-polref # use polynomials of order 0..# as extra 'orts';
[or -polort #] default is 0 (yielding a constant vector).
Use # = -1 to suppress this feature.
-fimfile fname fname = filename to save activation magnitudes in;
if not given, the last name on the command line will
be used
-corr if present, indicates to write correlation output to
image file 'fimfile.CORR' (next option is better)
-corfile fname fname = filename to save correlation image in;
if not present, and -corr is not present, correlation
image is not saved.
-cnrfile fname fname = filename to save contrast-to-noise image in;
if not present, will not be computed or saved;
CNR is scaled by 100 if images are output as shorts
and is written 'as-is' if output as floats (see -flim).
[CNR is defined here to be alpha/sigma, where
alpha = amplitude of normalized ideal in a pixel
sigma = standard deviation of pixel after removal
of orts and ideal
normalized ideal = ideal scaled so that trough-to-peak
height is one.]
-sigfile fname fname = filename to save standard deviation image in;
the standard deviation is of what is left after the
least squares removal of the -orts, -polrefs, and -ideal.
N.B.: This is always output in the -flim format!
-fitfile fname Image files of the least squares fit coefficients of
all the -ort and -polref time series that
are projected out of the data time series before
the -ideal is fit. The actual filenames will
be fname.01 fname.02 ....
Their order is -orts, then -polrefs, and last -ideal.
N.B.: These are always output in the -flim format!
-subort fname A new timeseries of images is written to disk, with
names of the form 'fname.0001', etc. These images
have the orts and polrefs (but not ideals) subtracted out.
N.B.: These are always output in the -flim format!
-flim If present, write outputs in mrilib 'float' format,
rather than scale+convert to integers
[The 'ftosh' program can later convert to short integers]
-clean if present, then output images won't have the +/- 10000
values forced into their corners for scaling purposes.
-clip if present, output correlations, etc., will be set to
zero in regions of low intensity.
-q if present, indicates 'quiet' operation.
-dfspace[:0] Indicates to use the 'dfspace' filter (a la imreg) to
register the images spatially before filtering.
-regbase fname Indicates to read image in file 'fname' as the base
image for registration. If not given, the first image
in the time series that is used in the correlation
computations will be used. This is also the image
that is used to define 'low intensity' for the -clip option.
|
|||
|
float_scan /binfs/freesurfer_alpha/afni/Linux/ |
#: 90 Sz: 12900 |
9/7/2000 3:28:39 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: float_scan [options] input_filename
Scans the input file of IEEE floating point numbers for
illegal values: infinities and not-a-number (NaN) values.
Options:
-fix = Writes a copy of the input file to stdout (which
should be redirected using '>'), replacing
illegal values with 0. If this option is not
used, the program just prints out a report.
-v = Verbose mode: print out index of each illegal value.
-skip n = Skip the first n floating point locations
(i.e., the first 4*n bytes) in the file
N.B.: This program does NOT work on compressed files, nor does it
work on byte-swapped files (e.g., files transferred between
Sun/SGI/HP and Intel platforms), nor does it work on images
stored in the 'flim' format!
The program 'exit status' is 1 if any illegal values were
found in the input file. If no errors were found, then
the exit status is 0. You can check the exit status by
using the shell variable $status. A C-shell example:
float_scan fff
if ( $status == 1 ) then
float_scan -fix fff > Elvis.Aaron.Presley
rm -f fff
mv Elvis.Aaron.Presley fff
endif
|
|||
|
from3d /binfs/freesurfer_alpha/afni/Linux/ |
#: 91 Sz: 213812 |
9/7/2000 3:28:40 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Copyright 1996 Medical College of Wisconsin
Program: from3d
Purpose: Extract 2d data files from 3d data set.
Usage: from3d [-v] [-nsize]
[-zfirst num] [-zlast num] [-tfirst num] [-tlast num]
-input fname -prefix rname
Options:
-v Print out verbose information.
-nsize Adjust size of 2d data file to be NxN, by padding
with zeros, where N is a power of 2.
-zfirst num Set 'num' = number of first z slice to be extracted.
(default = 1)
-zlast num Set 'num' = number of last z slice to be extracted.
(default = largest)
-tfirst num Set 'num' = number of first time slice to be extracted.
(default = 1)
-tlast num Set 'num' = number of last time slice to be extracted.
(default = largest)
-input fname Read 3d data set from file 'fname'.
'fname' may include a sub-brick selector list.
-prefix rname Write 2d data sets using prefix 'rname'.
|
|||
|
ftosh /binfs/freesurfer_alpha/afni/Linux/ |
#: 92 Sz: 91952 |
9/7/2000 3:28:40 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
MCW FTOSH: convert float images to shorts, by R.W. Cox
Copyright 1995, Medical College of Wisconsin
Usage: ftosh [options] image_files ...
where the image_files are in the same format to3d accepts
and where the options are
-prefix pname: The output files will be named in the format
-suffix sname: 'pname.index.sname' where 'pname' and 'sname'
-start si: are strings given by the first 2 options.
-step ss: 'index' is a number, given by 'si+(i-1)*ss'
for the i-th output file, for i=1,2,...
*** Default pname = 'sh'
*** Default sname = nothing at all
*** Default si = 1
*** Default ss = 1
-nsize: Enforce the 'normal size' option, to make
the output images 64x64, 128x128, or 256x256.
-scale sval: 'sval' and 'bval' are numeric values; if
-base bval: sval is given, then the output images are
-top tval: formed by scaling the inputs by the formula
'output = sval*(input-bval)'.
*** Default sval is determined by finding
V = largest abs(input-bval) in all the input
images and then sval = tval / V.
*** Default tval is 32000; note that tval is only
used if sval is not given on the command line.
*** Default bval is 0.
|
|||
|
imand /binfs/freesurfer_alpha/afni/Linux/ |
#: 93 Sz: 81568 |
9/7/2000 3:28:40 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: imand [-thresh #] input_images ... output_image * Only pixels nonzero in all input images * (and above the threshold, if given) will be output. |
|||
|
imaver /binfs/freesurfer_alpha/afni/Linux/ |
#: 94 Sz: 107364 |
9/7/2000 3:28:40 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: imaver out_ave out_sig input_images ...
(use - to skip output of out_ave and/or out_sig)
* Computes the mean and standard deviation, pixel-by-pixel,
of a whole bunch of images.
* Write output images in 'short int' format if inputs are
short ints, otherwise output images are floating point.
|
|||
|
imcalc /binfs/freesurfer_alpha/afni/Linux/ |
#: 95 Sz: 255148 |
9/7/2000 3:28:40 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Do arithmetic on 2D images, pixel-by-pixel.
Usage: imcalc options
where the options are:
-datum type = Coerce the output data to be stored as the given type,
which may be byte, short, or float.
[default = datum of first input image]
-a dname = Read image 'dname' and call the voxel values 'a'
in the expression. 'a' may be any letter from 'a' to 'z'.
** If some letter name is used in the expression, but not
present in one of the image options here, then that
variable is set to 0.
-expr "expression"
Apply the expression within quotes to the input images,
one voxel at a time, to produce the output image.
("sqrt(a*b)" to compute the geometric mean, for example)
-output name = Use 'name' for the output image filename.
[default='imcalc.out']
PROBLEMS:
** Complex-valued images cannot be processed (byte, short, and float are OK).
** Evaluation of expressions is not very efficient.
EXPRESSIONS:
Arithmetic expressions are allowed, using + - * / ** and parentheses.
As noted above, images are referred to by single letter variable names.
At this time, C relational, boolean, and conditional expressions are
NOT implemented. Built in functions include:
sin , cos , tan , asin , acos , atan , atan2,
sinh , cosh , tanh , asinh , acosh , atanh , exp ,
log , log10, abs , int , sqrt , max , min ,
J0 , J1 , Y0 , Y1 , erf , erfc , qginv, qg ,
rect , step , astep, bool , and , or , mofn ,
where qg(x) = reversed cdf of a standard normal distribution
qginv(x) = inverse function to qg,
min, max, atan2 each take 2 arguments,
J0, J1, Y0, Y1 are Bessel functions (see Watson),
erf, erfc are the error and complementary error functions.
The following functions are designed to help implement logical
functions, such as masking of images against some criterion:
step(x) = {1 if x>0 , 0 if x<=0},
astep(x,y) = {1 if abs(x) > y , 0 otherwise} = step(abs(x)-y)
rect(x) = {1 if abs(x)<=0.5, 0 if abs(x)>0.5},
bool(x) = {1 if x != 0.0 , 0 if x == 0.0},
and(a,b,...,c) = {1 if all arguments are nonzero, 0 if any are zero}
or(a,b,...,c) = {1 if any arguments are nonzero, 0 if all are zero}
mofn(m,a,...,c) = {1 if at least 'm' arguments are nonzero, 0 otherwise}
These last 3 functions take a variable number of arguments.
All computations are carried out in double precision before being
truncated to the final output 'datum'.
Note that the quotes around the expression are needed so the shell
doesn't try to expand * characters, or interpret parentheses.
(Try the 'ccalc' program to see how the expression evaluator works.)
|
|||
|
imdump /binfs/freesurfer_alpha/afni/Linux/ |
#: 96 Sz: 74700 |
9/7/2000 3:28:41 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: imdump input_image * Prints out nonzero pixels in an image; * Results to stdout; redirect (with >) to save to a file; * Format: x-index y-index value, one pixel per line. |
|||
|
immask /binfs/freesurfer_alpha/afni/Linux/ |
#: 97 Sz: 90096 |
9/7/2000 3:28:41 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: immask [-thresh #] [-mask mask_image] [-pos] input_image output_image * Masks the input_image and produces the output_image; * Use of -thresh # means all pixels with absolute value below # in input_image will be set to zero in the output_image * Use of -mask mask_image means that only locations that are nonzero in the mask_image will be nonzero in the output_image * Use of -pos means only positive pixels from input_image will be used * At least one of -thresh, -mask, -pos must be used; more than one is OK. |
|||
|
imreg /binfs/freesurfer_alpha/afni/Linux/ |
#: 98 Sz: 211640 |
9/7/2000 3:28:41 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: imreg [options] base_image image_sequence ...
* Registers each 2D image in 'image_sequence' to 'base_image'.
* If 'base_image' = '+AVER', will compute the base image as
the average of the images in 'image_sequence'.
* If 'base_image' = '+count', will use the count-th image in the
sequence as the base image. Here, count is 1,2,3, ....
OUTPUT OPTIONS:
-nowrite Don't write outputs, just print progress reports.
-prefix pname The output files will be named in the format
-suffix sname 'pname.index.sname' where 'pname' and 'sname'
-start si are strings given by the first 2 options.
-step ss 'index' is a number, given by 'si+(i-1)*ss'
for the i-th output file, for i=1,2,...
*** Default pname = 'reg.'
*** Default sname = nothing at all
*** Default si = 1
*** Default ss = 1
-flim Write output in mrilib floating point format
(which can be converted to shorts using program ftosh).
*** Default is to write images in format of first
input file in the image_sequence.
-quiet Don't write progress report messages.
-debug Write lots of debugging output!
-dprefix dname Write files 'dname'.dx, 'dname'.dy, 'dname'.phi
for use in time series analysis.
ALIGNMENT ALGORITHMS:
-bilinear Uses bilinear interpolation during the iterative
adjustment procedure, rather than the default
bicubic interpolation. NOT RECOMMENDED!
-modes c f r Uses interpolation modes 'c', 'f', and 'r' during
the coarse, fine, and registration phases of the
algorithm, respectively. The modes can be selected
from 'bilinear', 'bicubic', and 'Fourier'. The
default is '-modes bicubic bicubic bicubic'.
-mlcF Equivalent to '-modes bilinear bicubic Fourier'.
-wtim filename Uses the image in 'filename' as a weighting factor
for each voxel (the larger the value the more
importance is given to that voxel).
-dfspace[:0] Uses the 'iterated diffential spatial' method to
align the images. The optional :0 indicates to
skip the iteration of the method, and to use the
simpler linear differential spatial alignment method.
ACCURACY: displacments of at most a few pixels.
*** This is the default method (without the :0).
-dftime[:0] Similar to the above, but after determining the
displacements, it modifies the images by using a
local fit in each voxel. The optional :0 has the
same meaning as for -dfspace.
ACCURACY: unevaluated. This option is intended
for FMRI use only!
-dfspacetime[:0] Apply both algorithms: dfspace, then dftime.
The new two options are used to play with the -dfspace algorithm,
which has a 'coarse' fit phase and a 'fine' fit phase:
-fine blur dxy dphi Set the 3 'fine' fit parameters:
blur = FWHM of image blur prior to registration,
in pixels [must be > 0];
dxy = convergence tolerance for translations,
in pixels;
dphi = convergence tolerance for rotations,
in degrees.
-nofine Turn off the 'fine' fit algorithm. By default, the
algorithm is on, with parameters 1.0, 0.07, 0.21.
|
|||
|
imrotate /binfs/freesurfer_alpha/afni/Linux/ |
#: 99 Sz: 166068 |
9/7/2000 3:28:41 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: imrotate [-linear | -Fourier] dx dy phi input_image output_image Shifts and rotates an image: dx pixels rightwards (not necessarily an integer) dy pixels downwards phi degrees clockwise -linear means to use bilinear interpolation (default is bicubic) -Fourier means to use Fourier interpolaion Values outside the input_image are taken to be zero. |
|||
|
imstack /binfs/freesurfer_alpha/afni/Linux/ |
#: 100 Sz: 146232 |
9/7/2000 3:28:42 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: imstack [options] image_filenames ...
Stacks up a set of 2D images into one big file (a la MGH).
Options:
-datum type Converts the output data file to be 'type',
which is either 'short' or 'float'.
The default type is the type of the first image.
-prefix name Names the output files to be 'name'.b'type' and 'name'.hdr.
The default name is 'obi-wan-kenobi'.
|
|||
|
imstat /binfs/freesurfer_alpha/afni/Linux/ |
#: 101 Sz: 102384 |
9/7/2000 3:28:42 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Calculation of statistics of one or more images.
Usage: imstat [-nolabel] [-pixstat prefix] [-quiet] image_file ...
-nolabel = don't write labels on each file's summary line
-quiet = don't print statistics for each file
-pixstat prefix = if more than one image file is given, then
'prefix.mean' and 'prefix.sdev' will be written
as the pixel-wise statistics images of the whole
collection. These images will be in the 'flim'
floating point format. [This option only works
on 2D images!]
|
|||
|
imupsam /binfs/freesurfer_alpha/afni/Linux/ |
#: 102 Sz: 157768 |
9/7/2000 3:28:42 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: imupsam n input_image output_image
* Upsamples the input 2D image by a factor of n and
writes result into output_image; n must be an
integer in the range 2..30.
* 7th order polynomial interpolation is used in each
direction.
* Inputs can be complex, float, short, PGM, or PPM.
* Author: RW Cox -- 16 April 1999.
|
|||
|
killer.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 103 Sz: 3143 |
9/7/2000 3:28:42 PM | ASCII English text |
|
libcoxplot.a /binfs/freesurfer_alpha/afni/Linux/ |
#: 104 Sz: 177776 |
9/7/2000 3:28:43 PM | current ar archive |
|
libf2c.a /binfs/freesurfer_alpha/afni/Linux/ |
#: 105 Sz: 222670 |
9/7/2000 3:28:43 PM | current ar archive |
|
libmri.a /binfs/freesurfer_alpha/afni/Linux/ |
#: 106 Sz: 2024342 |
9/7/2000 3:28:47 PM | current ar archive |
|
libvolpack.a /binfs/freesurfer_alpha/afni/Linux/ |
#: 107 Sz: 429660 |
9/7/2000 3:28:48 PM | current ar archive |
|
machdep.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 108 Sz: 9501 |
9/7/2000 3:28:48 PM | ASCII C program text |
|
mcw_glob.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 109 Sz: 3443 |
9/7/2000 3:28:48 PM | ASCII C program text |
|
mcw_malloc.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 110 Sz: 1677 |
9/7/2000 3:28:48 PM | ASCII C program text |
|
model_beta.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 111 Sz: 14527 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_constant.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 112 Sz: 14244 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_convgamma.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 113 Sz: 17116 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_convgamma2a.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 114 Sz: 17726 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_diffexp.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 115 Sz: 14402 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_diffusion.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 116 Sz: 14212 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_gammavar.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 117 Sz: 14501 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_linear.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 118 Sz: 14306 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_null.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 119 Sz: 14047 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_quadratic.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 120 Sz: 14437 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_sinewave_ap.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 121 Sz: 14408 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_sinewave_apf.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 122 Sz: 14441 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_squarewave_ap.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 123 Sz: 14442 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_squarewave_apf.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 124 Sz: 14507 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_trnglwave_ap.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 125 Sz: 14569 |
9/7/2000 3:28:48 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
model_trnglwave_apf.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 126 Sz: 14634 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
mrilib.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 127 Sz: 25380 |
9/7/2000 3:28:49 PM | ASCII English text |
|
mritopgm /binfs/freesurfer_alpha/afni/Linux/ |
#: 128 Sz: 86992 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Converts an image to raw pgm format. Results go to stdout and should be redirected. Usage: mritopgm input_image Example: mritopgm fred.001 | ppmtogif > fred.001.gif |
|||
|
multivector.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 129 Sz: 1345 |
9/7/2000 3:28:49 PM | ASCII C program text |
|
nsize /binfs/freesurfer_alpha/afni/Linux/ |
#: 130 Sz: 81056 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Copyright 1994,1995 Medical College of Wisconsin Usage: nsize image_in image_out Zero pads 'image_in' to NxN, N=64,128,256,512, or 1024, whichever is the closest size larger than 'image_in'. [Works only for byte and short images.] |
|||
|
p2t /binfs/freesurfer_alpha/afni/Linux/ |
#: 131 Sz: 11332 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
*** NOTE: This program has been superseded by program 'cdf' ***
Usage #1: p2t p dof
where p = double sided tail probability for t-distribution
dof = number of degrees of freedom to use
OUTPUT = t value that matches the input p
Usage #2: p2t p N L M
where p = double sided tail probability of beta distribution
N = number of measured data points
L = number of nuisance parameters (orts)
M = number of fit parameters
OUTPUT = threshold for correlation coefficient
Usage #3: p2t p
where p = one sided tail probability of Gaussian distribution
OUTPUT = z value for which P(x>z) = p
Usage #4: p2t p dof N
where p = double sided tail probability for distribution of
the mean of N iid zero-mean t-variables
dof = number of degrees of freedom of each t-variable
N = number of t variables averaged
OUTPUT = threshold for the t average statistic
N.B.: The method used for this calculation is the Cornish-
Fisher expansion in N, and is only an approximation.
This also requires dof > 6, and the results will be
less accurate as dof approaches 6 from above!
|
|||
|
plug_3ddot.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 132 Sz: 21763 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_3Ddump_V2.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 133 Sz: 31019 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_4Ddump.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 134 Sz: 36558 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_clust.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 135 Sz: 26146 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_compress.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 136 Sz: 19422 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_coorder.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 137 Sz: 20496 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_copy.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 138 Sz: 22652 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_deconvolve.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 139 Sz: 44489 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_delay_V2.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 140 Sz: 61939 |
9/7/2000 3:28:49 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_drawdset.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 141 Sz: 51598 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_edit.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 142 Sz: 38797 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_extract.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 143 Sz: 34322 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_fourier.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 144 Sz: 28396 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_hemisub.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 145 Sz: 22174 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_histog.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 146 Sz: 38591 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_imreg.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 147 Sz: 26016 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_lsqfit.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 148 Sz: 31215 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_maskave.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 149 Sz: 28631 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_maskcalc.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 150 Sz: 33002 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_maxima.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 151 Sz: 37406 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_nlfit.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 152 Sz: 65173 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_notes.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 153 Sz: 44127 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_power.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 154 Sz: 31921 |
9/7/2000 3:28:50 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_realtime.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 155 Sz: 86712 |
9/7/2000 3:28:51 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_rename.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 156 Sz: 21451 |
9/7/2000 3:28:51 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_render.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 157 Sz: 170513 |
9/7/2000 3:28:51 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_reorder.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 158 Sz: 38476 |
9/7/2000 3:28:51 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_roiedit.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 159 Sz: 102885 |
9/7/2000 3:28:51 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_stats.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 160 Sz: 21343 |
9/7/2000 3:28:51 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_stavg.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 161 Sz: 27814 |
9/7/2000 3:28:51 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_tag.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 162 Sz: 53081 |
9/7/2000 3:28:51 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plug_volreg.so /binfs/freesurfer_alpha/afni/Linux/ |
#: 163 Sz: 34689 |
9/7/2000 3:28:51 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
plugout_ijk /binfs/freesurfer_alpha/afni/Linux/ |
#: 164 Sz: 27240 |
9/7/2000 3:28:51 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: plugout_ijk [-host name] [-v]
This program connects to AFNI and send (i,j,k)
dataset indices to control the viewpoint.
Options:
-host name Means to connect to AFNI running on the
computer 'name' using TCP/IP. The default is to
connect on the current host using shared memory.
-v Verbose mode.
-port pp Use TCP/IP port number 'pp'. The default is
8009, but if two plugins are running on the
same computer, they must use different ports.
-name sss Use the string 'sss' for the name that AFNI assigns
to this plugout. The default is something stupid.
|
|||
|
plugout_tt /binfs/freesurfer_alpha/afni/Linux/ |
#: 165 Sz: 27432 |
9/7/2000 3:28:52 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: plugout_tt [-host name] [-v]
This program connects to AFNI and receives notification
whenever the user changes Talairach coordinates.
Options:
-host name Means to connect to AFNI running on the
computer 'name' using TCP/IP. The default is to
connect on the current host using shared memory.
-ijk Means to get voxel indices from AFNI, rather
than Talairach coordinates.
-v Verbose mode: prints out lots of stuff.
-port pp Use TCP/IP port number 'pp'. The default is
8001, but if two copies of this are running on
the same computer, they must use different ports.
-name sss Use the string 'sss' for the name that AFNI assigns
to this plugout. The default is something stupid.
|
|||
|
plugout_tta /binfs/freesurfer_alpha/afni/Linux/ |
#: 166 Sz: 31240 |
9/7/2000 3:28:52 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: plugout_tta [options]
This program connects to AFNI and receives notification
whenever the user changes Talairach coordinates.
It then drives Netscape to display the closest figures
from the Talairach-Tournoux atlas. Note that Netscape must
be running on the same computer as this plugout, since it
communicates with Netscape using a temporary URL file.
Options:
-host name Means to connect to AFNI running on the
computer 'name' using TCP/IP. The default is to
connect on the current host using shared memory.
To connect to the current host with TCP/IP, use
'-host localhost', or use the '-port' option.
-v Verbose mode: prints out progress reports.
-port pp Use TCP/IP port number 'pp'; default is 8005.
The environment variable AFNI_TTAHOME controls where the atlas
images are loaded from. If not given, a default value is used.
|
|||
|
README /binfs/freesurfer_alpha/afni/Linux/ |
#: 167 Sz: 18301 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.bzip2 /binfs/freesurfer_alpha/afni/Linux/ |
#: 168 Sz: 46932 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.changes /binfs/freesurfer_alpha/afni/Linux/ |
#: 169 Sz: 29924 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.compression /binfs/freesurfer_alpha/afni/Linux/ |
#: 170 Sz: 6433 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.copyright /binfs/freesurfer_alpha/afni/Linux/ |
#: 171 Sz: 2004 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.environment /binfs/freesurfer_alpha/afni/Linux/ |
#: 172 Sz: 22224 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.func_types /binfs/freesurfer_alpha/afni/Linux/ |
#: 173 Sz: 5657 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.notes /binfs/freesurfer_alpha/afni/Linux/ |
#: 174 Sz: 6451 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.plugouts /binfs/freesurfer_alpha/afni/Linux/ |
#: 175 Sz: 553 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.registration /binfs/freesurfer_alpha/afni/Linux/ |
#: 176 Sz: 4405 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.render_scripts /binfs/freesurfer_alpha/afni/Linux/ |
#: 177 Sz: 6815 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.roi /binfs/freesurfer_alpha/afni/Linux/ |
#: 178 Sz: 6841 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.setup /binfs/freesurfer_alpha/afni/Linux/ |
#: 179 Sz: 9457 |
9/7/2000 3:28:30 PM | ASCII English text |
|
README.ziad /binfs/freesurfer_alpha/afni/Linux/ |
#: 180 Sz: 1004 |
9/7/2000 3:28:30 PM | ASCII English text |
|
RSFgen /binfs/freesurfer_alpha/afni/Linux/ |
#: 181 Sz: 22424 |
9/7/2000 3:28:30 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Program: RSFgen
Author: B. Douglas Ward
Date: 24 August 1999
Sample program to generate random stimulus functions.
Usage:
RSFgen
-nt n n = length of time series
-nstim p p = number of input stimuli (experimental conditions)
-nreps i r r = number of repetitions for stimulus i (1<=i<=p)
[-seed s] s = random number seed
[-prefix pname] pname = prefix for p output .1D stimulus functions
e.g., pname1.1D, pname2.1D, ..., pnamep.1D
Warning: This will overwrite pre-existing .1D files
that have the same name.
|
|||
|
sfim /binfs/freesurfer_alpha/afni/Linux/ |
#: 182 Sz: 100992 |
9/7/2000 3:28:52 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
MCW SFIM: Stepwise Functional IMages, by R.W. Cox
Copyright 1995, Medical College of Wisconsin.
Usage: sfim [options] image_files ...
+ image_files are in the same format AFNI accepts
+ options are from the following:
-sfint iname: 'iname' is the name of a file which has
the interval definitions; an example is
3*# 5*rest 4*A 5*rest 4*B 5*rest 4*A 5*rest
which says:
- ignore the 1st 3 images
- take the next 5 as being in task state 'rest'
- take the next 4 as being in task state 'A'
and so on;
task names that start with a nonalphabetic character
are like the '#' above and mean 'ignore'.
*** the default 'iname' is 'sfint'
-base bname: 'bname' is the task state name to use as the
baseline; other task states will have the mean
baseline state subtracted; if there are no task
states from 'iname' that match 'bname', this
subtraction will not occur.
*** the default 'bname' is 'rest'
-localbase: if this option is present, then each non-base
task state interval has the mean of the two
nearest base intervals subtracted instead of the
grand mean of all the base task intervals.
-prefix pname: 'pname' is the prefix for output image filenames for
all states: the i'th interval with task state name
'fred' will be writen to file 'pname.fred.i'.
*** the default 'pname' is 'sfim'
Output files are the base-mean-removed averages for each non-base
task interval, and simply the mean for each base task interval.
Output images are in the 'flim' (floating pt. image) format, and
may be converted to 16 bit shorts using the program 'ftosh'.
|
|||
|
sqwave /binfs/freesurfer_alpha/afni/Linux/ |
#: 183 Sz: 14797 |
9/7/2000 3:28:52 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
FatalError
Usage: [-on #] [-off #] [-length #] [-cycles #]
[-init #] [-onkill #] [-offkill #] [-initkill #] [-name name]
|
|||
|
tagset.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 184 Sz: 1846 |
9/7/2000 3:28:52 PM | ASCII English text |
|
tfim /binfs/freesurfer_alpha/afni/Linux/ |
#: 185 Sz: 102976 |
9/7/2000 3:28:52 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
MCW TFIM: t-tests on sets of functional images, by R.W. Cox
Copyright 1995, Medical College of Wisconsin
Usage 1: tfim [options] -set1 image_files ... -set2 image_files ...
Usage 2: tfim [options] -base1 bval -set2 image_files ...
In usage 1, the collection of images files after '-set1' and the
collection after '-set2' are averaged and differenced, and the
difference is tested for significance with a 2 sample Student t-test.
In usage 2, the collection of image files after '-set2' is averaged
and then has the constant numerical value 'bval' subtracted, and the
difference is tested for significance with a 1 sample Student t-test.
N.B.: The input images can be in the usual 'short' or 'byte'
formats, or in the floating point 'flim' format.
N.B.: If in either set of images, a given pixel has zero variance
(i.e., is constant), then the t-test is not performed.
In that pixel, the .tspm file will be zero.
Options are:
-prefix pname: 'pname' is used as the prefix for the output
filenames. The output image files are
+ pname.diff = average of set2 minus average of set1
(or minus 'bval')
+ pname.tspm = t-statistic of difference
Output images are in the 'flim' (floating pt. image)
format, and may be converted to 16 bit shorts using
the program 'ftosh'.
*** The default 'pname' is 'tfim', if -prefix isn't used.
-pthresh pval: 'pval' is a numeric value between 0 and 1, giving
the significance level (per voxel) to threshold the
output with; voxels with (2-sided) t-statistic
less significant than 'pval' will have their diff
output zeroed.
*** The default is no threshold, if -pthresh isn't used.
-eqcorr dval: If present, this option means to write out the file
pname.corr = equivalent correlation statistic
= t/sqrt(dof+t^2)
The number 'dval' is the value to use for 'dof' if
dval is positive. This would typically be the total
number of data images used in forming the image sets,
if the image sets are from sfim or fim.
If dval is zero, then dof is computed from the number
of images in -set1 and -set2; if these are averages
from program sfim, then dof will be smallish, which in
turn means that significant corr values will be higher
than you may be used to from using program fim.
*** The default is not to write, if -eqcorr isn't used.
-paired: If present, this means that -set1 and -set2 should be
compared using a paired sample t-test. This option is
illegal with the -base1 option. The number of samples
in the two sets of images must be equal.
[This test is implemented by subtracting -set1 images
from the -set2 images, then testing as in '-base1 0'.]
*** The default is to do an unpaired test, if -paired isn't
used. In that case, -set1 and -set2 don't need to have
the same number of images.
|
|||
|
thd_compress.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 186 Sz: 2027 |
9/7/2000 3:28:52 PM | ASCII C program text |
|
thd_iochan.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 187 Sz: 4651 |
9/7/2000 3:28:52 PM | ASCII C program text |
|
thd_maker.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 188 Sz: 1087 |
9/7/2000 3:28:52 PM | ASCII C program text |
|
to3d /binfs/freesurfer_alpha/afni/Linux/ |
#: 189 Sz: 1453376 |
9/7/2000 3:28:55 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
to3d: 2D slices into 3D datasets for MCW AFNI, by R.W. Cox, 1996.
Copyright 1994-6 Medical College of Wisconsin
Usage: to3d [options] image_files ...
Creates 3D datasets for use with AFNI from 2D image files
The available options are
-help show this message
-type declare images to contain data of a given type
where 'type' is chosen from the following options:
ANATOMICAL TYPES
spgr == Spoiled GRASS
fse == Fast Spin Echo
epan == Echo Planar
anat == MRI Anatomy
ct == CT Scan
spct == SPECT Anatomy
pet == PET Anatomy
mra == MR Angiography
bmap == B-field Map
diff == Diffusion Map
omri == Other MRI
abuc == Anat Bucket
FUNCTIONAL TYPES
fim == Intensity
fith == Inten+Thr
fico == Inten+Cor
fitt == Inten+Ttest
fift == Inten+Ftest
fizt == Inten+Ztest
fict == Inten+ChiSq
fibt == Inten+Beta
fibn == Inten+Binom
figt == Inten+Gamma
fipt == Inten+Poisson
fbuc == Func-Bucket
[for paired (+) types above, images are fim first,]
[then followed by the threshold (etc.) image files]
-statpar value value ... value [* NEW IN 1996 *]
This option is used to supply the auxiliary statistical parameters
needed for certain dataset types (e.g., 'fico' and 'fitt'). For
example, a correlation coefficient computed using program 'fim2'
from 64 images, with 1 ideal, and with 2 orts could be specified with
-statpar 64 1 2
-prefix name will write 3D dataset using prefix 'name'
-session name will write 3D dataset into session directory 'name'
-geomparent fname will read geometry data from dataset file 'fname'
N.B.: geometry data does NOT include time-dependence
-anatparent fname will take anatomy parent from dataset file 'fname'
-nosave will suppress autosave of 3D dataset, which normally occurs
when the command line options supply all needed data correctly
-view type [* NEW IN 1996 *]
Will set the dataset's viewing coordinates to 'type', which
must be one of these strings: orig acpc tlrc
TIME DEPENDENT DATASETS [* NEW IN 1996 *]
-time:zt nz nt TR tpattern OR -time:tz nt nz TR tpattern
These options are used to specify a time dependent dataset.
'-time:zt' is used when the slices are input in the order
z-axis first, then t-axis.
'-time:tz' is used when the slices are input in the order
t-axis first, then z-axis.
nz = number of points in the z-direction
nt = number of points in the t-direction
(thus exactly nt * nz slices must be read in)
TR = repetition interval between acquisitions of the
same slice, in milliseconds (or other units, as given below)
tpattern = Code word that identifies how the slices (z-direction)
were gathered in time. The values that can be used:
alt+z = altplus = alternating in the plus direction
alt-z = altminus = alternating in the minus direction
seq+z = seqplus = sequential in the plus direction
seq-z = seqminus = sequential in the minus direction
zero = simult = simultaneous acquisition
@filename = read temporal offsets from 'filename'
For example if nz = 5 and TR = 1000, then the inter-slice
time is taken to be dt = TR/nz = 200. In this case, the
slices are offset in time by the following amounts:
S L I C E N U M B E R
tpattern 0 1 2 3 4 Comment
---------- ---- ---- ---- ---- ---- -------------------------------
altplus 0 600 200 800 400 Alternating in the +z direction
altminus 400 800 200 600 0 Alternating in the -z direction
seqplus 0 200 400 600 800 Sequential in the -z direction
seqplus 800 600 400 200 0 Sequential in the -z direction
simult 0 0 0 0 0 All slices acquired at once
If @filename is used for tpattern, then nz ASCII-formatted numbers are
read from the file. These are used to indicate the time offsets (in ms)
for each slice. For example, if 'filename' contains
0 600 200 800 400
then this is equivalent to 'altplus' in the above example.
Notes:
* Time-dependent functional datasets are not yet supported by
to3d or any other MCW AFNI package software. For many users,
the proper dataset type for these datasets is '-epan'.
* Time-dependent datasets with more than one value per time point
(e.g., 'fith', 'fico', 'fitt') are also not allowed by to3d.
* If you use 'abut' to fill in gaps in the data and/or to
subdivide the data slices, you will have to use the @filename
form for tpattern, unless 'simult' or 'zero' is acceptable.
* At this time, the value of 'tpattern' is not actually used in
any MCW AFNI program. The values are stored in the dataset
.HEAD files, and will be used in the future.
* The values set on the command line can't be altered interactively.
* The units of TR can be specified by the command line options below:
-t=ms or -t=msec --> milliseconds (the default)
-t=s or -t=sec --> seconds
-t=Hz or -t=Hertz --> Hertz (for chemical shift images?)
Alternatively, the units symbol ('ms', 'msec', 's', 'sec',
'Hz', or 'Hertz') may be attached to TR in the '-time:' option,
as in '-time:zt 16 64 4.0sec alt+z'
COMMAND LINE GEOMETRY SPECIFICATION [* NEW IN 1996 *]
-xFOV <dimen1><direc1>-<dimen2><direc2>
or or
-xSLAB <dimen1><direc1>-<direc2>
(Similar -yFOV, -ySLAB, -zFOV and -zSLAB option are also present.)
These options specify the size and orientation of the x-axis extent
of the dataset. <dimen#> means a dimension (in mm); <direc> is
an anatomical direction code, chosen from
A (Anterior) P (Posterior) L (Left)
I (Inferior) S (Superior) R (Right)
Thus, 20A-30P means that the x-axis of the input images runs from
20 mm Anterior to 30 mm Posterior. For convenience, 20A-20P can be
abbreviated as 20A-P.
-xFOV is used to mean that the distances are from edge-to-edge of
the outermost voxels in the x-direction.
-xSLAB is used to mean that the distances are from center-to-center
of the outermost voxels in the x-direction.
Under most circumstance, -xFOV , -yFOV , and -zSLAB would be the
correct combination of geometry specifiers to use. For example,
a common type of run at MCW would be entered as
-xFOV 120I-S -yFOV 120A-P -zSLAB 60S-50I
INPUT IMAGE FORMATS [* SIGNIFICANTLY CHANGED IN 1996 *]
Image files may be single images of unsigned bytes or signed shorts
(64x64, 128x128, 256x256, 512x512, or 1024x1024) or may be grouped
images (that is, 3- or 4-dimensional blocks of data).
In the grouped case, the string for the command line file spec is like
3D:hglobal:himage:nx:ny:nz:fname [16 bit input]
3Ds:hglobal:himage:nx:ny:nz:fname [16 bit input, swapped bytes]
3Db:hglobal:himage:nx:ny:nz:fname [ 8 bit input]
3Di:hglobal:himage:nx:ny:nz:fname [32 bit input]
3Df:hglobal:himage:nx:ny:nz:fname [floating point input]
3Dc:hglobal:himage:nx:ny:nz:fname [complex input]
where '3D:' or '3Ds': signals this is a 3D input file of signed shorts
'3Db:' signals this is a 3D input file of unsigned bytes
'3Di:' signals this is a 3D input file of signed ints
'3Df:' signals this is a 3D input file of floats
'3Dc:' signals this is a 3D input file of complex numbers
(real and imaginary pairs of floats)
hglobal = number of bytes to skip at start of whole file
himage = number of bytes to skip at start of each 2D image
nx = x dimension of each 2D image in the file
ny = y dimension of each 2D image in the file
nz = number of 2D images in the file
fname = actual filename on disk to read
* The ':' separators are required. The k-th image starts at
BYTE offset hglobal+(k+1)*himage+vs*k*nx*ny in file 'fname'
for k=0,1,...,nz-1.
* Here, vs=voxel length=1 for bytes, 2 for shorts, 4 for ints and floats,
and 8 for complex numbers.
* As a special case, hglobal = -1 means read data starting at
offset len-nz*(vs*nx*ny+himage), where len=file size in bytes.
(That is, to read the needed data from the END of the file.)
* Note that there is no provision for skips between data rows inside
a 2D slice, only for skips between 2D slice images.
* The int, float, and complex formats presume that the data in
the image file are in the 'native' format for this CPU; that is,
there is no provision for data conversion (unlike the 3Ds: format).
* Whether the 2D image data is interpreted as a 3D block or a 3D+time
block depends on the rest of the command line parameters. The
various 3D: input formats are just ways of inputting multiple 2D
slices from a single file.
The 'raw pgm' image format is also supported; it reads data into 'byte' images.
Notes:
* Not all MCW AFNI programs support all datum types. Shorts and
floats are safest. (See the '-datum' option below.)
* If '-datum short' is used or implied, then int, float, and complex
data will be scaled to fit into a 16 bit integer. If the '-gsfac'
option below is NOT used, then each slice will be SEPARATELY
scaled according to the following choice:
(a) If the slice values all fall in the range -32767 .. 32767,
then no scaling is performed.
(b) Otherwise, the image values are scaled to lie in the range
0 .. 10000 (original slice min -> 0, original max -> 10000).
This latter option is almost surely not what you want! Therefore,
if you use the 3Di:, 3Df:, or 3Dc: input methods and store the
data as shorts, I suggest you supply a global scaling factor.
Similar remarks apply to '-datum byte' scaling, with even more force.
* To3d now incoporates POSIX filename 'globbing', which means that
you can input filenames using 'escaped wildcards', and then to3d
will internally do the expansion to the list of files. This is
only desirable because some systems limit the number of command-line
arguments to a program. It is possible that you would wish to input
more slice files than your computer supports. For example,
to3d exp.?.*
might overflow the system command line limitations. The way to do
this using internal globbing would be
to3d exp.\?.\*
where the \ characters indicate to pass the wildcards ? and *
through to the program, rather than expand them in the shell.
(a) Note that if you choose to use this feature, ALL wildcards in
a filename must be escaped with \ or NONE must be escaped.
(b) Using the C shell, it is possible to turn off shell globbing
by using the command 'set noglob' -- if you do this, then you
do not need to use the \ character to escape the wildcards.
(c) Internal globbing of 3D: file specifiers is supported in to3d.
For example, '3D:0:0:64:64:100:sl.\*' could be used to input
a series of 64x64x100 files with names 'sl.01', 'sl.02' ....
This type of expansion is specific to to3d; the shell will not
properly expand such 3D: file specifications.
(d) In the C shell (csh or tcsh), you can use forward single 'quotes'
to prevent shell expansion of the wildcards, as in the command
to3d '3D:0:0:64:64:100:sl.*'
The globbing code is adapted from software developed by the
University of California, Berkeley, and is copyrighted by the
Regents of the University of California (see file mcw_glob.c).
-2swap
This option will force all input 2 byte images to be byte-swapped
after they are read in.
-4swap
This option will force all input 4 byte images to be byte-swapped
after they are read in.
-gsfac value
will scale each input slice by 'value'. For example,
'-gsfac 0.31830989' will scale by 1/Pi (approximately).
This option only has meaning if one of '-datum short' or
'-datum byte' is used or implied. Otherwise, it is ignored.
-datum type
will set the voxel data to be stored as 'type', which is currently
allowed to be short, float, byte, or complex.
If -datum is not used, then the datum type of the first input image
will determine what is used. In that case, the first input image will
determine the type as follows:
byte --> byte
short --> short
int, float --> float
complex --> complex
If -datum IS specified, then all input images will be converted
to the desired type. Note that the list of allowed types may
grow in the future, so you should not rely on the automatic
conversion scheme. Also note that floating point datasets may
not be portable between CPU architectures.
-nofloatscan
tells to3d NOT to scan input float and complex data files for
illegal values - the default is to scan and replace illegal
floating point values with zeros (cf. program float_scan).
-in:1
Input of huge 3D: files (with all the data from a 3D+time run, say)
can cause to3d to fail from lack of memory. The reason is that
the images are from a file are all read into RAM at once, and then
are scaled, converted, etc., as needed, then put into the final
dataset brick. This switch will cause the images from a 3D: file
to be read and processed one slice at a time, which will lower the
amount of memory needed. The penalty is somewhat more I/O overhead.
NEW IN 1997:
-orient code
Tells the orientation of the 3D volumes. The code must be 3 letters,
one each from the pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the orientation of the
y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
Note that the -xFOV, -zSLAB constructions can convey this information.
OPTIONS THAT AFFECT THE X11 IMAGE DISPLAY
-gamma gg the gamma correction factor for the
monitor is 'gg' (default gg is 1.0; greater than
1.0 makes the image contrast larger -- this may
also be adjusted interactively)
-ncolors nn use 'nn' gray levels for the image
displays (default is 80)
-xtwarns turn on display of Xt warning messages
|
|||
|
vecmat.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 190 Sz: 12580 |
9/7/2000 3:28:55 PM | ASCII C program text |
|
volpack.h /binfs/freesurfer_alpha/afni/Linux/ |
#: 191 Sz: 25376 |
9/7/2000 3:28:55 PM | ASCII C program text |
|
waver /binfs/freesurfer_alpha/afni/Linux/ |
#: 192 Sz: 81420 |
9/7/2000 3:28:55 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: waver [options] > output_filename
Creates an ideal waveform timeseries file.
The output goes to stdout, and normally would be redirected to a file.
Options: (# refers to a number; [xx] is the default value)
-WAV = Sets waveform to Cox special [default]
-GAM = Sets waveform to form t^b * exp(-t/c)
(waveforms will also be chosen if
one of the options below is used)
These options set parameters for the -WAV waveform.
-delaytime # = Sets delay time to # seconds [2]
-risetime # = Sets rise time to # seconds [4]
-falltime # = Sets fall time to # seconds [6]
-undershoot # = Sets undershoot to # times the peak [0.2]
(this should be a nonnegative factor)
-restoretime # = Sets time to restore from undershoot [2]
These options set parameters for the -GAM waveform:
-gamb # = Sets the parameter 'b' to # [8.6]
-gamc # = Sets the parameter 'c' to # [0.547]
These options apply to any waveform type:
-peak # = Sets peak value to # [100]
-dt # = Sets time step of output AND input [0.1]
The default is just to output the waveform defined by the parameters
above. If an input file is specified by one the options below, then
the timeseries defined by that file will be convolved with the ideal
waveform defined above -- that is, each nonzero point in the input
timeseries will generate a copy of the waveform starting at that point
in time, with the amplitude scaled by the input timeseries value.
-xyout = Output data in 2 columns:
1=time 2=waveform (useful for graphing)
[default is 1 column=waveform]
-input infile = Read timeseries from 'infile';
convolve with waveform to produce output
-inline DATA = Read timeseries from command line DATA;
convolve with waveform to produce output
DATA is in the form of numbers and
count@value, as in
-inline 20@0.0 5@1.0 30@0.0 1.0 20@0.0 2.0
which means a timeseries with 20 zeros, then 5 ones, then 30 zeros,
a single 1, 20 more zeros, and a final 2.
[The '@' character may actually be any of: '@', '*', 'x', 'X'.
Note that * must be typed as \* to prevent the shell from
trying to interpret it as a filename wildcard.]
At least one option is required, or the program will just print this message
to stdout. Only one of the timeseries input options above can be used.
If you have the 'xmgr' graphing program, then a useful way to preview the
results of this program is through a command pipe like
waver -dt 0.25 -xyout -inline 16@1 40@0 16@1 40@0 | xmgr -source stdin
If a square wave is desired, see the 'sqwave' program.
|
|||
| /binfs/freesurfer_alpha/afni/SunOS/ Skipped directory per survey instructions | |||
| /binfs/freesurfer_alpha/average/ | |||
|
lh.average.tif /binfs/freesurfer_alpha/average/ |
#: 193 Sz: 4719734 |
4/5/2000 12:14:26 PM | TIFF image data, big-endian |
|
lh_trans_toSulc.gcs /binfs/freesurfer_alpha/average/ |
#: 194 Sz: 23744678 |
5/18/2001 5:30:48 AM | data |
|
rh.average.tif /binfs/freesurfer_alpha/average/ |
#: 195 Sz: 4719734 |
4/5/2000 12:14:29 PM | TIFF image data, big-endian |
|
rh_trans_toSulc.gcs /binfs/freesurfer_alpha/average/ |
#: 196 Sz: 23479274 |
5/18/2001 5:32:37 AM | data |
|
tissue_parms.txt /binfs/freesurfer_alpha/average/ |
#: 197 Sz: 974 |
6/22/2001 8:50:04 AM | ASCII text |
| /binfs/freesurfer_alpha/bin/ | |||
|
analyse /binfs/freesurfer_alpha/bin/ |
#: 198 Sz: 149296 |
8/26/2001 7:18:50 PM | ELF 32-bit MSB MIPS-II executable, MIPS, version 1 |
|
analyse3 /binfs/freesurfer_alpha/bin/ |
#: 199 Sz: 153924 |
8/26/2001 8:25:46 PM | ELF 32-bit MSB MIPS-II executable, MIPS, version 1 |
|
combine /binfs/freesurfer_alpha/bin/ |
#: 200 Sz: 23416 |
8/26/2001 7:20:25 PM | ELF 32-bit MSB MIPS-II executable, MIPS, version 1 |
|
sigcombine /binfs/freesurfer_alpha/bin/ |
#: 201 Sz: 24028 |
8/26/2001 7:20:26 PM | ELF 32-bit MSB MIPS-II executable, MIPS, version 1 |
|
sigcombine2 /binfs/freesurfer_alpha/bin/ |
#: 202 Sz: 23736 |
8/26/2001 7:20:27 PM | ELF 32-bit MSB MIPS-II executable, MIPS, version 1 |
| /binfs/freesurfer_alpha/bin/IRIX/ Skipped directory per survey instructions | |||
| /binfs/freesurfer_alpha/bin/Linux/ | |||
|
brik2bfloat /binfs/freesurfer_alpha/bin/Linux/ |
#: 203 Sz: 672388 |
8/28/2000 1:33:23 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
use: <brikfilestem> <outstem> <nskip>
### Convert AFNI brik (x,y,z,short; x,y,z,short; ..) to bfloat slices: ###
Args:
<brikfilestem> needs <brikfilestem>.HEAD, <brikfilestem>.BRIK
<outstem> e.g., sigco (correlation)
Output files: (usu. 64x64 floats)
[skips <nskip> x,y,z,short block in BRIK file--16 blocks max]
slice 1: <outstem>_000.bfloat
slice 1: <outstem>_000.hdr
slice 2: <outstem>_001.bfloat
slice 2: <outstem>_001.hdr
[etc]
Examples:
cd <functional_subdir>
brik2bfloat avgatt_fico+orig sigco 1
|
|||
|
byte_swap /binfs/freesurfer_alpha/bin/Linux/ |
#: 204 Sz: 4522 |
6/17/2001 11:43:26 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Skipped per survey instructions. Probably a program that expects console input |
|||
|
correct_offset /binfs/freesurfer_alpha/bin/Linux/ |
#: 205 Sz: 29584 |
9/28/2000 2:31:32 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
imnr0 1 imnr1 256 ptype 2 x 256 y 256 fov 0.256000 thick 0.001000 psiz 0.001000 locatn 0.000000 strtx -0.128000 endx 0.128000 strty -0.128000 endy 0.128000 strtz -0.128000 endz 0.128000 tr 0.000000 te 0.000000 ti 0.000000 ras_good_flag 1 x_ras -1.000000 0.000000 0.000000 y_ras 0.000000 0.000000 -1.000000 z_ras 0.000000 1.000000 0.000000 c_ras 0.000000 0.000000 0.000000 |
|||
|
dicomserver.06Aug01 /binfs/freesurfer_alpha/bin/Linux/ |
#: 206 Sz: 250734 |
8/6/2001 12:15:42 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
ERROR: invalid input arg |
|||
|
dicomserver.19Jul01 /binfs/freesurfer_alpha/bin/Linux/ |
#: 207 Sz: 250734 |
7/19/2001 6:32:26 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
ERROR: invalid input arg |
|||
|
dicomserver.26Feb01 /binfs/freesurfer_alpha/bin/Linux/ |
#: 208 Sz: 250583 |
2/26/2001 2:28:30 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
ERROR: invalid input arg |
|||
|
dicomserver.nofork /binfs/freesurfer_alpha/bin/Linux/ |
#: 209 Sz: 250583 |
6/21/2001 3:07:30 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
ERROR: invalid input arg |
|||
|
extract /binfs/freesurfer_alpha/bin/Linux/ |
#: 210 Sz: 5572 |
6/17/2001 11:43:21 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Skipped per survey instructions. Probably a program that expects console input |
|||
|
ge5_to_minc /binfs/freesurfer_alpha/bin/Linux/ |
#: 211 Sz: 53127 |
6/17/2001 7:27:37 AM | a /usr/local/bin/perl script text executable |
#! /usr/local/bin/perl # # Routines for converting mri files to minc format. Must be included # with routines for reading in data structures, specific to the input # file format. # # $Log: ge5_to_minc,v $ # Revision 1.1 2000/12/12 15:06:25 rhoge # created new perl directory and moved all minc perl stuff here # # Revision 1.1.1.1 2000/11/29 22:39:25 rhoge # adding source to repository on amoeba # # Global variable for indicating byte order |
|||
|
ima2mnc.06Aug01 /binfs/freesurfer_alpha/bin/Linux/ |
#: 212 Sz: 10936 |
8/6/2001 12:16:48 PM | a /usr/bin/perl script text executable |
#!/usr/bin/perl # program to launch dicomserver wrapper, then client # performs checking to prevent conflicts on port # by Rick Hoge #$Log: ima2mnc,v $ #Revision 1.22 2001/08/02 21:18:40 rhoge #fixed syntax error # #Revision 1.21 2001/08/02 21:17:49 rhoge #removed hard-coded paths # #Revision 1.20 2001/08/02 21:16:18 rhoge #removed return value tests for reopening STDIN, STOUT etc. as they #were system dependent # #Revision 1.19 2001/07/30 15:53:16 rhoge #added -wait option to force wait for server process termination # #Revision 1.18 2001/07/19 17:50:46 rhoge #added -nofork command line option which will be passed to server if invoked # #Revision 1.17 2001/07/19 17:36:03 rhoge #added -servparent option, which makes the server process to permit ima2mnc exit #upon completion of conversion (will also need -nofork option) # #Revision 1.16 2001/07/19 17:11:54 rhoge #added experimental dicom input file support - calls dcmtk instead of #siemens_dicom_send # #Revision 1.15 2001/06/01 18:55:14 rhoge #added support for input dicom files # #Revision 1.14 2001/05/30 12:07:49 rhoge #added real time sequence ep2drt_fid_64_27b1953 to list of special seq's # #Revision 1.13 2001/04/19 19:28:44 rhoge #added new dual-echo multi-acq sequence # #Revision 1.12 2001/04/13 23:59:16 rhoge #added new sequence # #Revision 1.11 2001/04/06 21:17:47 rhoge #added new 128^2 sequence # #Revision 1.10 2001/03/22 15:46:52 rhoge #removed exit status check in send command # #Revision 1.9 2001/03/19 20:23:55 rhoge #added remote host functionality (-host, -port, -aetitle) to connect to #remote dicom host # #Revision 1.8 2001/03/13 22:06:32 rhoge #changed exec to system for dicom send command, now exits with status 0 # #Revision 1.7 2001/02/26 22:06:31 rhoge #changed destination dir specification # #Revision 1.6 2001/02/26 13:39:34 rhoge #set default max_outstanding to 10, remove redirect of STDERR # #Revision 1.5 2001/02/26 06:12:42 rhoge #implemented -log and -dicom options # #Revision 1.4 2001/02/26 04:18:29 rhoge #Minor change to cmd line usage # #Revision 1.3 2001/02/26 04:16:18 rhoge #Cleaned up interface, improved port conflict testing. #Ready for preliminary release. # |
|||
|
ima2mnc.19Jul01 /binfs/freesurfer_alpha/bin/Linux/ |
#: 213 Sz: 9958 |
7/19/2001 6:32:44 PM | a /usr/bin/perl script text executable |
#!/usr/bin/perl # program to launch dicomserver wrapper, then client # performs checking to prevent conflicts on port # by Rick Hoge #$Log: ima2mnc,v $ #Revision 1.18 2001/07/19 17:50:46 rhoge #added -nofork command line option which will be passed to server if invoked # #Revision 1.17 2001/07/19 17:36:03 rhoge #added -servparent option, which makes the server process to permit ima2mnc exit #upon completion of conversion (will also need -nofork option) # #Revision 1.16 2001/07/19 17:11:54 rhoge #added experimental dicom input file support - calls dcmtk instead of #siemens_dicom_send # #Revision 1.15 2001/06/01 18:55:14 rhoge #added support for input dicom files # #Revision 1.14 2001/05/30 12:07:49 rhoge #added real time sequence ep2drt_fid_64_27b1953 to list of special seq's # #Revision 1.13 2001/04/19 19:28:44 rhoge #added new dual-echo multi-acq sequence # #Revision 1.12 2001/04/13 23:59:16 rhoge #added new sequence # #Revision 1.11 2001/04/06 21:17:47 rhoge #added new 128^2 sequence # #Revision 1.10 2001/03/22 15:46:52 rhoge #removed exit status check in send command # #Revision 1.9 2001/03/19 20:23:55 rhoge #added remote host functionality (-host, -port, -aetitle) to connect to #remote dicom host # #Revision 1.8 2001/03/13 22:06:32 rhoge #changed exec to system for dicom send command, now exits with status 0 # #Revision 1.7 2001/02/26 22:06:31 rhoge #changed destination dir specification # #Revision 1.6 2001/02/26 13:39:34 rhoge #set default max_outstanding to 10, remove redirect of STDERR # #Revision 1.5 2001/02/26 06:12:42 rhoge #implemented -log and -dicom options # #Revision 1.4 2001/02/26 04:18:29 rhoge #Minor change to cmd line usage # #Revision 1.3 2001/02/26 04:16:18 rhoge #Cleaned up interface, improved port conflict testing. #Ready for preliminary release. # |
|||
|
ima2mnc.19Mar01 /binfs/freesurfer_alpha/bin/Linux/ |
#: 214 Sz: 6672 |
3/19/2001 1:12:43 PM | a /usr/bin/perl script text executable |
#!/usr/bin/perl # program to launch dicomserver wrapper, then client # performs checking to prevent conflicts on port # by Rick Hoge #$Log: ima2mnc,v $ #Revision 1.9 2001/03/19 20:23:55 rhoge #added remote host functionality (-host, -port, -aetitle) to connect to #remote dicom host # #Revision 1.8 2001/03/13 22:06:32 rhoge #changed exec to system for dicom send command, now exits with status 0 # #Revision 1.7 2001/02/26 22:06:31 rhoge #changed destination dir specification # #Revision 1.6 2001/02/26 13:39:34 rhoge #set default max_outstanding to 10, remove redirect of STDERR # #Revision 1.5 2001/02/26 06:12:42 rhoge #implemented -log and -dicom options # #Revision 1.4 2001/02/26 04:18:29 rhoge #Minor change to cmd line usage # #Revision 1.3 2001/02/26 04:16:18 rhoge #Cleaned up interface, improved port conflict testing. #Ready for preliminary release. # |
|||
|
ima2mnc.30Jul01 /binfs/freesurfer_alpha/bin/Linux/ |
#: 215 Sz: 11381 |
7/30/2001 9:09:32 PM | a /usr/bin/perl script text executable |
#!/usr/bin/perl # program to launch dicomserver wrapper, then client # performs checking to prevent conflicts on port # by Rick Hoge #$Log: ima2mnc,v $ #Revision 1.19 2001/07/30 15:53:16 rhoge #added -wait option to force wait for server process termination # #Revision 1.18 2001/07/19 17:50:46 rhoge #added -nofork command line option which will be passed to server if invoked # #Revision 1.17 2001/07/19 17:36:03 rhoge #added -servparent option, which makes the server process to permit ima2mnc exit #upon completion of conversion (will also need -nofork option) # #Revision 1.16 2001/07/19 17:11:54 rhoge #added experimental dicom input file support - calls dcmtk instead of #siemens_dicom_send # #Revision 1.15 2001/06/01 18:55:14 rhoge #added support for input dicom files # #Revision 1.14 2001/05/30 12:07:49 rhoge #added real time sequence ep2drt_fid_64_27b1953 to list of special seq's # #Revision 1.13 2001/04/19 19:28:44 rhoge #added new dual-echo multi-acq sequence # #Revision 1.12 2001/04/13 23:59:16 rhoge #added new sequence # #Revision 1.11 2001/04/06 21:17:47 rhoge #added new 128^2 sequence # #Revision 1.10 2001/03/22 15:46:52 rhoge #removed exit status check in send command # #Revision 1.9 2001/03/19 20:23:55 rhoge #added remote host functionality (-host, -port, -aetitle) to connect to #remote dicom host # #Revision 1.8 2001/03/13 22:06:32 rhoge #changed exec to system for dicom send command, now exits with status 0 # #Revision 1.7 2001/02/26 22:06:31 rhoge #changed destination dir specification # #Revision 1.6 2001/02/26 13:39:34 rhoge #set default max_outstanding to 10, remove redirect of STDERR # #Revision 1.5 2001/02/26 06:12:42 rhoge #implemented -log and -dicom options # #Revision 1.4 2001/02/26 04:18:29 rhoge #Minor change to cmd line usage # #Revision 1.3 2001/02/26 04:16:18 rhoge #Cleaned up interface, improved port conflict testing. #Ready for preliminary release. # |
|||
|
ima2mnc.dng /binfs/freesurfer_alpha/bin/Linux/ |
#: 216 Sz: 7025 |
7/5/2001 1:50:00 PM | a /usr/bin/perl script text executable |
#!/usr/bin/perl # program to launch dicomserver wrapper, then client # performs checking to prevent conflicts on port # by Rick Hoge # This is a modification of ima2mnc in which the server # (ie, the dicom receiver) is launched as the parent # instead of the child so that ima2mnc does not terminate # until the dicom receiver is finished. The version of # the dicom server does not use a fork (ie, # dicomserver.nofork). #$Log: ima2mnc,v $ #Revision 1.9 2001/03/19 20:23:55 rhoge #added remote host functionality (-host, -port, -aetitle) to connect to #remote dicom host # #Revision 1.8 2001/03/13 22:06:32 rhoge #changed exec to system for dicom send command, now exits with status 0 # #Revision 1.7 2001/02/26 22:06:31 rhoge #changed destination dir specification # #Revision 1.6 2001/02/26 13:39:34 rhoge #set default max_outstanding to 10, remove redirect of STDERR # #Revision 1.5 2001/02/26 06:12:42 rhoge #implemented -log and -dicom options # #Revision 1.4 2001/02/26 04:18:29 rhoge #Minor change to cmd line usage # #Revision 1.3 2001/02/26 04:16:18 rhoge #Cleaned up interface, improved port conflict testing. #Ready for preliminary release. # |
|||
|
ima2mnc.dng~ /binfs/freesurfer_alpha/bin/Linux/ |
#: 217 Sz: 6672 |
7/5/2001 1:45:21 PM | a /usr/bin/perl script text executable |
#!/usr/bin/perl # program to launch dicomserver wrapper, then client # performs checking to prevent conflicts on port # by Rick Hoge #$Log: ima2mnc,v $ #Revision 1.9 2001/03/19 20:23:55 rhoge #added remote host functionality (-host, -port, -aetitle) to connect to #remote dicom host # #Revision 1.8 2001/03/13 22:06:32 rhoge #changed exec to system for dicom send command, now exits with status 0 # #Revision 1.7 2001/02/26 22:06:31 rhoge #changed destination dir specification # #Revision 1.6 2001/02/26 13:39:34 rhoge #set default max_outstanding to 10, remove redirect of STDERR # #Revision 1.5 2001/02/26 06:12:42 rhoge #implemented -log and -dicom options # #Revision 1.4 2001/02/26 04:18:29 rhoge #Minor change to cmd line usage # #Revision 1.3 2001/02/26 04:16:18 rhoge #Cleaned up interface, improved port conflict testing. #Ready for preliminary release. # |
|||
|
ima2mnc.nofork /binfs/freesurfer_alpha/bin/Linux/ |
#: 218 Sz: 6679 |
6/22/2001 1:25:59 PM | a /usr/bin/perl script text executable |
#!/usr/bin/perl # program to launch dicomserver wrapper, then client # performs checking to prevent conflicts on port # by Rick Hoge #$Log: ima2mnc,v $ #Revision 1.9 2001/03/19 20:23:55 rhoge #added remote host functionality (-host, -port, -aetitle) to connect to #remote dicom host # #Revision 1.8 2001/03/13 22:06:32 rhoge #changed exec to system for dicom send command, now exits with status 0 # #Revision 1.7 2001/02/26 22:06:31 rhoge #changed destination dir specification # #Revision 1.6 2001/02/26 13:39:34 rhoge #set default max_outstanding to 10, remove redirect of STDERR # #Revision 1.5 2001/02/26 06:12:42 rhoge #implemented -log and -dicom options # #Revision 1.4 2001/02/26 04:18:29 rhoge #Minor change to cmd line usage # #Revision 1.3 2001/02/26 04:16:18 rhoge #Cleaned up interface, improved port conflict testing. #Ready for preliminary release. # |
|||
|
ima2mnc~ /binfs/freesurfer_alpha/bin/Linux/ |
#: 219 Sz: 6013 |
3/14/2001 2:24:44 PM | a /usr/bin/perl script text executable |
#!/usr/bin/perl # program to launch dicomserver wrapper, then client # performs checking to prevent conflicts on port # by Rick Hoge #$Log: ima2mnc,v $ #Revision 1.8 2001/03/13 22:06:32 rhoge #changed exec to system for dicom send command, now exits with status 0 # #Revision 1.7 2001/02/26 22:06:31 rhoge #changed destination dir specification # #Revision 1.6 2001/02/26 13:39:34 rhoge #set default max_outstanding to 10, remove redirect of STDERR # #Revision 1.5 2001/02/26 06:12:42 rhoge #implemented -log and -dicom options # #Revision 1.4 2001/02/26 04:18:29 rhoge #Minor change to cmd line usage # #Revision 1.3 2001/02/26 04:16:18 rhoge #Cleaned up interface, improved port conflict testing. #Ready for preliminary release. # |
|||
|
minc_to_bshort /binfs/freesurfer_alpha/bin/Linux/ |
#: 220 Sz: 594548 |
8/13/2001 10:49:31 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: <minc file> <bshort stem> |
|||
|
minc_to_cor /binfs/freesurfer_alpha/bin/Linux/ |
#: 221 Sz: 1977004 |
9/28/2000 2:40:16 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
****************************************** This program is no longer current. Please use mri_convert in freesurfer_alpha ****************************************** usage: <minc file> <output directory> |
|||
|
mri_add_xform_to_header /binfs/freesurfer_alpha/bin/Linux/ |
#: 222 Sz: 1122948 |
8/28/2000 1:33:28 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mri_add_xform_to_header [xform file name] [input directory] [output directory] |
|||
|
mri_annotation2label /binfs/freesurfer_alpha/bin/Linux/ |
#: 223 Sz: 2854935 |
5/9/2001 12:19:17 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE:
--subject source subject
--hemi hemisphere (lh or rh) (with surface)
--labelbase output will be base-XXX.label
--annotation as found in SUBJDIR/labels <aparc>
--surface name of surface <white>
--help display help
--version display version
This program will convert an annotation into multiple label files.
User specifies the subject, hemisphere, label base, and (optionally)
the annotation base and surface. By default, the annotation base is
aparc. The program will retrieves the annotations from
SUBJECTS_DIR/subject/label/hemi_annotbase.annot. A separate label file
is created for each annotation index; the name of the file conforms to
labelbase-XXX.label, where XXX is the zero-padded 3 digit annotation
index. If labelbase includes a directory path, that directory must
already exist. If there are no points in the annotation file for a
particular index, no label file is created. The xyz coordinates in the
label file are obtained from the values at that vertex of the
specified surface. The default surface is 'white'. Other options
include 'pial' and 'orig'. The human-readable names that correspond
to the annotation indices for aparc can be found in
$MRI_DIR/christophe_parc.txt. This annotation key also appears at the
end of this help.
Bugs:
If the name of the label base does not include a forward slash (ie, '/')
then the program will attempt to put the label files in
$SUBJECTS_DIR/subject/label. So, if you want the labels to go into the
current directory, make sure to put a './' in front of the label base.
Example:
mri_annotation2label --subject LW --hemi rh --labelbase ./labels/aparc-rh
This will get annotations from $SUBJECTS_DIR/LW/label/rh_aparc.annot
and then create about 94 label files: aparc-rh-001.label,
aparc-rh-002.label, ... Note that the directory 'labels' must already
exist.
Testing:
1. Start tksurfer:
tksurfer -LW lh inflated
% read_annotations lh_aparc
When a point is clicked on, it prints out a lot of info, including
something like:
annot = S_temporalis_sup (93, 3988701) (221, 220, 60)
This indicates that annotion number 93 was hit. Save this point.
2. Start another tksurfer and load the label:
tksurfer -LW lh inflated
[edit label field and hit the 'Read' button]
Verify that label pattern looks like the annotation as seen in
the tksurfer window from step 1.
3. Load label into tkmedit
tkmedit LW T1
[Load the label]
[Goto the point saved from step 1]
Annotation Key
could not open translation file ./christophe_parc.txt
|
|||
|
mri_average /binfs/freesurfer_alpha/bin/Linux/ |
#: 224 Sz: 1743504 |
8/28/2000 1:33:37 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mri_average [options] <volume> ... <output volume> -a rigid alignment of input volumes before averaging |
|||
|
mri_ca_label /binfs/freesurfer_alpha/bin/Linux/ |
#: 225 Sz: 1628692 |
9/10/2001 12:56:26 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mri_ca_label [options] <input volume> <xform> <gca file> <output volume> |
|||
|
mri_ca_train /binfs/freesurfer_alpha/bin/Linux/ |
#: 226 Sz: 1572948 |
9/10/2001 12:56:38 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mri_ca_train [options] <subject 1> <subject 2> ... <output file> -spacing - spacing of classifiers in canonical space -gradient - use intensity gradient as input to classifier. |
|||
|
mri_convert /binfs/freesurfer_alpha/bin/Linux/ |
#: 227 Sz: 3700629 |
10/5/2001 5:33:19 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
-u usage: [options] <in volume> <out volume> options are: -ro, --read_only -nw, --no_write -ii, --in_info -oi, --out_info -is, --in_stats -os, --out_stats -iis, --in_i_size <size> -ijs, --in_j_size <size> -iks, --in_k_size <size> -iid, --in_i_direction <R direction> <A direction> <S direction> -ijd, --in_j_direction <R direction> <A direction> <S direction> -ikd, --in_k_direction <R direction> <A direction> <S direction> -ic, --in_center <R coordinate> <A coordinate> <S coordinate> -oni, -oic, --out_i_count <count> -onj, -ojc, --out_j_count <count> -onk, -okc, --out_k_count <count> -ois, --out_i_size <size> -ojs, --out_j_size <size> -oks, --out_k_size <size> -oid, --out_i_direction <R direction> <A direction> <S direction> -ojd, --out_j_direction <R direction> <A direction> <S direction> -okd, --out_k_direction <R direction> <A direction> <S direction> -oc, --out_center <R coordinate> <A coordinate> <S coordinate> -odt, --out_data_type <uchar|short|int|float> SPECIFYING THE INPUT AND OUTPUT FILE TYPES The file type can be specified in two ways. First, mri_convert will try to figure it out on its own from the format of the file name (eg, files that end in .img are assumed to be in spm analyze format). Second, the user can explicity set the type of file using --in_type and/or --out_type. Legal values for --in_type (-it) and --out_type (-ot) are: cor - MGH-NMR COR format minc - MNI's Medical Imaging NetCDF format (output may not work) analyze - 3D analyze (same as spm) analyze4d - 4D analyze (output only) spm - SPM Analyze format (same as analyze and analyze3d) ge - GE Genesis format (input only) gelx - GE LX (input only) lx - same as gelx siemens - Siemens IMA (input only) dicom - generic DICOM Format (iput only) siemens_dicom - Siemens DICOM Format (iput only) brik - AFNI format afni - same as brik bshort - MGH-NMR bshort format bfloat - MGH-NMR bfloat format sdt - Varian (??) outline - MGH-NMR Outline format otl - same as outline gdf - ??? CONVERTING TO SPM-ANALYZE FORMAT Converting to SPM-Analyze format can be done in two ways, depeding upon whether a single frame or multiple frames are desired. For a single frame, simply specify the output file name with a .img extension, and mri_convert will save the first frame into the file. For multiple frames, specify the base as the output file name and add --out_type spm. This will save each frame as baseXXX.img where XXX is the three-digit, zero-padded frame number. Frame numbers begin at one. By default, the width the of zero padding is 3. This can be controlled with --nspmzeropad N where N is the new width. |
|||
|
mri_convert.010718 /binfs/freesurfer_alpha/bin/Linux/ |
#: 228 Sz: 3440264 |
7/18/2001 3:01:09 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <in volume> <out volume> options are: -ro, --read_only -nw, --no_write -ii, --in_info -oi, --out_info -is, --in_stats -os, --out_stats -iis, --in_i_size <size> -ijs, --in_j_size <size> -iks, --in_k_size <size> -iid, --in_i_direction <R direction> <A direction> <S direction> -ijd, --in_j_direction <R direction> <A direction> <S direction> -ikd, --in_k_direction <R direction> <A direction> <S direction> -ic, --in_center <R coordinate> <A coordinate> <S coordinate> -oni, -oic, --out_i_count <count> -onj, -ojc, --out_j_count <count> -onk, -okc, --out_k_count <count> -ois, --out_i_size <size> -ojs, --out_j_size <size> -oks, --out_k_size <size> -oid, --out_i_direction <R direction> <A direction> <S direction> -ojd, --out_j_direction <R direction> <A direction> <S direction> -okd, --out_k_direction <R direction> <A direction> <S direction> -oc, --out_center <R coordinate> <A coordinate> <S coordinate> -odt, --out_data_type <uchar|short|int|float> |
|||
|
mri_convert.bu /binfs/freesurfer_alpha/bin/Linux/ |
#: 229 Sz: 1986932 |
3/29/2001 4:10:13 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <in volume> <out volume> options are: -ro, --read_only -nw, --no_write -ii, --in_info -oi, --out_info -is, --in_stats -os, --out_stats -iis, --in_i_size <size> -ijs, --in_j_size <size> -iks, --in_k_size <size> -iid, --in_i_direction <R direction> <A direction> <S direction> -ijd, --in_j_direction <R direction> <A direction> <S direction> -ikd, --in_k_direction <R direction> <A direction> <S direction> -ic, --in_center <R coordinate> <A coordinate> <S coordinate> -oni, -oic, --out_i_count <count> -onj, -ojc, --out_j_count <count> -onk, -okc, --out_k_count <count> -ois, --out_i_size <size> -ojs, --out_j_size <size> -oks, --out_k_size <size> -oid, --out_i_direction <R direction> <A direction> <S direction> -ojd, --out_j_direction <R direction> <A direction> <S direction> -okd, --out_k_direction <R direction> <A direction> <S direction> -oc, --out_center <R coordinate> <A coordinate> <S coordinate> -odt, --out_data_type <uchar|short|int|float> |
|||
|
mri_cor2label /binfs/freesurfer_alpha/bin/Linux/ |
#: 230 Sz: 2967384 |
5/9/2001 1:11:24 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE:
--c cordir directory to find COR volume
--id labelid 0-255 value in COR volume
--l labelfile name of output file
--help print out help information
Converts values in a COR volume to a label. The program searches the
COR volume in directory 'cordir' for values equal to 'labelid'. The
xyz values for each point are then computed assuming 1 mm^3 voxels and
that xyz=0 at the center of the volume. The xyz values are then stored
in 'labelfile' in the label file format; the vertex values are set to
zero as is the statistic value. While this program can be used with
any COR volume, it was designed to convert parcellation volumes, which
happen to be stored in COR format. See tkmedit for more information
on parcellations. The labelid must be within the range of 0 to 255.
Bugs:
If the name of the label does not include a forward slash (ie, '/')
then the program will attempt to put the label files in
$SUBJECTS_DIR/subject/label. So, if you want the labels to go into
the current directory, make sure to put a './' in front of the label.
Example:
mri_cor2label --c /space/final/frontier/myparcellation
--id 57 --l /home/brainmapper/spattemp/57.label
This will load the COR volume found in the directory
/space/final/frontier/myparcellation and then search the volume for
values equaling 57. The results are stored in 57.label in the directory
/home/brainmapper/spattemp, which must exist prior to execution.
Hidden options:
--synth synthesizes a label (ignores values in COR volume)
See also: tkmedit, mri_label2label.
|
|||
|
mri_em_register /binfs/freesurfer_alpha/bin/Linux/ |
#: 231 Sz: 2175604 |
9/10/2001 12:56:10 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mri_em_register <in volume> <template volume> <output transform> |
|||
|
mri_fill /binfs/freesurfer_alpha/bin/Linux/ |
#: 232 Sz: 2049396 |
6/1/2001 1:32:56 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <input MR directory> <output MR directory> where options are: -T <threshold> - specify fill_holes threshold (default=1) -lh <x> <y> <z> - the Talairach coords of the white matter seed for the left hemisphere -rh <x> <y> <z> - the Talairach coords of the white matter seed for the right hemisphere -P <x> <y> <z> - the Talairach coords of the seed for the pons -C <x> <y> <z> - the Talairach coords of the seed for the corpus callosum |
|||
|
mri_head /binfs/freesurfer_alpha/bin/Linux/ |
#: 233 Sz: 1123864 |
8/28/2000 1:33:57 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: -identify filename
-read filename
-h|-u|-?
|
|||
|
mri_info /binfs/freesurfer_alpha/bin/Linux/ |
#: 234 Sz: 1139716 |
8/28/2000 1:34:03 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
file name: --help file size: 2099560 file type: MINC width: 128 height: 128 depth: 128 number of frames: 1 data type: unknown |
|||
|
mri_label2label /binfs/freesurfer_alpha/bin/Linux/ |
#: 235 Sz: 2866004 |
5/17/2001 1:44:01 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE:
--srclabel input label file
--srcsubject source subject
--trgsubject target subject
--trglabel output label file
--regmethod registration method (surface, volume)
--hemi hemisphere (lh or rh) (with surface)
--srcicoorder when srcsubject=ico
--trgicoorder when trgsubject=ico
--trgsurf get xyz from this surface (white)
--surfreg surface registration (sphere.reg)
Purpose: Converts a label in one subject's space to a label
in another subject's space using either talairach or spherical
as an intermediate registration space.
Example 1: If you have a label from subject fred called
broca-fred.label defined on fred's left hemispherical
surface and you want to convert it to sally's surface, then
mri_label2label --srclabel broca-fred.label --srcsubject fred
--trglabel broca-sally.label --trgsubject sally
--regmethod surface --hemi lh
This will map from fred to sally using sphere.reg. The registration
surface can be changed with --surfreg.
Example 2: You could also do the same mapping using talairach
space as an intermediate:
mri_label2label --srclabel broca-fred.label --srcsubject fred
--trglabel broca-sally.label --trgsubject sally
--regmethod volume
Note that no hemisphere is specified with --regmethod volume.
Notes:
1. A label can be converted to/from talairach space by specifying
the target/source subject as 'talairach'.
2. A label can be converted to/from the icosahedron by specifying
the target/source subject as 'ico'. When the source or target
subject is specified as 'ico', then the order of the icosahedron
must be specified with --srcicoorder/--trgicoorder.
3. When the surface registration method is used, the xyz coordinates
in the target label file are derived from the xyz coordinates
from the target subject's white surface. This can be changed
using the --trgsurf option.
4. When the volume registration method is used, the xyz coordinates
in the target label file are computed as xyzTrg = inv(Ttrg)*Tsrc*xyzSrc
where Tsrc is the talairach transform in
srcsubject/mri/transforms/talairach.xfm, and where Ttrg is the talairach
transform in trgsubject/mri/transforms/talairach.xfm.
5. The registration surfaces are rescaled to a radius of 100 (including
the ico)
|
|||
|
mri_linear_register /binfs/freesurfer_alpha/bin/Linux/ |
#: 236 Sz: 3111272 |
8/28/2000 1:54:34 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mri_linear_register <in volume> <template volume> <output transform> |
|||
|
mri_make_register /binfs/freesurfer_alpha/bin/Linux/ |
#: 237 Sz: 1968901 |
9/28/2000 2:34:03 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <subject name> <fct stem> <path to T1 dir> [<structural dir>]
options are:
-r register_fname defaults to register.dat in the functional directory
-a analyse_fname defaults to analyse.dat in the functional directory
use '-r -' or '-a -' to suppress writing of register or analyse files
|
|||
|
mri_make_template /binfs/freesurfer_alpha/bin/Linux/ |
#: 238 Sz: 1738972 |
8/28/2000 1:34:20 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: SUBJECTS_DIR not defined in environment. |
|||
|
mri_matrix_multiply /binfs/freesurfer_alpha/bin/Linux/ |
#: 239 Sz: 1910149 |
9/28/2000 3:03:06 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: unknown option -help : no input files specified usage: [options] options are: -v verbose '-im file' specifies input matrix files '-iim file' specifies input matrix files to be inverted before multiplication '-om file' specifies output matrix files input and output files may be .dat or .xfm files |
|||
|
mri_normalize /binfs/freesurfer_alpha/bin/Linux/ |
#: 240 Sz: 1346420 |
2/5/2001 6:18:40 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mri_normalize [options] <input volume> <output volume> -n <# of 3d normalization iterations>, default=5 -g <max intensity/mm gradient>, default=0.6 -s <sigma>, intensity interval pct for 3d, default=0.15 |
|||
|
mri_parse_sdcmdir /binfs/freesurfer_alpha/bin/Linux/ |
#: 241 Sz: 2704801 |
10/3/2001 4:12:47 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE:
--d sdicomdir : path to siemens dicom directory
--o outfile : write results to outfile (default is stdout)
--sortbyrun : assign run numbers
--summarize : only print out info for run leaders
--help : how to use this program
This program parses the Siemens DICOM files in a given directory, and
prints out information about each file. The output is printed to stdout
unless a file name is passed with the --o flag.
The most useful information is that which cannot be easily obtained by
probing a dicom file. This includes: the run number, number of frames
in the run, number of slices in the run, and, for mosaics, the number
of rows and cols in the volume.
There are 14 columns in the output:
1. File Number
2. File Name
3. Series Number
4. Series Error Flag (1 for error)
5. Image Number
6. Mosaic Flag (1 for mosaics)
7. Number of Rows in the Volume
8. Number of Columns in the Volume
9. Number of Slices in the Volume for the Series
10. Number of Frames in the Series
11. Repetition Time (sec)
12. Echo Time (ms)
13. Protocol Name - white space stripped
Arguments:
--d sdicomdir : this is the name of the directory where the
dicom files are located (required).
--o outfile : this is the name of a file to which the results will be
printed. If unspecified, the results will be printed to stdout.
--summarize : forces print out of information for the first file in the run.
|
|||
|
mri_partial_ribbon /binfs/freesurfer_alpha/bin/Linux/ |
#: 242 Sz: 1693556 |
4/3/2001 9:25:44 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: mri_partial_ribbon inner_surface_fname outer_surface_fname input_volume_p ref output_volume_pref |
|||
|
mri_probedicom /binfs/freesurfer_alpha/bin/Linux/ |
#: 243 Sz: 929035 |
10/2/2001 1:38:10 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
mri_register /binfs/freesurfer_alpha/bin/Linux/ |
#: 244 Sz: 1737340 |
8/28/2000 1:34:35 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mri_register <in brain> <ref brain> <output file name> CONFLICTING -u OUTPUT: usage: mri_register [image file name] |
|||
|
mri_segment /binfs/freesurfer_alpha/bin/Linux/ |
#: 245 Sz: 1406900 |
10/12/2000 7:37:21 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mri_segment <input volume> <output volume> CONFLICTING -u OUTPUT: usage: mri_segment <classifier file> <input volume> <output volume> |
|||
|
mri_strip_skull /binfs/freesurfer_alpha/bin/Linux/ |
#: 246 Sz: 1526956 |
8/28/2000 1:36:16 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: [-]name <tri_file|option> [-] [-tcl script]
dash prefix on name: don't read MRI images
-----------------------------------------------------------------
option infile (~/bem) outfile (~/bem) datfile (cwd)
-----------------------------------------------------------------
0 ic4.tri [none] [none--defaults]
1(script) ic4.tri brain.tri + images brain.dat
2(script) ic4.tri inner_skull.tri inner_skull.dat
3(script) ic4.tri outer_skull.tri outer_skull.dat
4(script) ic4.tri outer_skin.tri outer_skin.dat
fname fname fname [none--defaults]
-----------------------------------------------------------------
lone dash: infile is outfile|cmdline (not sphere), skip scripts
option=1: images written to ~/mri/brain; otherwise: ~/mri/tmp
command line tcl script (movies): use option=0
[vers: 050304]
|
|||
|
mri_strip_skull_emeg /binfs/freesurfer_alpha/bin/Linux/ |
#: 247 Sz: 1225876 |
5/28/2001 6:39:14 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: [-]name <tri_file|option> [-] [-tcl script]
dash prefix on name: don't read MRI images
-----------------------------------------------------------------
option infile (~/bem) outfile (~/bem) datfile (cwd)
-----------------------------------------------------------------
0 ic4.tri [none] [none--defaults]
1(script) ic4.tri brain.tri + images brain.dat
2(script) ic4.tri inner_skull.tri inner_skull.dat
3(script) ic4.tri outer_skull.tri outer_skull.dat
4(script) ic4.tri outer_skin.tri outer_skin.dat
5(script) ic4.tri brain.tri brain.dat
fname fname fname [none--defaults]
-----------------------------------------------------------------
lone dash: infile is outfile|cmdline (not sphere), skip scripts
option=1: images written to ~/mri/brain; otherwise: ~/mri/tmp
command line tcl script (movies): use option=0
[vers: 050304]
|
|||
|
mri_surf2surf /binfs/freesurfer_alpha/bin/Linux/ |
#: 248 Sz: 3251235 |
9/25/2001 4:08:03 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: --srcsubject source subject --srcsurfval path of file with input values --srcfmt source format --trgsubject target subject --trgicoorder when trgsubject=ico --trgsurfval path of file in which to store output values --trgfmt target format --surfreg surface registration (sphere.reg) --mapmethod nnfr or nnf --hemi hemisphere (lh or rh) --frame save only nth frame (with --ofmt paint) --nsmooth number of smoothing steps This program will resample one surface onto another. |
|||
|
mri_tessellate /binfs/freesurfer_alpha/bin/Linux/ |
#: 249 Sz: 308724 |
8/7/2001 7:54:02 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: <input volume> <label> <output surface> |
|||
|
mri_vol2roi /binfs/freesurfer_alpha/bin/Linux/ |
#: 250 Sz: 3167341 |
8/13/2001 2:29:02 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: --roiavg output path for ROI average --srcvol input volume path --srcfmt input volume format --srcreg source registration (SrcXYZ = R*AnatXYZ) --srcoldreg interpret srcreg as old-style reg.dat --srcwarp source scanner warp table --label path to label file --labelreg label registration (LabelXYZ = L*AnatXYZ) --mskvol mask volume path --mskfmt mask volume format --mskreg mask registration (MaskXYZ = M*AnatXYZ) --msksamesrc mask volume has same FOV as source --mskthresh threshold (0.5) mask threshold --msktail <abs>, pos, or neg (mask tail) --mskframe 0-based mask frame <0> --finalmskvol path in which to save final mask --float2int float-to-int conversion method (<round>, floor, or tkreg ) This program will resample one volume into an ROI. |
|||
|
mri_vol2surf /binfs/freesurfer_alpha/bin/Linux/ |
#: 251 Sz: 1718868 |
4/26/2001 12:54:36 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: --srcvol input volume path --srcfmt input volume format --srcreg source anat2scanner registration --srcoldreg interpret srcreg as old-style reg.dat --srcwarp source scanner warp table --surf target surface (white) --hemi hemisphere (lh or rh) --trgsubject target subject (if different than reg) Options for use with --trgsubject --surfreg surface registration (sphere.reg) --nohash flag to keep the hash table from being used. --icoorder order of icosahedron when trgsubject=ico Options for projecting along the surface normal: --projfrac (0->1) projection along normal --thickness thickness file (thickness) Options for output --o output path --ofmt output format --frame save only nth frame (with --ofmt paint) --interp interpolation method (<nearest>, tli, or sinc) --float2int float-to-int conversion method (<round>, floor, or tkreg ) This program will resample one volume into another. |
|||
|
mri_volcluster /binfs/freesurfer_alpha/bin/Linux/ |
#: 252 Sz: 3454173 |
10/9/2001 4:55:12 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: --i input volid --reg register.dat --frame frameno <0> --thmin minthresh --thmax maxthresh --sign <abs>, neg, pos --minsize minimum volume (mm^3) --mindist distance threshold <0> --o outupt volid --label label file --nlabelcluster nth cluster --synth synthfunc (uniform,loguniform,gaussian) --help : how to use this program This program clusters. |
|||
|
mri_watershed /binfs/freesurfer_alpha/bin/Linux/ |
#: 253 Sz: 1349268 |
6/1/2001 1:34:46 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: mri_watershed [options] input_file output_file optional command -less : to shrink the surface optional command -more : to expand the surface optional command -wat : only the watershed algorithm optional command -wat+temp : watershed algo and first template smoothing optional command -surf: to save the surfaces optional command -s int_i int_j int_k : to add a seed point optional command -t int_threshold: to change the threshold in the watershed analyze process optional command -h int_hpf : to precize the preflooding height (in percent) optional command -n : not to use the watershed analyze process |
|||
|
mri_wmfilter /binfs/freesurfer_alpha/bin/Linux/ |
#: 254 Sz: 1129348 |
8/28/2000 1:36:23 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: subject_name [option ...] this program will read an input volume from $SUBJECTS_DIR/<subject_name>/brain and set all voxels which are determined to be other than white matter to 0, writing the output volume to $SUBJECTS_DIR/<subject_name>/wm. |
|||
|
mris_average_curvature /binfs/freesurfer_alpha/bin/Linux/ |
#: 255 Sz: 1558484 |
10/4/2000 12:01:59 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: no SUBJECTS_DIR in envoronment. |
|||
|
mris_ca_label /binfs/freesurfer_alpha/bin/Linux/ |
#: 256 Sz: 1596948 |
6/1/2001 1:32:54 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mris_ca_label [options] <subject> <hemi> <canon surf> <classifier> <output file> ALSO PRODUCES THIS INCORRECT OUTPUT: usage: mri_ca_label [options] <input volume> <xform> <gca file> <output volume> |
|||
|
mris_ca_train /binfs/freesurfer_alpha/bin/Linux/ |
#: 257 Sz: 1597300 |
6/1/2001 1:32:55 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: mris_ca_train [options] <hemi> <canon surf> <annot file> <subject 1> <sub ject 2> ... <output file> ALSO PRODUCES THE FOLLOWING INCORRECT OUTPUT: usage: mri_ca_train [options] <subject 1> <subject 2> ... <output file> -spacing - spacing of classifiers in canonical space -gradient - use intensity gradient as input to classifier. |
|||
|
mris_convert /binfs/freesurfer_alpha/bin/Linux/ |
#: 258 Sz: 1566548 |
2/1/2001 12:00:50 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <input surface file> <output surface file> This program will convert an MRI surface to ascii. valid options are: |
|||
|
mris_convert_g /binfs/freesurfer_alpha/bin/Linux/ |
#: 259 Sz: 3083655 |
1/10/2003 4:10:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <input surface file> <output surface file> This program will convert an MRI surface to ascii. valid options are: |
|||
|
mris_curvature /binfs/freesurfer_alpha/bin/Linux/ |
#: 260 Sz: 1419708 |
8/28/2000 1:34:56 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <input surface file> This program will the second fundamental form of a cortical surface. It will create two new files <hemi>.H and <hemi>.K with the mean and Gaussian curvature respectively. valid options are: |
|||
|
mris_euler_number /binfs/freesurfer_alpha/bin/Linux/ |
#: 261 Sz: 1556692 |
10/5/2000 1:06:38 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <input surface file> This program will compute the euler number of a cortical surface. valid options are: |
|||
|
mris_fix_topology /binfs/freesurfer_alpha/bin/Linux/ |
#: 262 Sz: 1686100 |
5/11/2001 4:51:05 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <subject name> <hemisphere> This program computes a mapping from the unit sphere onto the surface of the cortex from a previously generated approximation of the cortical surface, thus guaranteeing a topologically correct surface. valid options are: |
|||
|
mris_flatten /binfs/freesurfer_alpha/bin/Linux/ |
#: 263 Sz: 1561012 |
10/4/2000 12:01:40 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <input patch> <output patch> This program will flatten a surface patch valid options are: -w <# iterations> write out the surface every # of iterations. -distances <nbhd size> <# of vertices at each distance> specify size of neighborhood and number of vertices at each distance to be used in the optimization. |
|||
|
mris_inflate /binfs/freesurfer_alpha/bin/Linux/ |
#: 264 Sz: 1419612 |
8/28/2000 1:35:24 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <input surface file> <output surface file> This program will inflate a cortical surface. valid options are: -n <# of iterations> - set the maximum # of iterations (default = 55) -w <# of iterations> - write out a snapshot of the inflation every #th time step. -dist <distance coefficient> - specify the relative strength of the metric preserving term in the cost functional versus the smoothing term (default = 0.1). |
|||
|
mris_make_surfaces /binfs/freesurfer_alpha/bin/Linux/ |
#: 265 Sz: 2031156 |
6/1/2001 3:01:55 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <subject name> <hemisphere> This program positions the tessellation of the cortical surface at the white matter surface, then the gray matter surface and generate surface files for these surfaces as well as a 'curvature' file for the cortical thickness, and a surface file which approximates layer IV of the cortical sheet. valid options are: -q omit self-intersection and only generate gray/white surface. -c create curvature and area files from white matter surface -a <avgs> average curvature values <avgs> times (default=10) -whiteonly only generate white matter surface |
|||
|
mris_make_template /binfs/freesurfer_alpha/bin/Linux/ |
#: 266 Sz: 1418972 |
8/28/2000 1:35:40 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <hemi> <surface name> <subject> <subject> ... <output name> This program will add a template into an average surface. valid options are: |
|||
|
mris_register /binfs/freesurfer_alpha/bin/Linux/ |
#: 267 Sz: 1560244 |
10/4/2000 12:02:18 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <input surface> <average surface> <output surface> This program register a surface with an average surface. valid options are: |
|||
|
mris_smooth /binfs/freesurfer_alpha/bin/Linux/ |
#: 268 Sz: 1557300 |
10/4/2000 12:01:46 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <input surface> <output surface> This program smooths the tessellation of a cortical surface and write out the first and second order properties after smoothing to the files $hemi.curv (mean curvature) and $hemi.area (area). valid options are: -a <avgs> specify # of curvature averaging iterations (def=10). -n <niter> specify # of smoothing iterations (def=10). |
|||
|
mris_sphere /binfs/freesurfer_alpha/bin/Linux/ |
#: 269 Sz: 1562388 |
10/4/2000 12:01:33 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <surface file> <patch file name> <output patch> This program will add a template into an average surface. valid options are: |
|||
|
mris_thickness /binfs/freesurfer_alpha/bin/Linux/ |
#: 270 Sz: 1556724 |
10/4/2000 12:02:12 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <subject name> <hemi> <thickness file> This program measures the thickness of the cortical surface and writes the resulting measurement into a 'curvature' file <output file>. valid options are: |
|||
|
mris_twoclass /binfs/freesurfer_alpha/bin/Linux/ |
#: 271 Sz: 1930708 |
9/20/2001 7:42:18 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: -o <output subject> [options] <hemi> <surf> <curv> <out prefix> <c1_subject1> <c1_subject2>... : <c2_subject1> <c2_subject2>... where surf must be a spherical surface suitable for computing geodesics The <c1_subject> ... is a list of subjects from one class and the <c2_subject>... is a list of subjects from another class. valid options are: -wfile - not implemented yet (reading of *.w files) -optimal - compute optimal smoothing kernel -fixed <navgs> - apply a fixed smoothing kernel -conditions <c0> <c1>- write out sigavg<c?> and sigvar<c?> files -t <fthresh> - specify F threshold -o <subject> - specify output subject name -b - perform bonferroni correction This program will compute the autocorrelation function of a curvature file valid options are: |
|||
|
nmovie /binfs/freesurfer_alpha/bin/Linux/ |
#: 272 Sz: 4530163 |
2/7/2001 1:06:30 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
nmovie <image file> <image file> ... |
|||
|
paint /binfs/freesurfer_alpha/bin/Linux/ |
#: 273 Sz: 1726484 |
9/28/2000 1:43:37 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: input_file hemi surf output_file -options
input_file - eg, stem_%03d.bfloat
surf - surface name (eg, orig, smoothwm, etc)
hemi - lh or rh
output_file - eg, stem-lh.w
options:
-imageoffset n - zero-based frame number to paint <0>
-nslices n - number of input slices
-regdat fname - name of register file <register.dat>
-dmax dist - distance (mm) to project along normal <0>
-dstep stepsize - size (mm) of projection step <0.25>
|
|||
|
siemens_dicom_send /binfs/freesurfer_alpha/bin/Linux/ |
#: 274 Sz: 105712 |
2/26/2001 1:01:10 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: host port AEtitle [directory] patient_num [first [last]] |
|||
|
spm2bfloat /binfs/freesurfer_alpha/bin/Linux/ |
#: 275 Sz: 310608 |
8/28/2000 1:36:32 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: in-spm-stem out-bfloat-stem out-registerdat-path subjname |
|||
|
sql.redhat61.so /binfs/freesurfer_alpha/bin/Linux/ |
#: 276 Sz: 184993 |
10/26/2000 12:18:45 PM | ELF 32-bit LSB shared object, Intel 80386, version |
|
stat_normalize /binfs/freesurfer_alpha/bin/Linux/ |
#: 277 Sz: 1553704 |
8/28/2000 1:36:47 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] <input sv prefix> <output sv prefix> options are: -r <resolution> - set output resolution (def=8mm) -f <field of view> - set output field of view (def=256) -S <hemisphere> <surface> - average in spherical coordinates This program will convert average a sequence of volume-based statistics in Talairach space: |
|||
|
statcombine /binfs/freesurfer_alpha/bin/Linux/ |
#: 278 Sz: 1497516 |
8/28/2000 1:36:39 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: subjname hemi cmd condinfix1 condinfix2 ... outinfix
cmd : avg,anova,diff,f,mean_diff
condinfix : cond num infile infix: {stem}{avg,var}{cond}-{hemi}.w
outinfix : e.g., from cond nums: 3_1
Flags:
-surf <str> (-s) surf for sampling data (default: orig)
-prefix <str> (-p) in/outfile prefix (default: sig)
-infixes <r> <i> (-x) real,imaginary infixes--default: 2 3
-outfixes <r> <i> (-x) real,imaginary outfixes--default: 2 3
|
|||
|
surf2surf /binfs/freesurfer_alpha/bin/Linux/ |
#: 279 Sz: 3123413 |
1/26/2001 4:18:18 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: --srcsubject source subject --srcsurfval path of file with input values --srcfmt source format --trgsubject target subject --trgicoorder when trgsubject=ico --trgsurfval path of file in which to store output values --trgfmt target format --surfreg surface registration (sphere.reg) --mapmethod nnfr or nnf --hemi hemisphere (lh or rh) --frame save only nth frame (with --ofmt paint) This program will resample one surface onto another. |
|||
|
tkmedit /binfs/freesurfer_alpha/bin/Linux/ |
#: 280 Sz: 8071062 |
10/10/2001 8:24:56 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
License file not found ! |
|||
|
tkmedit.010601 /binfs/freesurfer_alpha/bin/Linux/ |
#: 281 Sz: 4460321 |
6/1/2001 5:37:53 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tkmedit.010628 /binfs/freesurfer_alpha/bin/Linux/ |
#: 282 Sz: 4467121 |
6/28/2001 8:41:05 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tkmedit.010827 /binfs/freesurfer_alpha/bin/Linux/ |
#: 283 Sz: 4668286 |
8/27/2001 2:39:44 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tkmedit.010828 /binfs/freesurfer_alpha/bin/Linux/ |
#: 284 Sz: 4685534 |
8/28/2001 9:19:20 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tkmedit.010924 /binfs/freesurfer_alpha/bin/Linux/ |
#: 285 Sz: 4668286 |
9/24/2001 7:10:58 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tkmedit.dynamic /binfs/freesurfer_alpha/bin/Linux/ |
#: 286 Sz: 3449740 |
10/10/2001 8:24:55 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tkmedit.static /binfs/freesurfer_alpha/bin/Linux/ |
#: 287 Sz: 8071062 |
10/5/2001 8:30:30 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
License file not found ! |
|||
|
tkmedit.static.010828 /binfs/freesurfer_alpha/bin/Linux/ |
#: 288 Sz: 8043617 |
8/28/2001 9:20:59 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
License file not found ! |
|||
|
tkmedit.static.010924 /binfs/freesurfer_alpha/bin/Linux/ |
#: 289 Sz: 8045594 |
9/24/2001 7:11:18 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
License file not found ! |
|||
|
tkregister /binfs/freesurfer_alpha/bin/Linux/ |
#: 290 Sz: 2666056 |
10/10/2001 8:24:57 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
tkregister: env var MRI_DIR undefined (use setenv)
[dir containing mri distribution]
|
|||
|
tkregister.dynamic /binfs/freesurfer_alpha/bin/Linux/ |
#: 291 Sz: 1266268 |
10/10/2001 8:24:57 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
tkregister: env var MRI_DIR undefined (use setenv)
[dir containing mri distribution]
|
|||
|
tkregister.static /binfs/freesurfer_alpha/bin/Linux/ |
#: 292 Sz: 2666056 |
6/1/2001 6:37:54 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
tkregister: env var MRI_DIR undefined (use setenv)
[dir containing mri distribution]
|
|||
|
tksurfer /binfs/freesurfer_alpha/bin/Linux/ |
#: 293 Sz: 7841481 |
10/10/2001 8:25:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
tksurfer: env var MRI_DIR undefined (use setenv)
[dir containing mri distribution]
|
|||
|
tksurfer.010716 /binfs/freesurfer_alpha/bin/Linux/ |
#: 294 Sz: 2555600 |
7/16/2001 2:40:42 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tksurfer.dynamic /binfs/freesurfer_alpha/bin/Linux/ |
#: 295 Sz: 4634963 |
10/10/2001 8:24:58 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tksurfer.new /binfs/freesurfer_alpha/bin/Linux/ |
#: 296 Sz: 7841481 |
10/10/2001 8:25:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
tksurfer: env var MRI_DIR undefined (use setenv)
[dir containing mri distribution]
|
|||
|
tksurfer.new.010711 /binfs/freesurfer_alpha/bin/Linux/ |
#: 297 Sz: 4600470 |
7/11/2001 11:47:19 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tksurfer.new.010816 /binfs/freesurfer_alpha/bin/Linux/ |
#: 298 Sz: 4603605 |
8/16/2001 1:17:41 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tksurfer.new.010828 /binfs/freesurfer_alpha/bin/Linux/ |
#: 299 Sz: 4607509 |
8/28/2001 1:29:58 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tksurfer.new.010914 /binfs/freesurfer_alpha/bin/Linux/ |
#: 300 Sz: 4611834 |
9/14/2001 1:08:44 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tksurfer.new.011001 /binfs/freesurfer_alpha/bin/Linux/ |
#: 301 Sz: 4634739 |
10/1/2001 2:14:17 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tksurfer.new.dynamic /binfs/freesurfer_alpha/bin/Linux/ |
#: 302 Sz: 4634963 |
10/10/2001 8:24:58 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory |
|||
|
tksurfer.new.static /binfs/freesurfer_alpha/bin/Linux/ |
#: 303 Sz: 7841481 |
9/26/2001 8:00:37 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
tksurfer: env var MRI_DIR undefined (use setenv)
[dir containing mri distribution]
|
|||
|
tksurfer.new.static.010711 /binfs/freesurfer_alpha/bin/Linux/ |
#: 304 Sz: 6281230 |
7/11/2001 11:49:31 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
/binfs/freesurfer_alpha/bin/Linux/tksurfer.new.static.010711: Permission denied |
|||
|
tksurfer.new.static.010816 /binfs/freesurfer_alpha/bin/Linux/ |
#: 305 Sz: 7815255 |
8/16/2001 1:21:00 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
/binfs/freesurfer_alpha/bin/Linux/tksurfer.new.static.010816: Permission denied |
|||
|
tksurfer.static.010716 /binfs/freesurfer_alpha/bin/Linux/ |
#: 306 Sz: 0 |
7/16/2001 2:43:30 PM | empty |
|
tksurfer.static.new /binfs/freesurfer_alpha/bin/Linux/ |
#: 307 Sz: 7846613 |
10/1/2001 2:14:36 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
tksurfer: env var MRI_DIR undefined (use setenv)
[dir containing mri distribution]
|
|||
|
tksurfer.static.new.011001 /binfs/freesurfer_alpha/bin/Linux/ |
#: 308 Sz: 7846389 |
10/1/2001 2:14:33 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
tksurfer: env var MRI_DIR undefined (use setenv)
[dir containing mri distribution]
|
|||
|
vss-dump /binfs/freesurfer_alpha/bin/Linux/ |
#: 309 Sz: 2906483 |
1/22/2001 12:31:31 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
ERROR: file has unrecognized file code 0 |
|||
| /binfs/freesurfer_alpha/bin/noarch/ | |||
|
Art_csurf /binfs/freesurfer_alpha/bin/noarch/ |
#: 310 Sz: 2048 |
7/16/2000 6:17:05 PM | Bourne shell script text executable |
#! /bin/sh # force local (next line not seen by tcl) \ |
|||
|
bmh.tcl /binfs/freesurfer_alpha/bin/noarch/ |
#: 311 Sz: 0 |
7/16/2000 6:17:06 PM | empty |
|
browse-minc-header.tcl /binfs/freesurfer_alpha/bin/noarch/ |
#: 312 Sz: 10270 |
7/17/2000 12:18:16 PM | a /usr/bin/wish script text executable |
#!/usr/bin/wish |
|||
|
browse-sessions /binfs/freesurfer_alpha/bin/noarch/ |
#: 313 Sz: 2806 |
6/1/2001 3:06:06 PM | C shell script text executable |
#!/bin/csh -f # # $Id: browse-sessions,v 1.4 2001/06/01 22:05:44 greve Exp $ # This is just a wrapper for unpack_mnc.tcl. It sets the TCL and TK # libraries to be version 8.0 (which is uncompatible with other programs) # |
|||
|
check_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 314 Sz: 1846 |
12/1/2000 4:48:13 AM | a /usr/bin/perl script text executable |
#!/usr/bin/perl |
|||
|
cor_to_minc /binfs/freesurfer_alpha/bin/noarch/ |
#: 315 Sz: 476 |
7/17/2000 12:18:16 PM | Bourne shell script text executable |
#!/bin/sh |
|||
|
csurf /binfs/freesurfer_alpha/bin/noarch/ |
#: 316 Sz: 383386 |
7/16/2001 12:54:40 PM | Bourne shell script text executable |
#! /bin/sh # force local (next line not seen by tcl) \ |
|||
|
csurf.010599 /binfs/freesurfer_alpha/bin/noarch/ |
#: 317 Sz: 0 |
7/16/2000 6:17:07 PM | empty |
|
csurf.010604 /binfs/freesurfer_alpha/bin/noarch/ |
#: 318 Sz: 378532 |
6/4/2001 8:01:59 AM | Bourne shell script text executable |
#! /bin/sh # force local (next line not seen by tcl) \ |
|||
|
csurf.new /binfs/freesurfer_alpha/bin/noarch/ |
#: 319 Sz: 0 |
7/16/2000 6:17:10 PM | empty |
|
csurf.Old110499 /binfs/freesurfer_alpha/bin/noarch/ |
#: 320 Sz: 0 |
7/16/2000 6:17:09 PM | empty |
|
csurf33d /binfs/freesurfer_alpha/bin/noarch/ |
#: 321 Sz: 0 |
7/16/2000 6:17:12 PM | empty |
|
fix_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 322 Sz: 117 |
11/30/2000 12:38:26 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
fix_subject_corrected /binfs/freesurfer_alpha/bin/noarch/ |
#: 323 Sz: 84 |
7/2/2000 4:50:07 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
fix_subject_corrected-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 324 Sz: 794 |
7/16/2000 6:21:14 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
fix_subject_corrected-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 325 Sz: 705 |
7/16/2000 6:21:14 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
fix_subject-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 326 Sz: 472 |
11/30/2000 12:33:01 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
fix_subject-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 327 Sz: 471 |
11/30/2000 12:32:47 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
inflate_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 328 Sz: 456 |
11/30/2000 12:37:19 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef # this scripts needs to be rerun each time the # wm volume is edited |
|||
|
inflate_subject_new /binfs/freesurfer_alpha/bin/noarch/ |
#: 329 Sz: 471 |
4/5/2000 12:17:12 PM | C shell script text executable |
#!/bin/csh # this scripts needs to be rerun each time the # wm volume is edited |
|||
|
inflate_subject_new-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 330 Sz: 341 |
7/16/2000 6:21:14 PM | Tenex C shell script text executable |
#!/bin/tcsh |
|||
|
inflate_subject_new-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 331 Sz: 345 |
7/16/2000 6:21:14 PM | Tenex C shell script text executable |
#! /bin/tcsh -f |
|||
|
inflate_subject3 /binfs/freesurfer_alpha/bin/noarch/ |
#: 332 Sz: 481 |
4/5/2000 12:17:12 PM | Tenex C shell script text executable |
#!/bin/tcsh -f # this scripts needs to be rerun each time the # wm volume is edited |
|||
|
inflate_subject-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 333 Sz: 332 |
11/30/2000 12:37:41 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
inflate_subject-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 334 Sz: 331 |
11/30/2000 12:37:52 PM | Tenex C shell script text executable |
#! /bin/tcsh -ef |
|||
|
label_elderly_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 335 Sz: 266 |
6/23/2001 4:53:32 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
label_elderly_subject~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 336 Sz: 499 |
6/23/2001 4:53:13 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
label_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 337 Sz: 313 |
9/14/2001 12:38:34 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
label_subject_flash /binfs/freesurfer_alpha/bin/noarch/ |
#: 338 Sz: 272 |
6/22/2001 8:50:57 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
label_subject_mixed /binfs/freesurfer_alpha/bin/noarch/ |
#: 339 Sz: 276 |
6/25/2001 1:12:07 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
label_subject_mixed~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 340 Sz: 228 |
6/22/2001 8:46:32 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
label_subject~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 341 Sz: 228 |
6/1/2001 9:11:36 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
make_final_surfaces_corrected_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 342 Sz: 172 |
4/5/2000 12:17:12 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
make_final_surfaces_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 343 Sz: 130 |
11/30/2000 12:39:51 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
make_final_surfaces_subject-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 344 Sz: 395 |
12/6/2000 7:22:54 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
make_final_surfaces_subject-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 345 Sz: 395 |
12/6/2000 7:22:57 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
make_quick_surfaces_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 346 Sz: 149 |
4/5/2000 12:17:12 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
minc2seqinfo /binfs/freesurfer_alpha/bin/noarch/ |
#: 347 Sz: 3082 |
11/10/2000 4:09:55 PM | C shell script text executable |
#!/bin/csh -f # # Name: minc2seqinfo # $Id: minc2seqinfo,v 1.1 2000/11/11 00:05:51 greve Exp greve $ # # Author: Douglas Greve # Date: 10/28/00 # Purpose: extracts the relevent information for the seq.info file # that is part of the Sessions Database. # # The seq.info file has a tag-value following format. # Example, for a data set with 16 slices, each slice 64x64, with 100 TRs, # TR = 2 seconds, slice thickness of 5 mm, pixel size of 3.125 # collected with a sequence called ep2d_fid_ts_20b2604, then the # seq.info file is shown below. The order is actually unimportant. If there # is no temporal dimension, then there would be no "ntrs" and "TR" fields. # # ------ cut here ------- # sequencename ep2d_fid_ts_20b2604 # nrows 64 # ncols 64 # nslcs 16 # rowpixelsize 3.125 # colpixelsize 3.125 # slcpixelsize 5.000 # ntrs 100 # TR 2.0 # ------ cut here ------- |
|||
|
mkfsdist /binfs/freesurfer_alpha/bin/noarch/ |
#: 348 Sz: 8310 |
5/31/2001 4:42:30 PM | C shell script text executable |
#!/bin/csh -f # mkfsdist # $Id: mkfsdist,v 1.2 2001/05/31 23:41:04 greve Exp $ # # Usage: mkfsdist targetdir # # Purpose: creates a FreeSurfer distribution in the directory # specified on the command-line. The distribution can be installed # by following the instructions in freesurfer_alpha/INSTALL. # # These files are created in the target directory: # INSTALL -- installation instructions (copied from freesurfer_alpha); # license.freesurfer -- license agreement (copied from freesurfer_alpha); # fsa.tar.gz -- the freesurfer_alpha tree # minc.tar.gz -- ~inverse/minc (for running functional autoreg) # talairach.tar.gz -- $SUBJECTS_DIR/talairach (MNI 305) # bert.001.tar.gz -- tutorial data, run 1 # bert.002.tar.gz -- tutorial data, run 2 # bert.003.tar.gz -- tutorial data, run 3 # # Symbolic Links in freesurfer_alpha: # # It does not follow symbolic links, so any symbolic link # in freesurfer_alpha must have a pointer relative to someplace in the # freesurfer_alpha tree. # # Dynamic and Statically Linked Programs # # The only programs that are dynamically linked are tksurfer, tkmedit, # and tkregister. These programs are replaced by their statically # linked counterparts. The dynamically linked programs are included # with a .dynamic extension. The process that does this is fairly # involved. See comments in the code for more detail. # # Excluding files and directories from freesurfer_alpha: # # Files and directories within the freesurfer_alpha tree can be targeted # for exclusion by entering them into freesurfer_alpha/tar-exclude. This # is useful for excluding the license file (.license) as well as other # files that just take up space. When adding items to the exclude file, # put only one name on each line and make sure there are no trailing # white spaces. This name will be exluded where ever it is found in the # tree, either as a file or as a directory. It will also exclude the # files found in freesurfer_alpha/tar-exclude-more. # # |
|||
|
mkima_index.tcl /binfs/freesurfer_alpha/bin/noarch/ |
#: 349 Sz: 0 |
4/28/2000 12:08:25 PM | empty |
|
mkmnc_index.tcl /binfs/freesurfer_alpha/bin/noarch/ |
#: 350 Sz: 0 |
4/28/2000 12:08:25 PM | empty |
|
mksubjdirs /binfs/freesurfer_alpha/bin/noarch/ |
#: 351 Sz: 263 |
9/19/2001 8:00:02 AM | C shell script text executable |
#! /bin/csh |
|||
|
morph_only_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 352 Sz: 67 |
4/5/2000 12:17:12 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
morph_only_subject-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 353 Sz: 429 |
7/16/2000 6:21:14 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
morph_only_subject-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 354 Sz: 428 |
7/16/2000 6:21:14 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
morph_rgb-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 355 Sz: 1382 |
1/24/2001 3:23:21 PM | Tenex C shell script text executable |
#!/bin/tcsh -f # Do not edit this file unless you have checked it out properly! # Note: this file is being maintained in # /homes/nmrnew/home/fischl/dev/scripts # # $Id: morph_rgb-lh,v 1.2 2000/08/16 16:00:24 greve Exp $ |
|||
|
morph_rgb-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 356 Sz: 1382 |
1/24/2001 3:23:34 PM | Tenex C shell script text executable |
#!/bin/tcsh -f # Do not edit this file unless you have checked it out properly! # Note: this file is being maintained in # /homes/nmrnew/home/fischl/dev/scripts # # $Id: morph_rgb-rh,v 1.2 2000/08/16 16:02:59 greve Exp $ |
|||
|
morph_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 357 Sz: 58 |
11/30/2000 12:39:24 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
morph_subject-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 358 Sz: 1162 |
11/30/2000 12:34:33 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
morph_subject-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 359 Sz: 931 |
11/30/2000 12:34:16 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
morph_tables-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 360 Sz: 513 |
10/3/2000 3:03:36 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
morph_tables-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 361 Sz: 437 |
10/3/2000 3:03:27 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
mri_autorecon /binfs/freesurfer_alpha/bin/noarch/ |
#: 362 Sz: 18326 |
10/19/2000 11:45:19 AM | C shell script text executable |
#!/bin/csh -f # mri_autorecon # Performs the automatic portion of anatomical recontruction. This is # broken into two stages: # Stage 1: # a. Creating the subject's directory structure # b. Copying/Converting input data # c. Motion Correction # d. Creating symbolic link # Stage 2: # a. Segmentation # b. Fixing # c. Morphing # d. Making Final Surfaces # |
|||
|
mri_motion_correct /binfs/freesurfer_alpha/bin/noarch/ |
#: 363 Sz: 10850 |
7/13/2001 10:33:40 AM | Bourne shell script text executable |
#!/bin/sh # # mri_motion_correct v.2 # # 18 May 2001 ch # # --------------------------------------------------------------------- # subroutines |
|||
|
mri_motion_correct~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 364 Sz: 10830 |
7/13/2001 10:27:34 AM | Bourne shell script text executable |
#!/bin/sh # # mri_motion_correct v.2 # # 18 May 2001 ch # # --------------------------------------------------------------------- # subroutines |
|||
|
mri-func2sph /binfs/freesurfer_alpha/bin/noarch/ |
#: 365 Sz: 6320 |
4/5/2000 12:17:12 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
mri-funcvits /binfs/freesurfer_alpha/bin/noarch/ |
#: 366 Sz: 7141 |
9/27/2000 3:27:49 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
mri-sph2surf /binfs/freesurfer_alpha/bin/noarch/ |
#: 367 Sz: 4801 |
4/13/2000 2:32:02 PM | C shell script text executable |
#!/bin/csh -f # # |
|||
|
mri-structvits /binfs/freesurfer_alpha/bin/noarch/ |
#: 368 Sz: 7188 |
4/13/2000 2:33:10 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
new_surfer /binfs/freesurfer_alpha/bin/noarch/ |
#: 369 Sz: 180 |
9/26/2000 12:06:29 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
parcellate_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 370 Sz: 68 |
5/8/2001 11:10:09 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
parcellate_subject~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 371 Sz: 58 |
5/8/2001 11:02:27 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
parcellate_subject-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 372 Sz: 129 |
5/8/2001 11:05:59 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
parcellate_subject-lh~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 373 Sz: 126 |
5/8/2001 11:05:40 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
parcellate_subject-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 374 Sz: 129 |
5/8/2001 11:06:09 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
printdat /binfs/freesurfer_alpha/bin/noarch/ |
#: 375 Sz: 1750 |
6/6/2000 7:43:12 AM | Bourne shell script text executable |
#! /bin/sh # (next line not see by tcl) \ |
|||
|
progressbar.tcl /binfs/freesurfer_alpha/bin/noarch/ |
#: 376 Sz: 27497 |
7/28/2000 3:28:29 PM | ISO-8859 English text |
|
register.csh /binfs/freesurfer_alpha/bin/noarch/ |
#: 377 Sz: 1904 |
6/11/2000 5:23:01 PM | C shell script text executable |
#!/bin/csh -f # # # registers sets of COR files. |
|||
|
register_elderly_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 378 Sz: 499 |
6/23/2001 4:54:26 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
register_elderly_subject~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 379 Sz: 460 |
6/23/2001 4:54:17 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
register_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 380 Sz: 348 |
9/14/2001 12:38:10 PM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
register_subject_flash /binfs/freesurfer_alpha/bin/noarch/ |
#: 381 Sz: 361 |
6/22/2001 11:19:40 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
register_subject_mixed /binfs/freesurfer_alpha/bin/noarch/ |
#: 382 Sz: 328 |
6/26/2001 4:42:04 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
register_subject_mixed~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 383 Sz: 288 |
6/22/2001 8:47:15 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
register_subject~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 384 Sz: 460 |
6/22/2001 11:05:02 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
reinflate_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 385 Sz: 117 |
4/5/2000 12:17:12 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
reinflate_subject-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 386 Sz: 281 |
7/16/2000 6:21:14 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
reinflate_subject-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 387 Sz: 282 |
7/16/2000 6:21:14 PM | Tenex C shell script text executable |
#! /bin/tcsh -f |
|||
|
renormalize_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 388 Sz: 246 |
2/1/2001 12:09:30 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
renormalize_subject_keep_editting /binfs/freesurfer_alpha/bin/noarch/ |
#: 389 Sz: 252 |
2/1/2001 12:09:06 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
renormalize_T1_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 390 Sz: 112 |
4/5/2000 12:17:12 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
reregister_subject_mixed /binfs/freesurfer_alpha/bin/noarch/ |
#: 391 Sz: 288 |
6/25/2001 11:19:58 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
reregister_subject_mixed~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 392 Sz: 288 |
6/25/2001 11:19:45 AM | Tenex C shell script text executable |
#!/bin/tcsh -ef |
|||
|
segment_monkey /binfs/freesurfer_alpha/bin/noarch/ |
#: 393 Sz: 1087 |
12/21/2000 1:41:16 PM | Tenex C shell script text executable |
#! /bin/tcsh -ef # this script should only be run once per subject. |
|||
|
segment_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 394 Sz: 905 |
2/1/2001 12:08:57 PM | Tenex C shell script text executable |
#! /bin/tcsh -ef # this script should only be run once per subject. |
|||
|
segment_subject_notal /binfs/freesurfer_alpha/bin/noarch/ |
#: 395 Sz: 1124 |
2/1/2001 12:08:49 PM | Tenex C shell script text executable |
#! /bin/tcsh -ef # this script should only be run once per subject. |
|||
|
segment_subject_old_skull_strip /binfs/freesurfer_alpha/bin/noarch/ |
#: 396 Sz: 905 |
2/28/2001 2:27:30 PM | Tenex C shell script text executable |
#! /bin/tcsh -ef # this script should only be run once per subject. |
|||
|
sphere_subject /binfs/freesurfer_alpha/bin/noarch/ |
#: 397 Sz: 65 |
4/5/2000 12:17:12 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
sphere_subject-lh /binfs/freesurfer_alpha/bin/noarch/ |
#: 398 Sz: 235 |
7/16/2000 6:21:14 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
sphere_subject-rh /binfs/freesurfer_alpha/bin/noarch/ |
#: 399 Sz: 234 |
7/16/2000 6:21:14 PM | Tenex C shell script text executable |
#!/bin/tcsh -f |
|||
|
spm_t_to_b /binfs/freesurfer_alpha/bin/noarch/ |
#: 400 Sz: 1269 |
4/25/2000 9:44:44 AM | Bourne shell script text executable |
#!/bin/sh |
|||
|
spmmat2register /binfs/freesurfer_alpha/bin/noarch/ |
#: 401 Sz: 5064 |
8/28/2000 1:42:21 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
talairach /binfs/freesurfer_alpha/bin/noarch/ |
#: 402 Sz: 566 |
8/13/2001 12:52:52 PM | Bourne shell script text executable |
#!/bin/sh # for subject in /space/inverse/4/users/inverse/subjects/anders; do |
|||
|
talairach.log /binfs/freesurfer_alpha/bin/noarch/ |
#: 403 Sz: 256 |
6/23/2001 5:42:47 PM | ASCII text |
|
talairach~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 404 Sz: 563 |
6/9/2000 12:38:06 PM | Bourne shell script text executable |
#!/bin/sh # for subject in /space/inverse/4/users/inverse/subjects/anders; do |
|||
|
tkmedit_wrapper /binfs/freesurfer_alpha/bin/noarch/ |
#: 405 Sz: 516 |
6/27/2001 12:22:59 PM | Bourne shell script text executable |
#!/bin/sh |
|||
|
tkmedit_wrapper~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 406 Sz: 513 |
8/9/2000 12:31:12 PM | Bourne shell script text executable |
#!/bin/sh |
|||
|
unpack_ima.tcl /binfs/freesurfer_alpha/bin/noarch/ |
#: 407 Sz: 108726 |
9/18/2001 1:14:46 PM | a /usr/bin/wish script text executable |
#!/usr/bin/wish # this script looks at the headers of ima files in a predetermined archive direc tory. The default archive directory is over-ridden by the environment variable A RCHIVE_DIR. the user selects a session and the path to that session is proveded to the script that copies the relevant files via nfs to the local machine and un packs them locally into b shorts. # Copyright (C) 2001 Tony Harris tony@nmr.mgh.harvard.edu # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # http://www.gnu.org/copyleft/gpl.html # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. #--------------------------------------------------------------------------------------# #Structure of this script: #global variables #subroutines # dialogs # functions # session info # search # transfer # utils #widgets #bindings #main #--------------------------------------------------------------------------------------# # Alphabetical listing of functions (updated 07 Aug 2001) : # CheckDirOK # CheckScratchDirOK # CheckSourceDirOK # CheckTargetDirOK # ConvertMINCfiles # CreateAlertDialog # CreateFileBrowser # CreateMINCfiles # CreateOutputMonitor # CreateProgressBarWindow # CreateSearchDialog # CreateSequenceDialog # CreateSessionInfoView # DeleteOutputMonitor # DeleteSequenceListItem # DestroyAlertDialog # DestroyFileBrowser # DestroyProgressBarWindow # DestroySearchDialog # DestroySequenceDialog # DestroySessionInfoView # Dialog_Create # Dialog_Dismiss # Dialog_Wait # DicomPushMinc # GetHeaderInfo # GetMincSisterSession # GetSeqDir # GetSequences # GetSessionDescriptors # GetSessionInfoFromFile # Ima2sessions # KillPipe # LoadListBox # LocalSearch # Log # MountCDROM # QueryDB # ReadIncomingDir # ReadIndexFile # RestoreSessions # Run_unpackmincdir # SaveSessions # SelectCDROM # StartTransfer # TransferIMAfiles # TransferIMAtoMINC # TransferSortMincFiles # ViewCDROM #----------------------------------------------------------------------------------------# # global variable defined elsewhere # sessionNumber: integer 0-N, numerical order of sessions read # # session(sessionNumber, fieldValue) # A 2-D array containing a subset of header info from each session. # The field Keys are: # 0 patient_name # 1 patient_ID # 2 study_date # 3 registration_date # 4 registration_time # 5 experimenter # 6 experiment_name # 7 path to first file in session directory # # functions which write to "session" array: QueryDB ReadIncomingDir ReadIndexFile |
|||
|
unpack_ima1.tcl /binfs/freesurfer_alpha/bin/noarch/ |
#: 408 Sz: 44705 |
8/9/2000 12:55:00 PM | a /usr/bin/wish script text executable |
#!/usr/bin/wish # this cript looks at the headers of ima files in a predetermined archive direct ory. The default archive directory is over-ridden by the environment variable AR CHIVE_DIR. the user selcets a session and the path to that session is proveded t o the script that copies the relevant files via nfs to the local machine and unp acks them locally into b shorts. #--------------------------------------------------------------------------------------# #export ALPHA_BIN=/space/annecy/5/users/inverse/freesurfer_alpha/bin #cp unpack_ima.tcl $ALPHA_BIN/noarch #export PATH=$PATH:$ALPHA_BIN/noarch #export PATH=$PATH:$ALPHA_BIN/Linux #-----------------------------------------------------------------------------------------# # global variable defined elsewhere # session(sessionNumber, fieldValue) A 2-D array conataining all that is known about the sessions. # The field Keys are: # 0 patient_name # 1 patient_ID # 2 study_date # 3 path to first file in session directory # # displayedSessions A list containing the "session" indices which are currently displayed # in the list box #-----------------------------------------------------------------------------------------# #define needed variables |
|||
|
unpack_mnc.24Apr00 /binfs/freesurfer_alpha/bin/noarch/ |
#: 409 Sz: 20066 |
4/14/2000 11:51:14 AM | a /usr/bin/wish script text executable |
#!/usr/bin/wish # this cript looks at the headers of minc files in a predetermined archive direc tory. The default archive directory is over-ridden by the environment variable A RCHIVE_DIR. the user selcets a session and the path to that session is proveded to the script that copies the relevant files via nfs to the local machine and un packs them locally into b shorts. #--------------------------------------------------------------------------------------# #export ALPHA_BIN=/space/annecy/5/users/inverse/freesurfer_alpha/bin #cp unpack_mnc.tcl $ALPHA_BIN/noarch #export PATH=$PATH:$ALPHA_BIN/noarch #export PATH=$PATH:$ALPHA_BIN/Linux #wrapper program is "browse-sessions" #define needed variables |
|||
|
unpack_mnc.tcl /binfs/freesurfer_alpha/bin/noarch/ |
#: 410 Sz: 38258 |
7/25/2001 2:08:08 PM | a /usr/bin/wish script text executable |
#!/usr/bin/wish # This script looks at the headers of minc files in a predetermined archive dire ctory. The default archive directory is over-ridden by the environment variable ARCHIVE_DIR. The scripts attempts to read an index file, "index.txt", which is a sister to the archive directory. This index is produced by "mkmnc_index.tcl" an d contains header info and paths to sessions in other directries. The user selec ts a session.The path to that session is provided to the script "unpackmincdir," which copies the relevant files via nfs to the local machine and unpacks them l ocally into b shorts. #--------------------------------------------------------------------------------------# #export ALPHA_BIN=/space/annecy/5/users/inverse/freesurfer_alpha/bin #cp unpack_mnc.tcl $ALPHA_BIN/noarch #export PATH=$PATH:$ALPHA_BIN/noarch #export PATH=$PATH:$ALPHA_BIN/Linux #wrapper program is "browse-sessions" #define needed variables |
|||
|
unpackimadir.06Aug01 /binfs/freesurfer_alpha/bin/noarch/ |
#: 411 Sz: 6030 |
8/22/2001 10:40:57 AM | C shell script text executable |
#!/bin/csh -f # Name: unpackimadir # Purpose: converts data in an IMA directory to MINC and # then calls unpackmincdir to convert to Sessions format # (deletes the original MINC). Any arguments that unpackimadir # does not recognize are passed to unpackmincdir. The # temporary minc files can be kept by specifying -keepminc. # The temporary minc directory can be specified with -mincdir, # otherwise it will be put in the output directory. |
|||
|
unpackimadir.06Aug01~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 412 Sz: 6038 |
8/6/2001 12:19:03 PM | C shell script text executable |
#!/bin/csh -f # Name: unpackimadir # Purpose: converts data in an IMA directory to MINC and # then calls unpackmincdir to convert to Sessions format # (deletes the original MINC). Any arguments that unpackimadir # does not recognize are passed to unpackmincdir. The # temporary minc files can be kept by specifying -keepminc. # The temporary minc directory can be specified with -mincdir, # otherwise it will be put in the output directory. |
|||
|
unpackimadir.31July01 /binfs/freesurfer_alpha/bin/noarch/ |
#: 413 Sz: 6024 |
7/30/2001 9:20:57 PM | C shell script text executable |
#!/bin/csh -f # Name: unpackimadir # Purpose: converts data in an IMA directory to MINC and # then calls unpackmincdir to convert to Sessions format # (deletes the original MINC). Any arguments that unpackimadir # does not recognize are passed to unpackmincdir. The # temporary minc files can be kept by specifying -keepminc. # The temporary minc directory can be specified with -mincdir, # otherwise it will be put in the output directory. |
|||
|
unpackimadir~ /binfs/freesurfer_alpha/bin/noarch/ |
#: 414 Sz: 6030 |
7/30/2001 3:02:17 PM | C shell script text executable |
#!/bin/csh -f # Name: unpackimadir # Purpose: converts data in an IMA directory to MINC and # then calls unpackmincdir to convert to Sessions format # (deletes the original MINC). Any arguments that unpackimadir # does not recognize are passed to unpackmincdir. The # temporary minc files can be kept by specifying -keepminc. # The temporary minc directory can be specified with -mincdir, # otherwise it will be put in the output directory. |
|||
|
unpackmincdir /binfs/freesurfer_alpha/bin/noarch/ |
#: 415 Sz: 17966 |
5/15/2001 2:19:39 PM | C shell script text executable |
#!/bin/csh -f # Name: unpackmincdir # Purpose: unpacks the functionals and anatomicals and copies others |
|||
|
unpacksdcmdir /binfs/freesurfer_alpha/bin/noarch/ |
#: 416 Sz: 32008 |
10/3/2001 4:05:55 PM | a /usr/bin/tclsh script text executable |
#!/usr/bin/tclsh #------------------------------------------------------------------# |
|||
|
xsanatreg /binfs/freesurfer_alpha/bin/noarch/ |
#: 417 Sz: 4428 |
9/15/2000 8:57:20 AM | C shell script text executable |
#!/bin/csh -f # xsanatreg -- cross-session anatomical registration. This is a front end # for minctracc. The inputs are directories pointing to COR volumes. |
|||
| /binfs/freesurfer_alpha/bin/noarch/no scratch dir set/ | |||
| /binfs/freesurfer_alpha/bin/noarch/old/ | |||
|
csurf /binfs/freesurfer_alpha/bin/noarch/old/ |
#: 418 Sz: 281637 |
4/18/2000 2:43:02 PM | Bourne shell script text executable |
#! /bin/sh # force local (next line not seen by tcl) \ |
|||
| /binfs/freesurfer_alpha/bin/Solaris/ Skipped directory per survey instructions | |||
| /binfs/freesurfer_alpha/data/ | |||
|
gradientNonlinearityAllegra.dat /binfs/freesurfer_alpha/data/ |
#: 419 Sz: 222404 |
9/19/2001 3:58:24 PM | data |
| /binfs/freesurfer_alpha/docs/ | |||
|
citation.minc /binfs/freesurfer_alpha/docs/ |
#: 420 Sz: 540 |
8/2/2001 1:48:06 PM | ASCII English text |
|
copywrite.minc /binfs/freesurfer_alpha/docs/ |
#: 421 Sz: 1066 |
8/2/2001 1:53:12 PM | ASCII English text |
|
copywrite.minc~ /binfs/freesurfer_alpha/docs/ |
#: 422 Sz: 527 |
8/2/2001 1:47:15 PM | ASCII English text |
|
FreeSurferManual.pdf /binfs/freesurfer_alpha/docs/ |
#: 423 Sz: 7122837 |
9/7/2000 3:29:49 PM | PDF document, version 1.1 |
|
license.afni /binfs/freesurfer_alpha/docs/ |
#: 424 Sz: 580 |
8/2/2001 2:24:10 PM | ASCII English text |
|
license.afni~ /binfs/freesurfer_alpha/docs/ |
#: 425 Sz: 577 |
8/2/2001 1:52:33 PM | ASCII English text |
|
license.freesurfer /binfs/freesurfer_alpha/docs/ |
#: 426 Sz: 9191 |
9/7/2000 3:29:49 PM | ISO-8859 English text |
|
license.gnu /binfs/freesurfer_alpha/docs/ |
#: 427 Sz: 25267 |
9/7/2000 3:29:49 PM | ASCII English text |
|
license.html_lib /binfs/freesurfer_alpha/docs/ |
#: 428 Sz: 2022 |
9/7/2000 3:29:49 PM | ASCII English text |
|
license.tcltk /binfs/freesurfer_alpha/docs/ |
#: 429 Sz: 1734 |
9/7/2000 3:29:49 PM | ASCII English text |
|
license.tix /binfs/freesurfer_alpha/docs/ |
#: 430 Sz: 1594 |
9/7/2000 3:29:49 PM | ASCII English text |
|
recon1.ps /binfs/freesurfer_alpha/docs/ |
#: 431 Sz: 12642693 |
9/7/2000 3:30:26 PM | PostScript document text conforming at level 3.0 |
|
recon2.ps /binfs/freesurfer_alpha/docs/ |
#: 432 Sz: 9008305 |
9/7/2000 3:30:53 PM | PostScript document text conforming at level 3.0 |
|
registration.notes /binfs/freesurfer_alpha/docs/ |
#: 433 Sz: 852 |
9/7/2000 3:30:53 PM | ASCII English text |
| /binfs/freesurfer_alpha/fsfast-20011005/ | |||
| /binfs/freesurfer_alpha/fsfast-20011005/bin/ | |||
|
addmcparams /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 434 Sz: 519 |
11/7/2000 1:39:00 PM | C shell script text executable |
#!/bin/csh -f # Computes total displacement from the AFNI motion correction parameter # file and prints out the old set of parameters with total distplacement # as the last column (11th) # $Id$ |
|||
|
afni2bvol /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 435 Sz: 3354 |
4/4/2001 4:23:22 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
autoreg-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 436 Sz: 9335 |
9/5/2001 1:12:45 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
avgraw /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 437 Sz: 6433 |
3/9/2001 4:17:38 PM | C shell script text executable |
#!/bin/csh -f # average raw fMRI on a time-point by time-point basis |
|||
|
bfile2afni /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 438 Sz: 5451 |
4/4/2001 3:11:25 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
bfileconvert /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 439 Sz: 4290 |
3/9/2001 3:28:07 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
bfvcheck /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 440 Sz: 2749 |
5/21/2001 5:38:54 PM | C shell script text executable |
#!/bin/csh -f # bfvcheck - given the stem of a volume stored in bfile format, this # script checks the entire volume to assure that all the sizes and # parameters are consistent. |
|||
|
cat-bvolume /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 441 Sz: 4135 |
5/21/2001 2:31:33 PM | C shell script text executable |
#!/bin/csh -f # $Id$ # Name: cat-bvolume # Purpose: concatenates multiple bvolumes into one bvolume. The # source bvolumes must have the same spatial dimension but can # differ in the number of frames. They must have the same precision # and the same endianness. This script assures that the correct # values are in the output header files. |
|||
|
checkmincdir /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 442 Sz: 1935 |
7/3/2001 1:08:35 PM | C shell script text executable |
#!/bin/csh -f # # Name: checkmincdir # # Purpose: given a directory with minc files from a single exam # and a list of run numbers, determines whether all the expected # minc files are there and if they are about the right size. # This is supposed to help determine if/when ima2mnc has finished # converting all the ima files into minc. If there's something # wrong, a message is printed to stdout and a non-zero status is # returned. If successful, nothing is printed and 0 is returned. # # "img-getrunlist' can be used to get the list of run numbers # directly from the ima directory. # |
|||
|
clusterspec2mask /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 443 Sz: 6059 |
8/3/2001 1:25:54 PM | C shell script text executable |
#!/bin/csh -f # # Creates a weightd mask from a list of cluster specs. Each cluster # is a rectangular solid. The values in the mask can be floating # point. # # The cluster spec consists of 8 numbers: # 1. amplitude - base value for the cluster # 2. hanrad - hanning radius for off-center voxels in the cluster # 3-5. rowmin, colmin, slicemin - lower corner of the bounding box # 6-8. rowmax, colmax, slicemax - upper corner of the bounding box # # Notes: # 1. hanrad is not implemented yet. # 2. if clusters overlap, the value is set by the last cluster. # |
|||
|
compress-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 444 Sz: 7297 |
5/11/2001 2:33:22 PM | C shell script text executable |
#!/bin/csh -f # compress-sess # |
|||
|
concat-bvolumes /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 445 Sz: 1839 |
7/27/2001 5:47:24 PM | C shell script text executable |
#!/bin/csh -f # $Id$ |
|||
|
condfit /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 446 Sz: 6517 |
10/15/2000 8:57:55 AM | C shell script text executable |
#!/bin/csh -f |
|||
|
condfit-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 447 Sz: 10071 |
10/19/2000 8:23:45 AM | C shell script text executable |
#!/bin/csh -f # condfit-sess - random effects intersubject averaging condition fitting # |
|||
|
conjunct-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 448 Sz: 8249 |
4/18/2001 3:00:18 PM | C shell script text executable |
#!/bin/csh -f # conjunct-sess - conjunction of two or more contrasts # |
|||
|
cp-bvolume /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 449 Sz: 1401 |
6/2/2000 10:13:49 AM | C shell script text executable |
#!/bin/csh -f # $Id: cp-bvolume,v 1.1 2000/03/07 00:53:36 greve Exp greve $ |
|||
|
df-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 450 Sz: 660 |
2/22/2001 4:36:27 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
diag-fmri /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 451 Sz: 12081 |
8/28/2001 5:26:48 PM | C shell script text executable |
#!/bin/csh -f # $Id: diag-fmri,v 1.5 2000/01/20 23:51:05 greve Exp greve $ # This program is used to stress the fmri analysis software # to look for bugs or anything else that might be amiss. # It synthesizes and processes data, examining the errors in # the hemodynamic estimages and the false-positive rate. |
|||
|
diag-optseq /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 452 Sz: 978 |
1/20/2000 2:50:25 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
difffsfast /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 453 Sz: 1800 |
8/7/2001 9:57:00 AM | C shell script text executable |
#!/bin/csh -f |
|||
|
du-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 454 Sz: 378 |
2/22/2001 4:13:39 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
editmask /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 455 Sz: 5037 |
5/21/2001 12:42:26 PM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: editmask ############################################################ |
|||
|
fast-log-preamble.csh /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 456 Sz: 1149 |
8/21/2000 2:40:55 PM | ASCII English text |
|
fftfunc-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 457 Sz: 8744 |
8/8/2001 12:00:35 PM | C shell script text executable |
#!/bin/csh -f # fftfunc-sess - # # $Id$ |
|||
|
fimg2bshort /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 458 Sz: 1290 |
10/13/1999 4:07:26 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
fixseqinfo-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 459 Sz: 5860 |
11/10/2000 1:23:37 PM | C shell script text executable |
#!/bin/csh -f # fixseqinfo-sess - fixes the seq.info file # # $Id: fixseqinfo-sess,v 1.1 2000/11/10 21:23:23 greve Exp greve $ |
|||
|
fmreigen /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 460 Sz: 9712 |
2/22/2000 11:30:56 AM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: fmreigen ############################################################ |
|||
|
fmreigen-jk /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 461 Sz: 10473 |
2/22/2000 11:31:18 AM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: fmreigen-jk -- jackknifing ############################################################ |
|||
|
fpr /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 462 Sz: 4738 |
1/19/2001 12:18:35 PM | C shell script text executable |
#!/bin/csh -f ############################################################ |
|||
|
fsfast-version /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 463 Sz: 169 |
5/10/2001 5:21:56 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
func2label /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 464 Sz: 7975 |
5/31/2000 3:07:00 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
func2roi-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 465 Sz: 18894 |
8/13/2001 2:29:12 PM | C shell script text executable |
#!/bin/csh -f # func2roi-sess |
|||
|
func2sph-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 466 Sz: 10929 |
8/28/2001 5:45:19 PM | C shell script text executable |
#!/bin/csh -f # func2sph-sess -- with version 1.7, the old vss functions are no longer used. # Passing "-old" as an argument will invoke the old func2sphere-sess (now called # func2sphere-sess-vss). |
|||
|
func2sph-sess-new /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 467 Sz: 125 |
3/16/2001 1:52:38 PM | C shell script text executable |
#!/bin/csh -f # Name: func2sph-sess-new # This is just a front end for func2sph-sess. |
|||
|
func2sph-sess-vss /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 468 Sz: 7255 |
1/23/2001 11:33:23 AM | C shell script text executable |
#!/bin/csh -f # func2sph-sess-vss - this corresponds to func2sph-sess version 1.6 (01/1/19). # It uses the old vss (vertex-sampled space) libraries and functions which # have now been replaced. This version can be accessed from func2sph-sess # by including a "-old" flag. |
|||
|
func2tal /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 469 Sz: 8367 |
9/6/2001 11:15:55 AM | C shell script text executable |
#!/bin/csh -f # func2tal # $Id: func2tal,v 1.4 2000/08/08 21:07:34 greve Exp greve $ |
|||
|
func2tal-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 470 Sz: 7331 |
5/23/2001 10:20:30 AM | C shell script text executable |
#!/bin/csh -f # func2tal-sess # |
|||
|
funcvits-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 471 Sz: 6007 |
1/23/2001 11:34:27 AM | C shell script text executable |
#!/bin/csh -f # funcvits-sess # |
|||
|
getbext /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 472 Sz: 667 |
9/19/2000 12:42:15 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
getbfvdim /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 473 Sz: 609 |
5/21/2001 2:16:28 PM | C shell script text executable |
#!/bin/csh -f # getbfvdim - gets the dimensions of a volume stored in bfile format |
|||
|
getendian /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 474 Sz: 489 |
5/21/2001 2:16:04 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
getfirstrundir-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 475 Sz: 772 |
4/13/2000 1:28:21 PM | C shell script text executable |
#!/bin/csh -f # getfirstrundir-sess # gets first 3 digit, zero-padded directory. # $Id: getfirstrundir-sess,v 1.2 2000/04/13 20:36:39 greve Exp greve $ |
|||
|
getfirstsliceno /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 476 Sz: 475 |
3/30/2000 1:38:34 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
geticoorder /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 477 Sz: 1028 |
9/26/2001 12:02:49 PM | C shell script text executable |
#!/bin/csh -f # Get Ico Order |
|||
|
getlastsliceno /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 478 Sz: 655 |
4/4/2000 5:46:27 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
getmatlab /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 479 Sz: 464 |
9/11/2001 12:59:17 PM | C shell script text executable |
#!/bin/csh -f # $Id: getmatlab,v 1.1 2000/01/20 23:51:05 greve Exp greve $ #set MATLAB = /usr/pubsw/packages/matlab/6.1/bin/matlab #echo $MATLAB #exit 0; |
|||
|
getncols /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 480 Sz: 486 |
2/23/2001 1:33:24 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
getnconds /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 481 Sz: 2846 |
3/1/2000 2:15:03 PM | C shell script text executable |
#!/bin/csh -f # getnconds - returns a list of the number of conditions # for each session specified. The number of conditions # does not include any condition with an id of 0. # # $Id$ |
|||
|
getnframes /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 482 Sz: 492 |
11/7/2000 2:10:01 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
getnrows /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 483 Sz: 486 |
2/23/2001 1:33:13 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
getnslices /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 484 Sz: 657 |
8/29/2000 12:53:57 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
getpwdcmd /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 485 Sz: 464 |
9/21/2000 12:14:51 PM | C shell script text executable |
#!/bin/csh -f # This script returns the pwd command to use. If the command # pawd exists, then that is used, otherwise pwd is used. # pawd is used with amd and returns the current directory # with out all the automounter stuff prepended to it. # # $Id$ |
|||
|
getrunlist /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 486 Sz: 668 |
10/9/2001 12:04:31 PM | C shell script text executable |
#!/bin/csh -f # getrunlist - finds all the subdirectories with name # of the form %03d in the given directory. # # $Id$ |
|||
|
getsesspath /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 487 Sz: 4891 |
2/5/2001 3:01:44 PM | C shell script text executable |
#!/bin/csh -f # getsesspath - gets the full paths of the sessions # listed in groupdef files. The candidate paths are # given in a searchdir file. # # $Id: getsesspath,v 1.2 2000/09/14 18:05:55 greve Exp greve $ |
|||
|
getsliceno /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 488 Sz: 710 |
3/7/2000 12:25:16 PM | C shell script text executable |
#!/bin/csh -f ########################################## # Name: getsliceno # Purpose: gets XXX portion of stem_XXX.bxxxx # $Id ########################################## |
|||
|
getslicestr /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 489 Sz: 712 |
3/7/2000 12:29:07 PM | C shell script text executable |
#!/bin/csh -f ########################################## # Name: getslicestr # Purpose: gets XXX portion of stem_XXX.bxxxx # $Id ########################################## |
|||
|
getspacetype /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 490 Sz: 1040 |
8/29/2000 11:42:52 AM | C shell script text executable |
#!/bin/csh -f # parses space names into space type and averaging method (fx) |
|||
|
getstem /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 491 Sz: 971 |
5/19/1999 10:44:18 AM | C shell script text executable |
#!/bin/csh -f ########################################## # Name: getstem # Purpose: strips off the _XXX.bxxxx portion # of its argument to obtain the stem. This # seems like a hokey way to do it, but it # works. # '$Id: getstem,v 1.2 1999/05/19 16:39:10 greve Exp $' ########################################## |
|||
|
gettalres /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 492 Sz: 600 |
8/29/2000 12:58:48 PM | C shell script text executable |
#!/bin/csh -f # Gets the talairach resolution (in mm) based on the number of slices |
|||
|
grecon2bshort /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 493 Sz: 3796 |
5/3/1999 4:01:59 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
hdrerror /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 494 Sz: 5620 |
1/26/2000 12:44:55 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
ima-checkdir /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 495 Sz: 2347 |
8/11/2000 12:28:34 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
ima-checkimgno /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 496 Sz: 1483 |
8/11/2000 12:01:14 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
ima-checkseries /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 497 Sz: 2620 |
7/3/2001 12:02:09 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
ima-getfirstimg /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 498 Sz: 2698 |
6/27/2000 3:52:15 PM | C shell script text executable |
#!/bin/csh -f # # ima-getfirstimg - gets the first image number given # the ima series and run number. # # The script gets the first image in the alphabetically sorted # list of all images in the series/run. The image number is extracted # from this image. This image number is decremented and used to # create a new file name. If this file exists, the image number is # decremented again. Decremation continues until the file does not # exist indicating that the first image in the run has been reached. # It was necessary to do it this way so as to avoid reading in 1000's # of file names. # |
|||
|
ima-getrunlist /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 499 Sz: 845 |
7/3/2001 12:21:35 PM | C shell script text executable |
#!/bin/csh -f # # Name: ima-getrunlist # Purpose: given a directory with ima files from one exam, # returns a list of the run numbers. |
|||
|
ima-parse-name /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 500 Sz: 398 |
4/10/2000 11:37:18 AM | C shell script text executable |
#!/bin/csh |
|||
|
inorm /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 501 Sz: 6744 |
5/21/2001 5:31:08 PM | C shell script text executable |
#!/bin/csh -f # fMRI Intensity normalization program |
|||
|
inorm-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 502 Sz: 7512 |
7/10/2001 11:06:49 AM | C shell script text executable |
#!/bin/csh -f # inorm-sess - # # $Id: inorm-sess,v 1.6 2001/05/17 21:55:23 greve Exp greve $ |
|||
|
intergroupavg-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 503 Sz: 9958 |
8/23/2001 10:03:02 AM | C shell script text executable |
#!/bin/csh -f # isxavg-fe-sess # |
|||
|
isargflag /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 504 Sz: 364 |
1/10/2001 3:00:44 PM | C shell script text executable |
#!/bin/csh -f # USAGE: isargflag string # # Returns 1 if string begins with a "-" otherwise returns 0. If the # string = -1, returns 0. # # $Id$ |
|||
|
isroiavg /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 505 Sz: 4839 |
1/20/2000 2:52:45 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
isxavg-fe /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 506 Sz: 7428 |
5/21/2001 5:21:54 PM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: isxavg # Purpose: # Usage: isxavg -fs N -ns N -weight <string> -effect <string> # -i instem1 -i instem2 -o outstem ############################################################ |
|||
|
isxavg-fe-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 507 Sz: 10526 |
5/23/2001 10:32:57 AM | C shell script text executable |
#!/bin/csh -f # isxavg-fe-sess # |
|||
|
isxavg-fe-sess-1.3 /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 508 Sz: 8079 |
8/29/2000 8:13:43 AM | C shell script text executable |
#!/bin/csh -f # isxavg-fe-sess # |
|||
|
isxavg-re /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 509 Sz: 7427 |
9/18/2001 9:35:53 AM | C shell script text executable |
#!/bin/csh -f |
|||
|
isxavg-re-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 510 Sz: 10759 |
9/11/2001 1:09:12 PM | C shell script text executable |
#!/bin/csh -f # isxavg-re-sess - random effects intersubject averaging # |
|||
|
ksgrinder /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 511 Sz: 8247 |
3/9/2001 4:46:23 PM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: ksgrinder - front end for KSS_grinder ############################################################ |
|||
|
ksgrinder-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 512 Sz: 6561 |
4/18/2001 3:03:16 PM | C shell script text executable |
#!/bin/csh -f # ksgrinder-sess # |
|||
|
mc-afni /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 513 Sz: 8971 |
8/2/2001 2:26:37 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
mc-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 514 Sz: 6539 |
8/2/2001 2:27:49 PM | C shell script text executable |
#!/bin/csh -f # mc-sess - motion correction # # $Id: mc-sess,v 1.5 2001/01/03 20:19:24 greve Exp greve $ |
|||
|
meanimg /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 515 Sz: 8858 |
9/11/2001 12:55:21 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
mergecontrasts-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 516 Sz: 8715 |
10/1/2001 12:09:28 PM | C shell script text executable |
#!/bin/csh -f # mergecontrasts-sess - AND conjunction of two contrasts # |
|||
|
mkanalysis-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 517 Sz: 11303 |
5/23/2001 10:32:06 AM | C shell script text executable |
#!/bin/csh -f # mkanalysis-sess -- sets up post-processing environment for # functional analysis |
|||
|
mkanalysis-sess.new /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 518 Sz: 17240 |
9/28/2001 11:50:05 AM | C shell script text executable |
#!/bin/csh -f # mkanalysis-sess -- sets up post-processing environment for # functional analysis |
|||
|
mkblockpar /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 519 Sz: 3434 |
4/13/2000 2:55:02 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
mkcontrast /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 520 Sz: 10785 |
9/5/2001 9:50:56 AM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: mkcontrast # Purpose: make a contrast matrix ############################################################ |
|||
|
mkcontrast-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 521 Sz: 8854 |
8/7/2001 4:53:30 PM | C shell script text executable |
#!/bin/csh -f # stxgrinder-sess # |
|||
|
mkfieldsign /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 522 Sz: 5420 |
5/22/2001 2:54:51 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
mkmosaic /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 523 Sz: 5731 |
8/11/2000 8:46:47 AM | C shell script text executable |
#! /bin/csh -f ########################################################## # Name: mkmosiac # Usage: <csh> mkmosaic instem <outdir> <-heq>" # # Purpose: Creates an NxM mosaic from slice files. If # the slices files have multiple time points, then the # mosaic will have multiple time points. For example, # if the slices are of dimension 64x64x10, then the mosiac # will be 256x256x10. # # Notes: ########################################################## |
|||
|
mkmosaic16 /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 524 Sz: 6037 |
2/22/2000 11:35:09 AM | C shell script text executable |
#! /bin/csh -f ########################################################## # Name: mkmosiac16 # Usage: <csh> mkmosaic16 instem <outdir> <-heq>" # # Purpose: Creates a 4x4 mosaic from 16 slice files. If # the slices files have multiple time points, then the # mosaic will have multiple time points. For example, # if the slices are of dimension 64x64x10, then the mosiac # will be 256x256x10. # # Notes: ########################################################## |
|||
|
mkmosaic-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 525 Sz: 8991 |
8/30/2000 4:01:12 PM | C shell script text executable |
#!/bin/csh -f # mkmosaic-sess # |
|||
|
mktalreg /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 526 Sz: 3410 |
8/29/2000 3:47:25 PM | C shell script text executable |
#!/bin/csh -f # Contructs a register file to go from tal space to subject # |
|||
|
MR2bshort /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 527 Sz: 4029 |
5/3/1999 7:47:00 AM | C shell script text executable |
#!/bin/csh -f ########################################################### |
|||
|
mtp-repack /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 528 Sz: 8723 |
6/14/2000 3:13:39 PM | C shell script text executable |
#!/bin/csh -f # mtp-repack - repacks data given the indices in the incomplete data # before which a sham volume should be inserted. # # Notes: # 1. fillmethod is ignored -- uses interpolation # |
|||
|
optseq /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 529 Sz: 13570 |
7/27/2001 9:53:42 AM | C shell script text executable |
#!/bin/csh -f |
|||
|
paint-fieldsign-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 530 Sz: 9701 |
5/24/2001 5:24:13 PM | C shell script text executable |
#!/bin/csh -f # paint-fieldsign-sess # |
|||
|
paint-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 531 Sz: 15607 |
10/4/2001 9:30:14 AM | C shell script text executable |
#!/bin/csh -f # paint-sess # |
|||
|
paint-sess-new /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 532 Sz: 116 |
3/16/2001 1:53:00 PM | C shell script text executable |
#!/bin/csh -f # Name: paint-sess-new # This is just a front end for paint-sess. |
|||
|
paint-sess-old /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 533 Sz: 11592 |
2/9/2001 4:53:10 PM | C shell script text executable |
#!/bin/csh -f # paint-sess-old: version 1.8 of paint-sess. Uses the old paint command and # the old vss functions. # |
|||
|
par2kspar /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 534 Sz: 4430 |
3/9/2001 3:43:18 PM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: par2kspar - convert a paradigm file to something # suitable for KSS_grinder ############################################################ |
|||
|
par2par01-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 535 Sz: 4102 |
7/27/2001 10:44:12 AM | C shell script text executable |
#!/bin/csh -f # par2par01-sess # # Compresses all conditions in a paradigm file into a single condition. # This is mainly used for testing. |
|||
|
pctsigch /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 536 Sz: 4720 |
2/22/2000 11:35:41 AM | C shell script text executable |
#!/bin/csh -f |
|||
|
qsurfer /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 537 Sz: 4508 |
5/31/2001 1:32:57 PM | C shell script text executable |
#!/bin/csh -f # qsurfer - quick surfer # |
|||
|
rawavg-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 538 Sz: 3026 |
1/14/2001 2:43:42 PM | C shell script text executable |
#!/bin/csh -f # vertically averages data -- not finished yet |
|||
|
roc /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 539 Sz: 2255 |
1/24/2001 4:52:16 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
rocview /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 540 Sz: 6008 |
7/17/2001 3:26:20 PM | C shell script text executable |
#!/bin/csh -f # rocview # # $Id$ |
|||
|
roiavg /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 541 Sz: 6111 |
1/20/2000 2:53:09 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
roiavgraw /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 542 Sz: 8932 |
1/27/2000 9:58:38 AM | C shell script text executable |
#!/bin/csh -f |
|||
|
roisummary-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 543 Sz: 5811 |
4/18/2001 3:05:01 PM | C shell script text executable |
#!/bin/csh -f # func2roi-sess |
|||
|
roitxt2tbl /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 544 Sz: 2713 |
4/6/2001 1:57:44 PM | C shell script text executable |
#!/bin/csh -f # # Converts the text files created by func2roi-sess into a table # with one column so that it is easier to read into external # statistics programs. Each row has the following meaning: # # 1. nlabel - number of functional voxels in the label specified # when running func2roi-sess. This number is zero if no label # is specified. # 2. nroi - number of functional voxels in the final ROI (intersection # of label and mask) # 3. offset - mean of the offsets in each voxel of the ROI. This # can be used to compute percent signal change. # 4. eresstd - mean of the standard deviations of the residual error # at each voxel in the ROI. # 5. DOF - degrees of freedom in eresstd # 6. TER - for event-related studies, this is the time between estimates # that come later. This can be helpful for plotting. # 7. tPreStim - for event-related studies, this is the prestimulus # window. This can be helpful for plotting. # 8. nconditions - number of non-null conditions # 9. nestspercond - number of estimates per condition # 10-N. These are the estimates for each condition. There will be a # block for each condition. Each block is length nestspercond. # |
|||
|
selfreqavg /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 545 Sz: 16085 |
9/27/2001 1:43:56 PM | C shell script text executable |
#!/bin/csh -f # fMRI selective frequency averaging (for phase-encoding analysis) |
|||
|
selfreqcomb /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 546 Sz: 6660 |
7/2/2001 8:36:36 AM | C shell script text executable |
#!/bin/csh -f # fMRI selective frequency combining of averages (for phase-encoding analysis) |
|||
|
selfreqcomb.bak /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 547 Sz: 4791 |
4/20/2000 3:53:35 PM | C shell script text executable |
#!/bin/csh -f # fMRI selective frequency combiner -- combines averages from selfreqavg |
|||
|
selxavg /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 548 Sz: 24097 |
11/7/2000 3:14:49 PM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: selxavg ############################################################ |
|||
|
selxavg2 /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 549 Sz: 15905 |
8/27/2001 9:07:22 AM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: selxavg2 ############################################################ |
|||
|
selxavg-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 550 Sz: 8917 |
9/28/2001 11:48:11 AM | C shell script text executable |
#!/bin/csh -f # selxavg-sess # # $Id: selxavg-sess,v 1.8 2001/01/04 22:13:43 greve Exp greve $ |
|||
|
selxavg-sess-perrun /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 551 Sz: 6359 |
4/12/2001 3:08:57 PM | C shell script text executable |
#!/bin/csh -f # selxavg-sess # # $Id: selxavg-sess-perrun,v 1.1 2001/01/11 22:21:10 greve Exp greve $ |
|||
|
seqefficiency /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 552 Sz: 6852 |
10/1/2001 9:59:00 AM | C shell script text executable |
#!/bin/csh -f |
|||
|
sfa-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 553 Sz: 9610 |
9/27/2001 2:27:35 PM | C shell script text executable |
#!/bin/csh -f # sfa-sess # # $Id$ |
|||
|
skb-import /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 554 Sz: 6919 |
9/26/2000 4:03:58 PM | C shell script text executable |
#!/bin/csh -f # Script to import data from old SKB study |
|||
|
sliceview-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 555 Sz: 15165 |
8/2/2001 12:22:56 PM | C shell script text executable |
#!/bin/csh -f # sliceview-sess # |
|||
|
sliceview-sess-perrun /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 556 Sz: 12011 |
1/5/2001 2:48:15 PM | C shell script text executable |
#!/bin/csh -f # sliceview-sess # |
|||
|
spatfil /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 557 Sz: 9056 |
1/20/2000 2:53:56 PM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: spatfiil ############################################################ |
|||
|
sphsmooth-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 558 Sz: 7746 |
9/26/2001 12:16:49 PM | C shell script text executable |
#!/bin/csh -f # isxavg-fe-sess # |
|||
|
splitstr /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 559 Sz: 619 |
3/7/2000 12:19:05 PM | C shell script text executable |
#!/bin/csh -f ########################################## # Name: splitstr # Purpose: splits the argument string with spaces # $Id ########################################## |
|||
|
spmimg2bvolume /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 560 Sz: 10387 |
8/10/2001 3:27:25 PM | C shell script text executable |
#!/bin/csh -f # spmimg2bvolume - convert an spm .img series of files into # a bvolume (ie, bshort or bfloat) # |
|||
|
stfreqgrinder /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 561 Sz: 6484 |
4/20/2000 3:11:37 PM | C shell script text executable |
#!/bin/csh -f # fMRI selective frequency grinding (for phase-encoding analysis) |
|||
|
stripsessargs /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 562 Sz: 607 |
3/8/2000 10:39:35 AM | C shell script text executable |
#!/bin/csh -f # selxavg-sess # # $Id$ |
|||
|
stxgpredict /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 563 Sz: 5202 |
7/27/2001 3:46:28 PM | C shell script text executable |
#!/bin/csh -f # stxpredict - computes a prediction of the statistical map # given the averages from an already analyzed data set as well # as a list of paradigm files. |
|||
|
stxgrinder /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 564 Sz: 15892 |
1/31/2001 3:57:07 PM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: stxgrinder # Purpose: uses the same command-line args as stxgrinder ############################################################ |
|||
|
stxgrinder-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 565 Sz: 8996 |
6/27/2001 9:48:44 AM | C shell script text executable |
#!/bin/csh -f # stxgrinder-sess # |
|||
|
stxgrinder-sess-perrun /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 566 Sz: 5935 |
1/5/2001 2:46:45 PM | C shell script text executable |
#!/bin/csh -f # stxgrinder-sess # |
|||
|
subject-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 567 Sz: 924 |
11/1/2000 3:01:45 PM | C shell script text executable |
#!/bin/csh -f # subjectname-sess # # $Id$ |
|||
|
surf-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 568 Sz: 17838 |
9/5/2001 9:07:26 AM | C shell script text executable |
#!/bin/csh -f # surf-sess # |
|||
|
surf-sess-new /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 569 Sz: 113 |
3/16/2001 1:53:26 PM | C shell script text executable |
#!/bin/csh -f # Name: surf-sess-new # This is just a front end for surf-sess. |
|||
|
sxacfg-get /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 570 Sz: 974 |
2/15/2000 10:01:29 AM | C shell script text executable |
#!/bin/csh -f # $Id: sxacfg-get,v 1.1 2000/02/15 19:03:20 greve Exp greve $ # Extracts variable values from a selxavg configuration file. |
|||
|
synthfmri /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 571 Sz: 9717 |
8/8/2000 11:42:00 AM | C shell script text executable |
#!/bin/csh -f ############################################################ |
|||
|
synth-phenc /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 572 Sz: 9161 |
4/20/2000 4:28:32 PM | C shell script text executable |
#!/bin/csh -f # fMRI phase-encoding synthsizer |
|||
|
synthrawroi /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 573 Sz: 3963 |
1/20/2000 2:59:00 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
synth-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 574 Sz: 16655 |
8/17/2001 1:47:05 PM | C shell script text executable |
#!/bin/csh -f # synth-sess # # $Id: synth-sess,v 1.3 2001/08/17 19:21:32 greve Exp greve $ |
|||
|
synthstudy /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 575 Sz: 2235 |
5/30/2001 3:19:07 PM | C shell script text executable |
#!/bin/csh -f # synthstudy # |
|||
|
tkmedit-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 576 Sz: 18210 |
8/21/2001 12:32:06 PM | C shell script text executable |
#!/bin/csh -f # tkmedit-sess # |
|||
|
tkregister-sess /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 577 Sz: 8065 |
1/29/2001 10:13:20 AM | C shell script text executable |
#!/bin/csh -f # tkregister-sess # |
|||
|
yakview /binfs/freesurfer_alpha/fsfast-20011005/bin/ |
#: 578 Sz: 13001 |
4/5/2001 10:36:21 AM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: yakview # Purpose: allows viewing of structurals with statistical # overlays along with a seperate window to view hemodynamic # responses. ############################################################ |
|||
| /binfs/freesurfer_alpha/fsfast-20011005/bin/IRIX/ | |||
|
afni_to_bshort /binfs/freesurfer_alpha/fsfast-20011005/bin/IRIX/ |
#: 579 Sz: 25852 |
3/7/2000 2:12:37 PM | ELF 32-bit MSB MIPS-I executable, MIPS, version 1 |
|
synthbfile /binfs/freesurfer_alpha/fsfast-20011005/bin/IRIX/ |
#: 580 Sz: 33020 |
4/3/2000 5:19:41 PM | ELF 32-bit MSB MIPS-I executable, MIPS, version 1 |
| /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ | |||
|
afni_to_bshort /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 581 Sz: 26388 |
3/7/2000 2:09:37 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: <input brik file> <output bshort stem> <voxels in x> <voxels in y> <numb er of slices> <time points> |
|||
|
bavg /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 582 Sz: 31730 |
11/23/1999 9:15:41 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Extension --help not recognized |
|||
|
brescale /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 583 Sz: 18797 |
11/23/1999 9:15:43 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: brescale multfactor instem outstem firstslice nslices
Version: $Id: brescale.c,v 1.2 1999/06/16 23:01:31 greve Exp $
|
|||
|
btail /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 584 Sz: 13803 |
11/23/1999 9:15:44 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: btail infile outfile offset |
|||
|
btavg /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 585 Sz: 18830 |
11/23/1999 9:15:42 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: btavg bfile r1 c1 r2 c2
Version: $Id$
|
|||
|
cmpmodtime /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 586 Sz: 23641 |
11/23/1999 9:15:45 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: cmpmodtime file1 file2 Returns: +1 : file1 modified more recently than file2 0 : mod dates/times are equal -1 : file2 modified more recently than file1 |
|||
|
cor2bshort /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 587 Sz: 19598 |
11/23/1999 9:15:40 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
&cor = 804b1e0 usage: [options] -s subject -o outstem options are: -v cor volume id <T1> -p slice plane orientation (<ax>, cor, sag) -b between plane resolution (mm) <1> -i within plane resolution (mm) <1> This program converts COR files to bshort, sub-sampling and re-orienting along the way. |
|||
|
diffw /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 588 Sz: 25427 |
10/5/1999 3:21:51 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
n = 1, avg = 6.16298e-33, std = nan, min = 6.16298e-33, max = 6.16298e-33 |
|||
|
dumpw /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 589 Sz: 21881 |
10/5/1999 3:21:49 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
-- ilat = 17475, num = 1
0 0.00000
|
|||
|
fast_condfit /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 590 Sz: 67987 |
10/2/2000 5:06:48 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
/binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/fast_condfit: No such file or directory |
|||
|
fast_inorm /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 591 Sz: 47500 |
11/7/2000 12:09:59 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
/binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/fast_inorm: No such file or directory |
|||
|
I2bshort-func /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 592 Sz: 24042 |
11/23/1999 9:15:43 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: I2bshort-func f1 nf a1 na rows cols
f1 - number of first functional slice
nf - number functional slices
a1 - number of first anatomical slice
na - number anatomical slices
rows - number of rows in each functional slice
cols - number of cols in each functional slice
Input files are: I.fff.saa where fff goes from
f1 to f1+nf and aa goes from a1 to a1+na
Output files are: I_aaa.bshort
|
|||
|
parboxcar /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 593 Sz: 17652 |
11/23/1999 9:15:46 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: parboxcar inpar tboxcar TR outpar |
|||
|
pkfinder /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 594 Sz: 65440 |
1/21/2000 10:18:25 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: pkfinder -i instem (required) -frame number of frame in input to process (0) -cluster minimum cluster size (required) -ngrowmax grow cluster over ngrowmax box (1) -pval maximum pval (1e-05) -distance min dist between peaks (12) mm -xcenter column at which x=0 (23) -ycenter row at which y=0 (26) -no1988 dont subtract 12mm from ycenter -zcenter slice at which z=0 (24) -xres distance between columns (3.125) mm -yres distance between rows (3.125) mm -zres distance between slices (3.125) mm -pos create coordinate list based on positive changes (default) -neg create coordinate list based on negative changes -abs create coordinate list based on absolute changes -nopeaks do not create an instem.peaks.bfloat file -raw threshold = pval -ln threshold = -ln(pval) (default) -log10 threshold = -log10(pval) -verbose print out A LOT of information NOTE: 12 mm is subtracted from ycenter in output lists for 1988 atlas |
|||
|
setbfileroi /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 595 Sz: 18743 |
11/23/1999 9:15:42 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
USAGE: setbfileroi infile r1 c1 r2 c2 val <outfile> |
|||
|
synthbfile /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 596 Sz: 33721 |
11/23/1999 9:15:42 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: [options] -o outstem options are: -e extention (bfloat) -d dof (0 - do not gen dof file) -f first anat slice (0) -n number of anat slices (16) -r number of rows (64) -c number of cols (64) -p number of time points (2) -t specify values of time points -m average of all voxels (5) -a noise amp for all voxels (0) -l axis : alternate average for slices along x,y, or z -s random seed (53) -i inc: increment the amplitude by inc for each slice (0) This program synthesizes simple bshort or bfloat files |
|||
|
talcoor /binfs/freesurfer_alpha/fsfast-20011005/bin/Linux/ |
#: 597 Sz: 66099 |
1/3/2000 3:06:22 PM | ELF 32-bit LSB executable, Intel 80386, version 1 |
talcoor version 1.0 - RL Buckner MGH-NMR (e-mail commments to: buckner@nmr.mgh.harvard.edu)
(C) Copyright 1997 Randy L. Buckner All Rights Reserved
Usage: talcoor [-options] -i <instem>
Example: talcoor -nslices 16 -i S120r43
<instem> : prefix of .ks.bfloat input files
Key options:
-help : get more detailed help
-firstslice <int> : first slice number to process (default = 0)
-nslices <int> : number of slices to process (default = 39)
-pos : create coordinate list based on positive changes (default)
-neg : create coordinate list based on negative changes
-cluster <int> : number of cluster voxels required
-pval <float> : p-value threshold for finding peaks (default = .00001)
-distance <float> : mm distance 2 points must be separated - else weight l
ocation by -logp (default = 12.0)
-noweight : do not weight locations, simply keep the most significant
-nosort : do not sort output by -logp value, default is to sort
-nopeaks : do not produce ...peaks.bfloat file, default is to produce
-quiet : quite mode
-nohead : don't output header (good for bringing into stats packages)
Format options:
-kslogp : use ...kslogp.bfloat not ...ks.bfloat
-selavg <int> : use ...#.bfloat (where # is int) not ...ks.bfloat
-simple : use dont use any fancy extension not ...ks.bfloat
-expand : creates a separate peak bfloat for each slice, default
is on concatenated file
Dimension options:
-xcenter <int> : Talairach x-center (default = 23)
-ycenter <int> : Talairach y-center (default = 26) NOTE: 12 mm are subt
racted in output lists for 1988 atlas
-zcenter <int> : Talairach z-center (default = 24)
-xres <float> : resolution of input image in the x-dimension (default = 3.125)
-yres <float> : resolution of input image in the y-dimension (default = 3.125)
-zres <float> : resolution of input image in the z-dimension (default = 3.125)
----------------------------------------------------------------------
talcoor -help
talcoor version 1.0 (C) 1997 Randy L. Buckner e-mail comments to buckner@nmr.mgh.harvard.edu
The purpose of this program is to take in .bfloat images that contain statistical
probability values (-log[p]) and find the locations of the peaks in Talairach and Tournoux
1988 atlas space.
The program, essentially, screens for peaks based on the following criteria:
(1) The voxel must reach a certain threshold specified by the -pval <float> option. The float
should be the actual p-value (e.g., "-pval .0001").
(2) The voxel must be the largest of its neighbors.
(3) If the -cluster <int> constraint is set, its neighbors must contain at least <int>
members that reach the critical p-value (e.g., "-cluster 8").
(4) If the -distance <float> constraint is set then peaks within <float> mm are not
considered. In these instances the weighted location is kept unless the -noweight option
option is selected. Then, the largest peak is kept. (e.g., "-distance 8.0 -noweight")
The ouput of the program is twofold. First, a text list of all identified peaks are
generated in a file with the .coor extension. These peaks are numbered and sorted
largest to smallest unless the -nosort option is used. Then they appear in the order
they were detected. The second item produced is a .bfloat image stack that contains
one image for each slice of the brain. A square dot is placed in these images
corresponding to the identified peaks. The intenisty value of these dots is the p-value.
These stacks can be viewed by %xds <name>.peaks.bfloat &. Alternatively, these stacks
can be placed in a mosaic and viewed on top of an anatomic image. Yet another alternative,
which can be used to decide whether the peak search algorith is working, is to display the
mosaic of the .peaks.bfloat file on top of a mosaic of the statistical map that produced
it (e.g., %xds -A mosTAL_AVG10stemallfix.peaks.bfloat mosTAL_AVG10stemallfix.ks.bfloat &).
talcoor is meant (but not required) to be used with talreg and taltime. "talreg" will take
in coordinates identified by talcoor and automatically define regions around it. "taltime"
will take in a region and get its timecourse. Still yet another program "normalizer" will
take in the timeseries produced by taltime and drift correct, smooth, and convert it to
percent change. Collectively, these programs can thus be used to automatically interogate
fMRI timecourse data.
Options:
-expand This program, by default, makes a single .bfloat stack that contains all peaks.
Other programs output one image per slice so that they can be made to correspond
to single slice data such as .bshort timeseries. Choosing the "-expand" forces
this program to conform to that convention producing one image per slice.
-nopeaks Do not produce the .peaks.bfloat images.
|
|||
| /binfs/freesurfer_alpha/fsfast-20011005/bin/SunOS/ | |||
|
afni_to_bshort /binfs/freesurfer_alpha/fsfast-20011005/bin/SunOS/ |
#: 598 Sz: 20558 |
3/7/2000 2:17:19 PM | ELF 32-bit MSB executable, SPARC, version 1 (SYSV) |
|
KSS_grinder /binfs/freesurfer_alpha/fsfast-20011005/bin/SunOS/ |
#: 599 Sz: 131072 |
3/9/2001 1:43:49 PM | SPARC demand paged dynamically linked executable n |
| /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ | |||
|
apconvert /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ |
#: 600 Sz: 593 |
10/27/1999 10:55:26 AM | C shell script text executable |
#!/bin/csh -f |
|||
|
avgavg-re /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ |
#: 601 Sz: 2562 |
6/8/1999 7:07:53 PM | C shell script text executable |
#!/bin/csh -f # avgavg-re -fs fs -ns ns -i in1 -i in2 -o outstem # $Id$ |
|||
|
isavgstg /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ |
#: 602 Sz: 5476 |
10/27/1999 5:48:30 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
isxavg /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ |
#: 603 Sz: 6719 |
10/26/1999 10:32:11 AM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: isxavg # Purpose: # Usage: isxavg -fs N -ns N -weight <string> -effect <string> # -i instem1 -i instem2 -o outstem ############################################################ |
|||
|
isxgrinder /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ |
#: 604 Sz: 12658 |
10/27/1999 4:18:24 PM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: isxgrinder # Purpose: intersubject statistical grinding. Operates # on data created by isxavg (which averages the # outputs of selxavg across subjects). ############################################################ |
|||
|
mkcmtx /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ |
#: 605 Sz: 8554 |
11/10/1999 10:40:35 AM | C shell script text executable |
#!/bin/csh -f ############################################################ # Name: mkcmtx # Purpose: make a contrast matrix ############################################################ |
|||
|
mri-func2sph /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ |
#: 606 Sz: 6106 |
11/12/1999 12:02:52 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
mri-funcvits /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ |
#: 607 Sz: 6131 |
11/12/1999 12:02:52 PM | C shell script text executable |
#!/bin/csh -f |
|||
|
mri-sph2label /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ |
#: 608 Sz: 6011 |
5/19/2000 3:18:04 PM | C shell script text executable |
#!/bin/csh -f # mri-sph2label |
|||
|
mri-structvits /binfs/freesurfer_alpha/fsfast-20011005/bin/trash/ |
#: 609 Sz: 7061 |
11/12/1999 12:02:52 PM | C shell script text executable |
#!/bin/csh -f |
|||
| /binfs/freesurfer_alpha/fsfast-20011005/docs/ | |||
|
avgavg.info /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 610 Sz: 425 |
9/17/1999 10:02:57 AM | ASCII text |
|
bert-functional.howto.aux /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 611 Sz: 2553 |
8/15/2001 12:41:09 PM | LaTeX auxiliary file |
|
bert-functional.howto.log /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 612 Sz: 10174 |
8/15/2001 12:41:09 PM | TeX transcript text |
|
bert-functional.howto.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 613 Sz: 51202 |
8/15/2001 12:41:09 PM | PostScript document text conforming at level 2.0 |
|
bert-functional.howto.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 614 Sz: 25530 |
8/15/2001 1:09:08 PM | LaTeX 2e document text |
|
bfile.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 615 Sz: 37666 |
3/23/2001 12:43:01 PM | PostScript document text conforming at level 2.0 |
|
bfile.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 616 Sz: 2650 |
3/23/2001 12:41:53 PM | ASCII English text |
|
CHANGES /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 617 Sz: 757 |
11/9/2000 3:41:52 PM | ASCII English text |
|
condfit.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 618 Sz: 33805 |
8/7/2001 11:00:42 AM | PostScript document text conforming at level 2.0 |
|
condfit.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 619 Sz: 1894 |
10/6/2000 12:09:40 PM | ASCII English text |
|
COPYWRITE /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 620 Sz: 175 |
4/5/2000 11:54:07 AM | ASCII English text |
|
DISCLAIMER /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 621 Sz: 634 |
4/5/2000 11:36:52 AM | ASCII text |
|
fmri-analysis-theory.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 622 Sz: 124053 |
3/7/2000 2:47:35 PM | PostScript document text conforming at level 2.0 |
|
fmri-analysis-theory.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 623 Sz: 17982 |
8/10/1999 12:41:14 PM | LaTeX 2e document text |
|
func2roi-sess.pdf /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 624 Sz: 136879 |
8/23/2001 9:57:35 AM | PDF document, version 1.2 |
|
func2roi-sess.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 625 Sz: 113625 |
8/7/2001 11:00:43 AM | PostScript document text conforming at level 2.0 |
|
func2roi-sess.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 626 Sz: 19868 |
4/19/2001 2:59:40 PM | ASCII English text |
|
hbm99-abstract.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 627 Sz: 73257 |
8/13/1999 2:32:21 PM | PostScript document text conforming at level 2.0 |
|
inorm.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 628 Sz: 83665 |
8/7/2001 11:01:36 AM | PostScript document text conforming at level 2.0 |
|
inorm.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 629 Sz: 12800 |
8/7/2001 11:01:31 AM | ASCII English text |
|
INSTALL /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 630 Sz: 2822 |
5/14/2001 1:58:23 PM | ASCII English text |
|
INSTALL.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 631 Sz: 31461 |
6/27/2000 12:28:09 PM | PostScript document text conforming at level 2.0 |
|
INSTALL.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 632 Sz: 4249 |
6/27/2000 12:28:05 PM | LaTeX 2e document text |
|
intergroup-sess.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 633 Sz: 54598 |
8/3/2001 12:25:53 PM | PostScript document text conforming at level 2.0 |
|
intergroup-sess.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 634 Sz: 5156 |
8/3/2001 12:25:24 PM | ASCII English text |
|
isxavg-fe.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 635 Sz: 44799 |
3/7/2000 2:47:39 PM | PostScript document text conforming at level 2.0 |
|
isxavg-fe.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 636 Sz: 2908 |
3/7/2000 12:48:48 PM | ASCII English text |
|
isxavg-re.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 637 Sz: 49177 |
3/7/2000 2:47:41 PM | PostScript document text conforming at level 2.0 |
|
isxavg-re.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 638 Sz: 4068 |
3/7/2000 12:53:43 PM | ASCII English text |
|
license.gnu /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 639 Sz: 25267 |
4/5/2000 11:03:41 AM | ASCII English text |
|
Makefile /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 640 Sz: 478 |
8/10/1999 2:21:47 PM | ASCII make commands text |
|
MANIFEST /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 641 Sz: 12455 |
10/5/2001 8:22:43 AM | ASCII text |
|
mc-afni.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 642 Sz: 61523 |
3/23/2000 10:59:13 AM | PostScript document text conforming at level 2.0 |
|
mc-afni.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 643 Sz: 5058 |
3/23/2000 10:59:04 AM | ASCII English text |
|
MGH-NMR-StdProc-Handbook.doc /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 644 Sz: 1811968 |
3/13/2001 11:05:36 AM | Microsoft Office Document |
|
mkcontrast.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 645 Sz: 72726 |
3/7/2000 2:47:44 PM | PostScript document text conforming at level 2.0 |
|
mkcontrast.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 646 Sz: 7554 |
3/7/2000 10:22:55 AM | ASCII English text |
|
mkmosaic.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 647 Sz: 42376 |
3/7/2000 2:47:46 PM | PostScript document text conforming at level 2.0 |
|
mkmosaic.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 648 Sz: 2878 |
3/7/2000 12:59:42 PM | ASCII English text |
|
mkmosaic16.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 649 Sz: 45539 |
3/7/2000 2:47:48 PM | PostScript document text conforming at level 2.0 |
|
mkmosaic16.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 650 Sz: 2564 |
1/20/2000 2:48:35 PM | ASCII English text |
|
mtp-repack.pdf /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 651 Sz: 66926 |
6/14/2000 3:23:37 PM | PDF document, version 1.2 |
|
mtp-repack.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 652 Sz: 52878 |
6/20/2000 9:30:12 AM | PostScript document text conforming at level 2.0 |
|
mtp-repack.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 653 Sz: 5429 |
6/20/2000 9:29:51 AM | ASCII English text |
|
optseq.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 654 Sz: 83658 |
9/26/2000 9:08:17 AM | PostScript document text conforming at level 2.0 |
|
optseq.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 655 Sz: 11611 |
9/25/2000 9:25:32 AM | ASCII English text |
|
overview.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 656 Sz: 61574 |
8/7/2001 11:01:37 AM | PostScript document text conforming at level 2.0 |
|
overview.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 657 Sz: 7607 |
1/13/2001 12:46:32 PM | ASCII English text |
|
paint.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 658 Sz: 45302 |
3/7/2000 2:47:53 PM | PostScript document text conforming at level 2.0 |
|
paint.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 659 Sz: 2905 |
1/20/2000 2:49:01 PM | ASCII English text |
|
paradigm.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 660 Sz: 31006 |
3/7/2000 2:47:54 PM | PostScript document text conforming at level 2.0 |
|
paradigm.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 661 Sz: 2562 |
1/20/2000 2:49:01 PM | ASCII English text |
|
README.afni /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 662 Sz: 156 |
4/5/2000 11:03:49 AM | ASCII English text |
|
register.info /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 663 Sz: 6371 |
8/13/1999 9:40:34 AM | ASCII English text |
|
selfreq.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 664 Sz: 74426 |
8/7/2001 11:01:37 AM | PostScript document text conforming at level 2.0 |
|
selfreq.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 665 Sz: 10692 |
3/5/2001 8:18:11 AM | ASCII English text |
|
selxavg.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 666 Sz: 91391 |
3/7/2000 2:47:56 PM | PostScript document text conforming at level 2.0 |
|
selxavg.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 667 Sz: 17916 |
8/27/2001 11:02:27 AM | ASCII English text |
|
seq.info.example /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 668 Sz: 217 |
11/10/2000 11:21:31 AM | ASCII text |
|
seqefficiency.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 669 Sz: 42064 |
3/7/2000 2:47:58 PM | PostScript document text conforming at level 2.0 |
|
seqefficiency.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 670 Sz: 2343 |
1/20/2000 2:49:02 PM | ASCII English text |
|
sliceview.tal.txt /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 671 Sz: 866 |
8/21/2001 12:29:35 PM | ASCII English text |
|
stgrinder2.info /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 672 Sz: 1350 |
9/17/1999 10:03:05 AM | ASCII text |
|
stxgrinder.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 673 Sz: 96144 |
3/7/2000 2:48:00 PM | PostScript document text conforming at level 2.0 |
|
stxgrinder.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 674 Sz: 16792 |
3/7/2000 10:19:16 AM | LaTeX 2e document text |
|
version /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 675 Sz: 9 |
10/5/2001 8:22:42 AM | ASCII text |
|
vol2roi.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 676 Sz: 71228 |
1/2/2001 2:56:33 PM | PostScript document text conforming at level 2.0 |
|
vol2roi.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 677 Sz: 10512 |
1/2/2001 2:56:25 PM | ASCII English text |
|
yakview.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 678 Sz: 65110 |
6/20/2000 9:21:46 AM | PostScript document text conforming at level 2.0 |
|
yakview.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/ |
#: 679 Sz: 7050 |
6/20/2000 9:20:38 AM | ASCII English text |
| /binfs/freesurfer_alpha/fsfast-20011005/docs/log/ | |||
|
sliceview-sess.log /binfs/freesurfer_alpha/fsfast-20011005/docs/log/ |
#: 680 Sz: 422 |
2/26/2001 3:02:27 PM | ASCII text |
| /binfs/freesurfer_alpha/fsfast-20011005/docs/minc/ | |||
|
prog_guide.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/minc/ |
#: 681 Sz: 132109 |
10/30/2000 8:15:10 AM | PostScript document text conforming at level 2.0 |
|
prog_guide.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/minc/ |
#: 682 Sz: 33924 |
10/30/2000 8:13:31 AM | ASCII English text |
|
prog_guide.toc /binfs/freesurfer_alpha/fsfast-20011005/docs/minc/ |
#: 683 Sz: 1822 |
10/30/2000 8:15:09 AM | LaTeX table of contents |
|
prog_ref.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/minc/ |
#: 684 Sz: 141112 |
10/30/2000 8:15:03 AM | PostScript document text conforming at level 2.0 |
|
prog_ref.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/minc/ |
#: 685 Sz: 45184 |
10/30/2000 8:13:31 AM | ASCII English text |
|
prog_ref.toc /binfs/freesurfer_alpha/fsfast-20011005/docs/minc/ |
#: 686 Sz: 1478 |
10/30/2000 8:15:02 AM | LaTeX table of contents |
|
volume_io.ps /binfs/freesurfer_alpha/fsfast-20011005/docs/minc/ |
#: 687 Sz: 296194 |
10/30/2000 8:14:36 AM | PostScript document text conforming at level 2.0 |
|
volume_io.tex /binfs/freesurfer_alpha/fsfast-20011005/docs/minc/ |
#: 688 Sz: 115155 |
10/30/2000 8:13:31 AM | LaTeX document text |
|
volume_io.toc /binfs/freesurfer_alpha/fsfast-20011005/docs/minc/ |
#: 689 Sz: 2400 |
10/30/2000 8:14:36 AM | LaTeX table of contents |
| /binfs/freesurfer_alpha/fsfast-20011005/src/ | |||
|
afni_to_bshort.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 690 Sz: 2632 |
3/7/2000 2:08:40 PM | ASCII C program text |
|
bavg.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 691 Sz: 3149 |
7/22/1999 10:45:41 AM | ASCII English text |
|
bf2bs.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 692 Sz: 3198 |
12/10/1998 2:00:48 PM | ASCII English text |
|
brescale.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 693 Sz: 3769 |
6/16/1999 4:04:21 PM | ASCII C program text |
|
brueker2bshort.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 694 Sz: 4285 |
4/12/1999 3:35:12 PM | ASCII English text |
|
bs2bf.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 695 Sz: 3183 |
12/9/1998 2:31:37 PM | ASCII English text |
|
btail.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 696 Sz: 1076 |
3/31/1999 12:53:58 PM | ASCII C program text |
|
btavg.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 697 Sz: 3252 |
6/9/1999 2:54:59 PM | ASCII English text |
|
cmpmodtime.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 698 Sz: 839 |
10/26/1999 5:58:45 PM | ASCII C program text |
|
cor2bshort.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 699 Sz: 7705 |
5/24/1999 10:12:56 AM | ASCII C program text |
|
diffw.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 700 Sz: 4153 |
7/12/1999 1:20:41 PM | ASCII English text |
|
dumpw.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 701 Sz: 2313 |
7/8/1999 1:17:17 PM | ASCII C program text |
|
extractroi.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 702 Sz: 1872 |
1/6/2000 2:26:48 PM | ASCII C program text |
|
I2bshort.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 703 Sz: 2011 |
4/5/1999 11:31:48 AM | ASCII English text |
|
I2bshort-anat.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 704 Sz: 2435 |
4/5/1999 11:31:44 AM | ASCII C program text |
|
I2bshort-func.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 705 Sz: 3016 |
4/5/1999 11:31:46 AM | ASCII C program text |
|
inorm.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 706 Sz: 2908 |
8/9/1999 5:00:02 PM | ASCII English text |
|
Makefile /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 707 Sz: 1908 |
4/19/2000 1:42:02 PM | ASCII English text |
|
parboxcar.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 708 Sz: 718 |
1/4/2000 10:35:39 AM | ASCII C program text |
|
pkfinder.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 709 Sz: 10325 |
1/21/2000 10:12:51 AM | ASCII C program text |
|
pkfutil.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 710 Sz: 22108 |
1/21/2000 10:18:20 AM | ASCII C program text |
|
pkfutil.h /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 711 Sz: 3112 |
1/21/2000 10:17:06 AM | ASCII C program text |
|
pkfutil.o /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 712 Sz: 49820 |
1/26/2000 11:24:53 AM | ELF 32-bit MSB relocatable, SPARC, version 1 (SYSV |
|
setbfileroi.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 713 Sz: 3751 |
7/29/1999 2:55:25 PM | ASCII English text |
|
synthbfile /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 714 Sz: 33020 |
4/3/2000 5:19:41 PM | ELF 32-bit MSB MIPS-I executable, MIPS, version 1 |
|
synthbfile.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 715 Sz: 9525 |
1/4/2000 10:37:39 AM | ASCII C program text |
|
synthw.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 716 Sz: 4433 |
7/12/1999 1:00:48 PM | ASCII English text |
|
talcoor.c /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 717 Sz: 35144 |
1/4/2000 10:33:37 AM | ASCII C program text |
|
talcoor.h /binfs/freesurfer_alpha/fsfast-20011005/src/ |
#: 718 Sz: 84 |
1/3/2000 7:30:58 AM | ASCII C program text |
| /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ | |||
|
afni2bvol.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 719 Sz: 3473 |
4/4/2001 4:04:32 PM | MatLab script |
function r = afni2bvol(varargin) % r = afni2bvol(varargin) % '$Id' %% Print useage if there are no arguments %% |
|||
|
arCorrFun.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 720 Sz: 654 |
8/13/1999 1:18:58 PM | MatLab script |
function R = arCorrFun(alpha, rho, nMaxDelay, Sided) % % function R = arCorrFun(alpha, rho, nMaxDelay, <Sided>) % % nMaxDelay + 1 = number of components in the One-Sided ACor. % % The alpha-rho model of the correlation function: % r(0) = 1 % r(n) = (1-alpha)*rho^n, 0 < n <= nMaxDelay % % Defaults: Sided = 1 % % $Id: arCorrFun.m,v 1.1 1999/08/13 20:16:58 greve Exp $ |
|||
|
avgrandeff.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 721 Sz: 4498 |
6/9/1999 10:24:56 AM | MatLab script |
% avgrandeff % % Average using a Random Effects Model % % InputStems, SubtCond0, FirstSlice, nSlices, OutStem % RescaleAvg, ROI |
|||
|
basename.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 722 Sz: 577 |
8/17/2000 2:23:41 PM | MatLab script |
function name = basename(path) % name = basename(path) % % This is an attempt to recreate the unix basename % command in matlab. % $Id$ |
|||
|
bliweights.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 723 Sz: 2443 |
9/11/2000 1:34:27 PM | MatLab script |
function [ind, wind] = bliweights(szmtx, rc_hat) % [ind wind] = bliweights(szmtx, rc_hat) % % Weights and indices for bilinear interpolation. % % szmtx is number of rows and columns in matrix % rc_hat - off-grid rows and columns to interpolate (N x 2) % % ind (N x 4) % w (N x 4) % % See also: uliweights, tliweights |
|||
|
boldview.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 724 Sz: 5795 |
3/9/2000 12:50:39 PM | MatLab script |
function boldview(cbflag,data) |
|||
|
ComputeFPR.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 725 Sz: 290 |
11/3/1999 3:24:10 PM | MatLab script |
function [FPR, alpha] = ComputeFPR(p, pDelta) % % [FPR alpha] = ComputeFPR(p, <pDelta>) % |
|||
|
cor2bshort.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 726 Sz: 3865 |
3/9/2001 11:01:30 AM | MatLab script |
function cor2bshort(subject, volid, bpres, ipres) % % cor2bshort(subjname, volid, bpres, ipres) % % Converts a corronal volume found in $SUBJECTS_DIR/subject/mri/volid % into bshort format with bpres between-plane resolution and ipres % in-plane resolution. When a resolution more than 1 mm, all the COR % slices within that resolution are averaged together. % % The bshorts are put in % $SUBJECTS_DIR/subject/mri/volid/bshort%d%d % where the first %d is the bpres and the second is ipres. Also creates % register.dat and analyze.dat. % % The bshorts can be viewed against the originals with % tkregister local $SUBJECTS_DIR/subject/mri/volid % |
|||
|
defmossize.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 727 Sz: 1082 |
3/12/2001 11:11:05 AM | MatLab script |
function tszmos = defmossize(N, tszmos) % tszmos = defmossize(N, <tszmos>) % % Computes default mosaic size in terms of number of tile rows and % colums. % % Inputs: % N - minimum number of slices from which to construct the mosaic. % tszmos - mosaic size [rows cols] in tiles (optional). % % Returns: % tszoms - mosaic size [rows cols] in tiles. % % The tszmos input argument can be used to specify the number of % tile rows or the number of tile colums. |
|||
|
dirname.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 728 Sz: 462 |
8/17/2000 2:31:08 PM | MatLab script |
function name = dirname(path) % name = dirname(path) % % This is an attempt to recreate the unix dirname command % in matlab. % $Id$ |
|||
|
drclip.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 729 Sz: 808 |
10/16/2000 11:49:57 AM | MatLab script |
function [y, xthresh, nclip, psqueeze] = drclip(x,thr,clipval) % % [y, xthresh, nclip, psqueeze] = drclip(x,thr,<clipval>) % % Squeezes dynamic range by clipping a fraction (thr) of the % elements of greatest value to clipval. % % % $Id$ |
|||
|
drsqueeze.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 730 Sz: 636 |
4/23/1999 8:49:21 AM | MatLab script |
function [y, xthresh, nclip, psqueeze] = drsqueeze(x,thr) % % y = drsqueeze(x) % % Squeezes dynamic range by clipping a fraction (thr) of the % elements of greatest value. % % % $Id: drsqueeze.m,v 1.1 1999/03/24 22:11:30 greve Exp $ |
|||
|
editmask.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 731 Sz: 12103 |
5/22/2001 10:30:52 AM | MatLab script |
function r = editmask(varargin) % r = editmask(varargin) % Edit a functional mask % '$Id$' |
|||
|
fast_acorr.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 732 Sz: 855 |
2/9/2001 2:18:34 PM | MatLab script |
function R = fast_acorr(x) % R = fast_acorr(x) % % Computes the autocorrelation of x using an FFT. This should % produce the same results as the native matlab function xcorr % when invoked as xcorr(x,nMaxLag,'unbiased'), except that xcorr() % is slow and will not compute a separate R for each column of x. % |
|||
|
fast_baselinemtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 733 Sz: 297 |
12/4/2000 6:39:35 PM | MatLab script |
function Xbaseline = fast_baselinemtx(run,ntrs,nruns) % Xbaseline = fast_baselinemtx(run,ntrs,nruns) |
|||
|
fast_bfileconvert.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 734 Sz: 8405 |
3/9/2001 4:29:13 PM | MatLab script |
function r = fast_bfileconvert(varargin) % r = fast_bfileconvert(varargin) % Converts a bfile into another bfile. Eg, bfloat into bshort, % Little endian into big endian, etc. % '$Id: fast_bfileconvert.m,v 1.1 2000/09/06 22:56:33 greve Exp greve $' |
|||
|
fast_cbm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 735 Sz: 1793 |
6/29/2001 5:36:03 PM | MatLab script |
function [cbm, idealcbm, cbmerr] = fast_cbm(seq,maxorder) % [cbm idealcbm cbmerr] = fast_cbm(seq,maxorder) % % Defines nth order counter balancing as the probability of % getting a particular stimulus n stimuli after another % stimulus. The counter-balancing matrix (CBM) is NxNxmaxorder % (N = number of event types) where the entry in the ith row % and jth column of the kth matrix is the probability of seeing % event j k events after event i. % % All the numbers within a column of the idealcbm are the same % and equal the number of times the jth type was presented divided % by the total number of presentations. The idealcbm is NxN and % is the same for all orders. % % The cbmerr is the difference between the actual cbm and the % idealcbm. % % Notes: event type 0 is removed before processing. % % See also fast_cbm2(). Unlike fast_cbm2(), the CBM of all orders % (upto and including maxorder) are computed. % |
|||
|
fast_cbm2.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 736 Sz: 2038 |
6/29/2001 5:32:13 PM | MatLab script |
function [cbm, idealcbm] = fast_cbm2(seq,order) % % [cbm idealcbm] = fast_cbm2(seq,order) % % Defines nth order counter balancing as the probability of % getting a particular stimulus after a order-length sequence % of stimuli. If there are N event types in the sequence, then % the number of possible order-length sequnces is M = N^order % The counter-balance matrix (CBM) has a size MxN. The entry in % the ith row and jth column is the probability of seeing event % type j after subsequence i. % % Eg. N=3, order=3. M = 27. CBM is MxN: % i=1 --> (1,1,1) % i=2 --> (1,1,2) % i=3 --> (1,1,3) % i=4 --> (1,2,1) % i=5 --> (1,2,2) % ... % % All the numbers within a column of the idealcbm are the same % and equal the number of times the jth type was presented divided % by the total number of presentations. The idealcbm is also MxN. % % See also fast_cbm(). Unlike fast_cbm(), the CBM of only the % specified order is computed. % % Order must be <= 3. |
|||
|
fast_clip.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 737 Sz: 871 |
9/22/2000 8:04:03 AM | MatLab script |
function vclip = fast_clip(v,thresh,clipdir) % vclip = fast_clip(v,<<thresh>,clipdir>) % % clipdir: <positive>, negative, both % % $Id$ |
|||
|
fast_compute_cvm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 738 Sz: 5780 |
3/27/2001 2:38:53 PM | MatLab script |
function r = fast_compute_cvm(varargin) % r = fast_compute_cvm(varargin) % '$Id$' % % Computes the temporal covariance matrix (CVM) of a functional volume. % Options: % - compute CVM from a set of voxels specified in mask % - compute complementary CVM from the set of voxels not % specified in mask % - specify the threhsold for mask % - remove mean before computing CVM (default) % - remove trend before computing CVM (default) % % Saves results in CVM format (.bfloat, .hdr, and .cvm files) % % See also: fmri_cvmstruct, fmri_svcvm, fmri_ldcvm % |
|||
|
fast_condctrstmtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 739 Sz: 2143 |
7/25/2001 5:17:55 PM | MatLab script |
function R = fast_condctrstmtx(TER,TW,TPS,SumDelays,WDelays,RmPrestim) % % R = fast_condctrstmtx(TER,TW,TPS,SumDelays,WDelays,RmPrestim) % % Computes the contrast matrix for a single condition. % % TER - temporal estimation resolution (s) % TW - total time window (s) % TPS - prestimulus window (s), including delay = 0 % % SumDelays = 1, forces Delays to be weighted by WDelays and summed. % Forces the contrast matrix to be a vector. % % WDelays - delay weighting vector. Ignored if SumDelays = 0. If % [], replaced with ones (ie, forces a simple average). % % RmPrestim = 1 subtract prestimulus average; will replace % the prestim components of WDelays. % % If the prestim is not removed and SumDelays=0 % then returns the identity of size nDelays = round(TW/TER). % % If the prestim is not removed and SumDelays=1, then returns % a vector of length nDelays with all the components 1/Nh. % |
|||
|
fast_condfit.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 740 Sz: 16331 |
10/15/2000 9:01:35 AM | MatLab script |
function r = fast_condfit(varargin) % r = fast_condfit(varargin) % Random effects fit of conditions to a weight |
|||
|
fast_contrastmtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 741 Sz: 2048 |
8/7/2001 4:17:04 PM | MatLab script |
function R = fast_contrastmtx(TER,TW,TPS,nConds,SumConds,WConds,SumDelays,WDelays,RmPrestim) % % R = fast_contrastmtx(TER,TW,TPS,nConds,SumConds,WConds, % SumDelays,WDelays,RmPrestim) % % SumConds = 1, forces Conditions to be weighted by WConds and summed. % % WConds - condition weighting vector. Ignored if SumConds = 0. If % [], replaced with ones (ie, forces a simple average). % % SumDelays = 1, forces Delays to be weighted by WDelays and summed. % Forces the contrast matrix to be a vector. % % WDelays - delay weighting vector. Ignored if SumDelays = 0. If % [], replaced with ones (ie, forces a simple average). % % RmPrestim = 1 subtract prestimulus average; will replace % the prestim components of WDelays. % |
|||
|
fast_cvm_condrgl.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 742 Sz: 1079 |
2/16/2001 9:20:15 AM | MatLab script |
function [mrgl, neigused, pve] = fast_cvm_condrgl(m,condmin) % [mrgl, neigused] = fast_cvm_condrgl(m,condmin) % % Regularization by specifying a minimum condition number for % the resulting regularized matrix. % |
|||
|
fast_cvm_normalize.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 743 Sz: 1814 |
2/9/2001 12:14:56 PM | MatLab script |
function [ocvm, acoravg, acorstd] = fast_cvm_normalize(icvm,nmax) % ocvm = fast_cvm_normalize(icvm,nmax) % % Covariance matrix normalization. % % icvm - input covariance matrix % ocvm - normalized covariance matrix % % Forces all the diagonals elements of ocvm to be equal. The value of the % output diagonal is equal to the mean of the input diagonal divided by % the mean of the main diagonal (this forces the elements of the main % diagonal to be one). If nmax is set, then diagonals beyond nmax are % set to 0. Setting the diagonals to be equal enforces the assumption % that the noise is stationary across observations. % % Each diagonal is set to a constant equal to the mean of that diagonal % divided by the mean of the main diagonal. This forces the main diagonal % to be 1. % |
|||
|
fast_cvm_normposdef.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 744 Sz: 936 |
5/11/2001 1:44:16 PM | MatLab script |
function [mrgl, r, s, W] = fast_cvm_normposdef(m,nmax) % [mrgl r] = fast_cvm_normposdef(m,nmax) % % Normalization and force to be positive by contructing a % cholesky decomposition matrix from the auotcorrelation % function |
|||
|
fast_cvm_normrgl.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 745 Sz: 784 |
2/16/2001 3:53:43 PM | MatLab script |
function [mrgl, niters, alpha] = fast_cvm_normrgl(m,condmin) % mrgl = fast_cvm_normrgl(m,condmin) % % Regularization and normalization. % |
|||
|
fast_cvm_pvergl.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 746 Sz: 906 |
2/16/2001 9:46:24 AM | MatLab script |
function [mrgl, neigused, mrglcond] = fast_cvm_pvergl(m,pvemin) % [mrgl, neigused, mrglcond] = fast_cvm_pvergl(m,pvemin) % % Regularization by setting a minimum on the eigenvalues equal % to the the eigenvalue of the nth eigenvector needed to % account for pvemin percent of the variance. % |
|||
|
fast_cvm_regularize.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 747 Sz: 1079 |
2/16/2001 2:58:42 PM | MatLab script |
function [mrgl, neigused, pve] = fast_cvm_condrgl(m,condmin) % [mrgl, neigused] = fast_cvm_condrgl(m,condmin) % % Regularization by specifying a minimum condition number for % the resulting regularized matrix. % |
|||
|
fast_cvm2acor.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 748 Sz: 360 |
7/10/2001 2:21:29 PM | MatLab script |
function acor = fast_cvm2acor(cvm) % % acor = fast_cvm2acor(cvm) % % Computes the autocorrelation function from the % covariance matrix |
|||
|
fast_cvm2corm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 749 Sz: 473 |
8/9/2001 2:32:21 PM | MatLab script |
function cormtx = fast_cvm2corm(cvm) % cormtx = fast_cvm2corm(cvm) % Converts a covariance matrix into a correlation coefficient % matrix. It computes the correlation coefficient for compoent % i,j as cvm(i,j) / sqrt(cvm(i,i) * cvm(j,j)) |
|||
|
fast_cvm2whtn.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 750 Sz: 3250 |
5/14/2001 4:52:28 PM | MatLab script |
function [W, r, s, nunder ] = fast_cvm2whtn(cvm,nmax,pctrmagmin) % [W, r, s, nunder] = fast_cvm2whtn(cvm,nmax,pctrmagmin) % % Computes whitening matrix from a covariance matrix. % % Algorithm: computes the autocorrelation function (r) as the % average of the diagonal components of the CVM. This % toeplitzization (sorry) of the CVM enforces the assumption % that the underlying process is time-invariant. The magnitude % and phase of the FFT of the autocorrelation function is computed. % The magnitude of the whitening filter is then computed as the % inverse of the square root of that of the autocorrelation % function. The phase of the whitening filter is computed as the % negative of that of the autocorrelation function. The whitening % filter is then converted back to the time domain to become the % whitening function (s). This is then used to compute an upper % triangular toeplitz matrix, the whitening matrix (W), which has % the same size as cvm. % % If nmax is specified, then only the first nmax components of % the whitening function are used (the rest are padded to zero). % % If pctrmagmin is specified, then the the frequency components of % the magnitude of the FFT of the autocorrelation function are not % allowed to go below Rmagmin = max(Rmag)*pctrmagmin/100, ie, a % a percentage of maximum magnitude. The number that fall under this % threshold is returned as nunder. % % $Id$ % Testing: % ntrs = 100; ncols = 1000; alpha = .5; rho = .7; % nmax = 20; pctmin = 10; % y = synthcornoise(ntrs,ncols,alpha,rho); % ycvm = y*y'; %' % [W r s nunder] = fast_cvm2whtn(ycvm,nmax,pctmin); % ycvm2 = W*ycvm*W'; %' % [W2 r2 s2 nunder2] = fast_cvm2whtn(ycvm2); % plot(2:nmax,r(2:nmax),2:nmax,r2(2:nmax)); |
|||
|
fast_ecm2invlambda.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 751 Sz: 117 |
12/4/2000 6:06:25 PM | MatLab script |
function invLambda = fast_ecm2invlambda(ecm) |
|||
|
fast_esttrans.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 752 Sz: 1010 |
2/12/2001 5:24:45 PM | MatLab script |
function [d1, d2, d3, match, vxc] = fast_esttrans(v1,v2,frame) % [d1, d2, d3, match, vxc] = fast_esttrans(v1,v2,frame) % % Estimate translation between two volumes. The result is % the amount that v2 must be translated to best match v1. % match is a number between 0 and 1 indicating how good % the match is. % % Example: % n = 64; % v1 = randn(n,n,n); % v2 = fast_mshift(v1, [ 1 2 3 ], 1); % [d1 d2 d3] = fast_esttrans(v1,v2); % v1b = fast_mshift(v2, [ d1 d2 d3 ], 1); % v1b will now be idendical to v1 |
|||
|
fast_fileexists.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 753 Sz: 301 |
8/15/2000 5:11:50 PM | MatLab script |
function r = fast_fileexists(filename) % r = fast_fileexists(filename) % 1 if it exists and is readable , 0 if not |
|||
|
fast_fmrimovie.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 754 Sz: 577 |
1/3/2001 3:22:39 PM | MatLab script |
function fmrimovie = fast_fmrimovie(f) % fmrimovie = fast_fmrimovie(f) % |
|||
|
fast_func2roi.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 755 Sz: 11018 |
9/13/2000 2:53:24 PM | MatLab script |
function r = fast_func2roi(varargin) % r = fast_func2roi(varargin) % '$Id' |
|||
|
fast_getvolformat.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 756 Sz: 321 |
8/15/2000 4:54:30 PM | MatLab script |
function volformat = fast_getvolformat(volid) % volformat = fast_getvolformat(volid) % % $Id$ |
|||
|
fast_hlist.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 757 Sz: 394 |
1/22/2001 3:47:23 PM | MatLab script |
function [avglist, stdlist] = fast_hlist(Nc,Nh) % [avglist stdlist] = fast_hlist(Nc,Nh) |
|||
|
fast_hypospec2cmtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 758 Sz: 7164 |
3/22/2001 11:37:07 AM | MatLab script |
function cmtx = fast_hypospec2cmtx(hsfile) % % cmtx = fast_hypospec2cmtx(hsfile) % % Converts a hypothesis specification file into % a contrast matrix. |
|||
|
fast_igxavg.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 759 Sz: 7116 |
3/14/2001 12:24:52 PM | MatLab script |
function r = fast_isxavg_fe(varargin) % Name: fast_isxavg_fe % Purpose: implements fixed-effects intersession averaging % for output of selxavg % Author: Douglas Greve % Questions or Comments: analysis-bugs@nmr.mgh.harvard.edu % Version: $Id$ % r = fast_isxavg_fe(varargin) |
|||
|
fast_inorm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 760 Sz: 19854 |
3/15/2001 3:45:44 PM | MatLab script |
function r = fast_inorm(varargin) % r = fast_inorm(varargin) % Intensity normalizes and does some simple data hygene analysis. % '$Id' |
|||
|
fast_intergroupavg.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 761 Sz: 10426 |
3/21/2001 9:15:55 AM | MatLab script |
function r = fast_intergroupavg(varargin) % Name: fast_intergroupavg % Purpose: implements inter-group averaging % % Author: Douglas Greve % Questions or Comments: analysis-bugs@nmr.mgh.harvard.edu % Version: $Id$ % r = fast_isxavg_fe(varargin) |
|||
|
fast_invlambda.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 762 Sz: 409 |
12/4/2000 6:53:08 PM | MatLab script |
function invLambda = fast_invlambda(ErrCovMtx,nEigen) % invLambda = fast_invlambda(ErrCovMtx,nEigen) |
|||
|
fast_isbvol.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 763 Sz: 549 |
8/15/2000 4:42:28 PM | MatLab script |
function isbvol = fast_isbvol(volid) % isbvol = fast_isbvol(volid) % % Returns 1 if volume is in bfile format, ie, there exist file % with name volid_%03d.bshort or .bfloat. Actually, it just % looks for the header volid_%03d.hdr. % % $Id$ |
|||
|
fast_isminc.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 764 Sz: 549 |
8/15/2000 4:44:20 PM | MatLab script |
function isbvol = fast_isbvol(volid) % isbvol = fast_isbvol(volid) % % Returns 1 if volume is in bfile format, ie, there exist file % with name volid_%03d.bshort or .bfloat. Actually, it just % looks for the header volid_%03d.hdr. % % $Id$ |
|||
|
fast_ismincvol.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 765 Sz: 569 |
8/15/2000 4:53:02 PM | MatLab script |
function isminc = fast_ismincvol(volid) % isminc = fast_ismincvol(volid) % % Returns 1 if volume is in MINC format. % % $Id$ |
|||
|
fast_isxavg_fe.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 766 Sz: 7116 |
3/16/2001 10:14:58 AM | MatLab script |
function r = fast_isxavg_fe(varargin) % Name: fast_isxavg_fe % Purpose: implements fixed-effects intersession averaging % for output of selxavg % Author: Douglas Greve % Questions or Comments: analysis-bugs@nmr.mgh.harvard.edu % Version: $Id$ % r = fast_isxavg_fe(varargin) |
|||
|
fast_isxavg_re.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 767 Sz: 12836 |
8/8/2001 3:36:44 PM | MatLab script |
function r = fast_isxavg_re(varargin) % r = fast_isxavg_re(varargin) % Random effects intersubect averaging |
|||
|
fast_ldbvolume.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 768 Sz: 3332 |
9/12/2000 2:53:55 PM | MatLab script |
function [fastvol, msg] = fast_ldbvolume(stem, rows, cols, slices, planes) % [fastvol msg] = fast_ldbvolume(stem, rows, cols, slices, planes) % Everything is one-based now. |
|||
|
fast_ldcorslice.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 769 Sz: 676 |
10/30/2000 12:56:59 PM | MatLab script |
function corslice = fast_ldcorslice(corslicefile); % % corslice = fast_ldcorslice(corslicefile); % |
|||
|
fast_ldlabel.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 770 Sz: 775 |
1/10/2001 9:42:14 AM | MatLab script |
function [vtxno, xyz, vstat, hdr, msg] = fast_ldlabel(labelfile) % % [vtxno xyz vstat hdr msg] = fast_ldlabel(labelfile) % % $Id$ |
|||
|
fast_ldmri.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 771 Sz: 388 |
9/13/2000 2:51:21 PM | MatLab script |
function [fastvol, msg] = fast_ldmri(volid, volformat, rows, cols, slices, planes) % fastvol = fast_ldmri(volid, volformat, rows, cols, slices, planes) |
|||
|
fast_ldslice.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 772 Sz: 363 |
8/15/2000 5:39:30 PM | MatLab script |
function slice = fast_ldslice(volid,sliceno) % slice = fast_ldslice(volid,sliceno) |
|||
|
fast_ldsxabfile.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 773 Sz: 2303 |
3/12/2001 11:25:26 AM | MatLab script |
function [havg, eresvar, sxadat] = fast_ldsxabfile(sxabfile) % % [havg eresvar sxadat] = fast_ldsxabfile(sxabfile) % % This function reads in the selxavg values from the given bfile % assuming that the data are stored in selavg format. % % havg - (nrows,ncols,Nhtot) % eresvar - (nrows,ncols) - residual error variance % sxadat - info from the .dat file % % $Id$ % % See also: fmri_svsxabvol() |
|||
|
fast_ldsxabvolume.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 774 Sz: 996 |
2/13/2001 1:48:38 PM | MatLab script |
function [havg, eresvar, sxadat] = fast_ldsxabvolume(sxastem) % % [havg eresvar sxadat] = fast_ldsxabvolume(sxabfile) % % This function reads in the selxavg values from the given bvolume % assuming that the data are stored in selavg format. % % havg - (nslices,nrows,ncols,Nhtot) % eresvar - (nslices,nrows,ncols) - residual error variance % sxadat - info from the .dat file % % $Id$ % % See also: fast_svsxabfile() |
|||
|
fast_ldtpexcl.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 775 Sz: 1278 |
2/8/2001 11:49:13 AM | MatLab script |
function [indTPExc, indTPInc] = fast_ldtpexcl(TPExcludeFile,TR,NTRs,nSkip) % [indTPExc indTPInc] = fast_ldtpexcl(TPExcludeFile,TR,NTRs,nSkip) % % Returns a list of indices of time points which should % be excluded and a list of those which should be included. These lists % are based on what is in the Time Point Exlude file and on the value % nSkip. The TPExcludeFile variable can be empty. % |
|||
|
fast_ldwfile.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 776 Sz: 33 |
1/19/2001 3:57:57 PM | MatLab script |
function w = fast_ldwfile(wfile) |
|||
|
fast_mrivolstruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 777 Sz: 339 |
9/12/2000 2:54:15 PM | MatLab script |
function fv = fast_mrivolstruct % fastvol = fast_mrivolstruct |
|||
|
fast_mshift.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 778 Sz: 2065 |
2/12/2001 4:26:01 PM | MatLab script |
function m2 = fast_mshift(m1, shift, wrap) % m2 = fast_mshift(m1, shift, wrap) % % Shifts m1 by shift. Uses wrap-around if wrap=1. The number of % elements in shift must equal to the dimension of m1. This is similar % the matlab native wshift() function except that wshift can only handle % two dimensions and forces wrap-around. % % Positives shift down or to the right. % % Examples: % % x = [1 2 3 4 5]; % x2 = fast_mshift(x,[0 +2]) --> x2 = [0 0 1 2 3] % x2 = fast_mshift(x,[0 +2],1) --> x2 = [4 5 1 2 3] % x2 = fast_mshift(x,[0 -2]) --> x2 = [3 4 5 0 0] % x2 = fast_mshift(x,[0 -2],1) --> x2 = [3 4 5 1 2] % % x = [1 2 3; % 4 5 6]; % x2 = fast_mshift(x,[0 +1]) % 0 1 2 % 0 4 5 % x2 = fast_mshift(x,[0 +1],1) % 3 1 2 % 6 4 5 % x2 = fast_mshift(x,[-1 +1],1) % 6 4 5 % 3 1 2 |
|||
|
fast_normcovmtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 779 Sz: 144 |
12/4/2000 6:08:19 PM | MatLab script |
function NormCovMtx = fast_normcovmtx(CovMtx) |
|||
|
fast_npernull.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 780 Sz: 1212 |
7/2/2001 3:49:57 PM | MatLab script |
function npernull = fast_npernull(nevents,nnullclocks) % % npernull = fast_npernull(nevents,nnullclocks) % % Given the total number of null clocks required (nnullclocks) % and the number of events, returns the number of null clocks % that should occur before each event. One can think of it % as inserting non-null events between each null event, so there % needs to be one more null events than non-null events. % % For example, npernull(m) indicates the number of null clocks % to place BEFORE the mth event. The last npernull is the number % of null clocks to place AFTER the last event. % % Sum(npernull) = nnullclocks. Length(npernull) = nevents + 1. % % Does not attempt to optimize the distribution of the lengths % or to optimize the sequence of the lengths so that they are % well counter-balanced. The distribution ends up being roughly % exponential. |
|||
|
fast_omnibusmtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 781 Sz: 931 |
7/25/2001 3:13:52 PM | MatLab script |
function R = fast_omnibusmtx(nEventTypes,TER,TW,TPS,RmPrestim) % % R = fast_omnibusmtx(nEventTypes,TER,TW,TPS,RmPrestim) % % Allows computation of an omnibus matrix that includes % zeroing the prestimulus baseline and computing and % computing the stat based on the poststim component. % % |
|||
|
fast_pixrep.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 782 Sz: 763 |
11/9/2000 12:34:17 PM | MatLab script |
function img2 = fast_pixrep(img) % % img2 = fast_pixrep(img) % % Double image size with pixel replication of the rows and % columns. Works with multiple frames. % |
|||
|
fast_rescalefactor.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 783 Sz: 482 |
12/3/2000 8:56:56 PM | MatLab script |
function [RescaleFactor, MeanVal] = fast_rescalefactor(MeanValFile, RescaleTarget) % fast_rescalefactor(MeanValFile, RescaleTarget) |
|||
|
fast_runlist.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 784 Sz: 562 |
8/6/2001 12:27:07 PM | MatLab script |
function runlist = fast_runlist(dirname) % runlist = fast_runlist(dirname) |
|||
|
fast_runlistfile.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 785 Sz: 558 |
8/6/2001 12:32:20 PM | MatLab script |
function runlist = fast_runlistfile(runlistfile) % runlist = fast_runlistfile(runlistfile) |
|||
|
fast_sched2Xfir.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 786 Sz: 3289 |
7/3/2001 9:41:01 AM | MatLab script |
function X = fast_sched2Xfir(tPres,ntrs,TR,TER,TPreStim,TimeWindow) % % X = fast_sched2Xfir(tPres,ntrs,TR,TER,TPreStim,TimeWindow) % % Creates a design matrix (aka stimulus convolution matrix) modeling % the hemodynamic response as an FIR with adjustable tap weights. The % matrix is for a single event type whose schedule is passed by tPres. % The size of the matrix will be ntrs by Nh, Nh = TimeWindow/TER. % % tPres - list of presentation times (ie, the schedule) in seconds % for one event type. Time=0 is defined as the time the first stored % image was collected (ie, ignore discarded acquisitions). An event % before t=0 will have an effect on the matrix if its Post Stimulus % Window encompasses t=0; otherwise it is ignored. Events found % after the termination of data collection are ignored (a warning % is printed). If tPres is empty, a matrix of zeros is returned. % % ntrs - number of functional volumes collected (do not include % discarded acquisitions). % % TR - TR of the exmperiment (ie, time between acquisitions of % functional volumes) in seconds. % % TER - temporal estimation resolution (in seconds). This is the % resolution at which the hemodynamic response is reconstructed. % The TER must be an integer divisor of the TR. Note: arbitrary % schedules cannot be used to perform sub TR estimation. The % schudule must have been designed for that purpose. % % TPreStim - prestimulus window (in seconds). This creates a matrix % which will allow averaging to begin before the stimulus onset. % Must be a integer multiple of the TER. % % TimeWindow - total time window (in seconds) in which the hemodynamic % response will be modeled, including the TPreStim. Must be a integer % multiple of the TER. The Post Stimulus Window = TimeWindow - TPreStim. % % $Id$ |
|||
|
fast_schedseq.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 787 Sz: 3055 |
7/2/2001 4:14:53 PM | MatLab script |
function tseq = fast_schedseq(seq, tpercond, TER, TScan, TPreScan) % % tseq = fast_schedseq(seq, tpercond, TER, TScan, TPreScan) % % Computes a (random) time at which each event in sequence seq % can occur. No optimization is performed here. % % seq is the sequence of events. Each event is coded 1-N. Zero cannot % be used as an event code. Event codes should be contiguous from 1-N. % % tpercond is the amount of time allocated for each event type. Its % length must be equal to the number of event types. % % TER is the temporal estimation resolution (in seconds). % % TScan is the length of the scan (in seconds) during which data % are collected AND stored (do not include discarded acquisitions). % % TPreScan is the amount of time before the onset of scanning that % stimuli should begin to appear. Where "the onset of scanning" is % defined as the first image collected AND stored. Note that TPreScan % is not inherently related to the number discarded acquisitions. % TPreScan allows the user to present stimuli before images are % collected. If this is done, then these presentations should be % considered during the analysis. % % tseq is a list of times at which the items in seq should be presented. % The times are in seconds relative to the first image that is % collected AND stored. % % $Id$ |
|||
|
fast_selxavg.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 788 Sz: 30762 |
8/28/2001 4:58:33 PM | MatLab script |
function r = fast_selxavg(varargin) % r = fast_selxavg(varargin) % '$Id: fast_selxavg.m,v 1.2 2001/05/11 21:04:48 greve Exp greve $' |
|||
|
fast_slicedelay.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 789 Sz: 830 |
12/3/2000 4:40:57 PM | MatLab script |
function delay = fast_slicedelay(TR,nSlices,Slice,AcqOrder) % delay = fast_slicedelay(TR,nSlices,Slice,AcqOrder) % % Computes the amount of time after the start of a TR that a slice % is aquired given the TR, the number of slices, and the order of % acquisition (linear or interleaved). % |
|||
|
fast_svcorslice.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 790 Sz: 856 |
10/31/2000 3:36:55 PM | MatLab script |
function err = fast_svcorslice(corslice,corslicefile) % % err = fast_svcorslice(corslice,corslicefile) % |
|||
|
fast_svlabel.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 791 Sz: 947 |
1/10/2001 9:38:07 AM | MatLab script |
function err = fast_svlabel(vtxno, xyz, vstat, hdr, filename) % err = fast_svlabel(vtxno, xyz, vstat, hdr, filename) % |
|||
|
fast_tnorm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 792 Sz: 448 |
10/19/2000 3:00:10 PM | MatLab script |
function ftnorm = fast_tnorm(f) % imgtnorm = fast_tnorm(f) % % Temporal Normalization f: N1xN2x...Nt % |
|||
|
fast_trendmtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 793 Sz: 320 |
12/3/2000 10:06:53 PM | MatLab script |
function Xtrend = fast_trendmtx(run,ntrs,nruns) % Xbasline = fast_trendmtx(run,ntrs,nruns) |
|||
|
fast_volstruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 794 Sz: 329 |
9/12/2000 12:43:03 PM | MatLab script |
function fv = fast_mrivolstruct % fastvol = fast_mrivolstruct |
|||
|
fmri_abjackknife.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 795 Sz: 475 |
11/3/1999 5:07:30 PM | MatLab script |
function [a, vtemplate] = fmri_abjackknife(v,alist,blist) % [a vtemplate] = fmri_abjackknife(v,alist,blist) % % size(v) = (Nh,Nvox,Nsamples) |
|||
|
fmri_accrandeff.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 796 Sz: 1259 |
1/20/2000 11:58:52 AM | MatLab script |
function [hsum, hsum2, dof] = fmri_accrandeff(h, hsum, hsum2, dof,... |
|||
|
fmri_acorr.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 797 Sz: 2201 |
4/23/1999 8:49:21 AM | MatLab script |
function [avgRxx, stdRxx] = fmri_acorr(x, nMaxLag, ind) % % [avgRxx stdRxx] = fmri_acorr(x) % [avgRxx stdRxx] = fmri_acorr(x, nMaxLag) % [avgRxx stdRxx] = fmri_acorr(x, nMaxLag, ind) % % Computes the autocorrelation of x using an FFT. This should % produce the same results as the native matlab function xcorr % when invoked as xcorr(x,nMaxLag,'unbiased'). This function % should be much faster because it uses an FFT. Rxx is scaled so % that the zeroth lag is 1. If x is a matrix, the Rxx of each column % is computed separately, and the average and std at each delay point % are returned. % % The input argument ind contains a list of columns in x to use % when computing the autocorrelation. % % Size of x: nRows, nCols, nTP, nRuns % % $Id: fmri_acorr.m,v 1.1 1999/03/24 22:11:30 greve Exp $ |
|||
|
fmri_acorr2covmtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 798 Sz: 1025 |
4/23/1999 8:49:21 AM | MatLab script |
function CVM = fmri_acorr2covmtx(R,nCVM,Sided) % % CVM = fmri_acorr2covmtx(R) % CVM = fmri_acorr2covmtx(R,nCVM) % CVM = fmri_acorr2covmtx(R,nCVM,Sided) % % Arguments: % R - correlation function (normalized) % nCVM - number of rows/cols of the final covariance matrix. % if unspecified, nCVM = length(R); % Sided - 1 or 2. % 1 indicates one-sided (ie, zero lag to maxlag) % 2 indicates two-sided (ie, symetric, -maxlag to maxlag) (default) % % $Id: fmri_acorr2covmtx.m,v 1.1 1999/03/24 22:11:30 greve Exp $ |
|||
|
fmri_acorrfit.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 799 Sz: 1403 |
4/23/1999 8:49:26 AM | MatLab script |
function [alpha, rho] = fmri_acorrfit(R,nFit) % % [alpha, rho] = fmri_acorrfit(R) % [alpha, rho] = fmri_acorrfit(R,nFit) % % Fits the autocorrelation function R to the model: % R(n) = 1, n = 0 % R(n) = (1-alpha)*rho^n, n != 0 % and returns alpha and rho. Components of R <= 0 are excluded % from the fit. % % R should be two-sided column vector, normalized with zero lag = 1. % If R has multiple columns, an alpha and rho are fit for each % column. If nFit is supplied, then only the first nFit components % of R are fit. nFit must be a scalar. % % $Id: fmri_acorrfit.m,v 1.4 1999/04/16 20:14:51 greve Exp $ |
|||
|
fmri_acorrsig.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 800 Sz: 635 |
4/23/1999 8:49:21 AM | MatLab script |
function [sig, nkeep] = fmri_acorrsig(Ravg,Rstd,pthresh) % % [sig, nkeep] = fmri_acorrsig(Ravg,Rstd,pthresh) % % Compute the significance of an autocorrelation function % at each delay given the avg and std at each point. Also % returns the number of contiguous components after delay % zero which have signficances below pthresh. % % $Id: fmri_acorrsig.m,v 1.1 1999/03/24 22:11:30 greve Exp $ |
|||
|
fmri_acorrsynth.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 801 Sz: 928 |
4/23/1999 8:49:21 AM | MatLab script |
function R = fmri_acorrsynth(alpha, rho, nMaxDelay) % % R = fmri_acorrsynth(alpha, rho, nMaxDelay) % % Synthesizes an autocorrelation function based on the model % R(0) = 1 % R(n) = (1-alpha)*rho^n, 0 < abs(n) <= nMaxDelay % % R(n) has 2*nMaxDelay elements. % % If alpha and rho have multiple elements, then multiple Rs % computed and occupy a seperate column in R. % % $Id: fmri_acorrsynth.m,v 1.1 1999/03/24 22:11:30 greve Exp $ |
|||
|
fmri_avgmtx_is.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 802 Sz: 1030 |
4/23/1999 8:49:21 AM | MatLab script |
function Misa = fmri_avgmtx_is(Nch, Ns, XtXs) % % Misa = fmri_avgmtx_is(Nch, Ns) % Misa = fmri_avgmtx_is(Nch, Ns, XtXs) % % Compute inter-session averaging matrix. % Nch - number conditions * number of estimates per event % Ns - number of sessions % XtXs - list of (sum(x'x)) (one for each session). % % Misa will have dimension Nch x Nch x Ns % % $Id: fmri_avgmtx_is.m,v 1.1 1999/03/26 17:32:20 greve Exp $ |
|||
|
fmri_avgrandeff.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 803 Sz: 582 |
1/20/2000 11:58:57 AM | MatLab script |
function [havg, hstd] = fmri_avgrandeff(hsum, hsum2, dof) % % [havg hstd] = fmri_avgrandeff(hsum, hsum2, dof) % % Comptutes the average and std dev for rand effects accumulated % values. % % $Id: fmri_avgrandeff.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_avgxavg.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 804 Sz: 2223 |
4/23/1999 8:49:21 AM | MatLab script |
function [havgavg, hstdavg, DOF, Ms] =fmri_avgxavg(effect, havg, hstd, xtx) % % [havgavg, hstdavg, DOF, Ms] = fmri_avgxavg(effect, havg, hstd) % [havgavg, hstdavg, DOF, Ms] = fmri_avgxavg(effect, havg, hstd, xtx) % |
|||
|
fmri_axaslice.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 805 Sz: 3705 |
4/26/1999 8:40:19 AM | MatLab script |
% HDRFiles, datFiles, OutFile % Effect, Weight |
|||
|
fmri_bfiledim.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 806 Sz: 1273 |
8/22/2001 3:03:43 PM | MatLab script |
function [nrows, ncols, ntp, fs, ns, endian, bext] = fmri_bfiledim(stem) % [nrows ncols ntp fs ns endian bext] = fmri_bfiledim(stem) % % $Id$ |
|||
|
fmri_boxcar.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 807 Sz: 709 |
11/22/1999 1:25:37 PM | MatLab script |
function parbox = fmri_boxcar(par,boxduration,TR) % % parbox = fmri_boxcar(par,boxduration,TR) % |
|||
|
fmri_bvoldim.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 808 Sz: 1378 |
8/22/2001 3:05:09 PM | MatLab script |
function [nslices, nrows, ncols, nt, endian, bext, hdrdat] = fmri_bvoldim(stem) % [nslices nrows ncols nt endian bext hdrdat] = fmri_bvoldim(stem) % % $Id: fmri_bvoldim.m,v 1.1 2000/01/27 01:20:39 greve Exp greve $ |
|||
|
fmri_cvmstruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 809 Sz: 607 |
9/21/2000 3:13:16 PM | MatLab script |
function cvmstruct = fmri_cvmstruct; % cvmstruct = fmri_cvmstruct % Creates covariance matrix structure |
|||
|
fmri_detrend.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 810 Sz: 3258 |
4/23/1999 8:49:21 AM | MatLab script |
function [ypost, coeff, hest] = fmri_detrend(ypre,X,Order,TPExclude) % % [ypost, coeff, hest] = fmri_detrend(ypre,X,Order,TPExclude) % % Removes all trends of order 0 (mean) to order Order-1 while % simultanesouly fitting for the hemodynamic response. Detrending % is done on a run-by-run basis. If you do not want the HDR to % be fit, pass X=[]. hest will be [] in that case. % % [ypost, coeff, hest] = fmri_detrend(ypre,X,Order) % % ypre: raw fMRI slices (nRows x nCols x nTP x nRuns) % X: Stim Conv Mtx (nTP x nTotEst x nRuns) % Order: number of trend components to remove (scalar-int) % % ypost: detrended fMRI slices (nRows x nCols x nTP x nRuns) % coeff: trend coefficients (nRows x nCols x Order x nRuns) % hest: HDR estimates for each run (nRows x nCols x Nch x nRuns) % % $Id: fmri_detrend.m,v 1.2 1999/04/16 20:15:49 greve Exp $ |
|||
|
fmri_dof.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 811 Sz: 604 |
4/23/1999 8:49:21 AM | MatLab script |
function dof = fmri_dof(X,DTOrder) % % Compute degrees of freedom. % % dof = fmri_dof(X,DTOrder) % % X - stim conv matricies: nTP x nTotEst x nRuns, where nTotEst % is (nHEst + nPreStim)*nNonNullCond. % DTOrder - number of trends removed. % % The dof is the number of observations (nRuns*nTP) minus % the number of parameters fit (HOrder*nNNCond + nRuns*PPOrder). % % $Id: fmri_dof.m,v 1.1 1999/03/24 22:11:30 greve Exp $ % |
|||
|
fmri_ecovar.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 812 Sz: 756 |
4/23/1999 8:49:21 AM | MatLab script |
function Ce = fmri_ecovar(e,VoxId) % % Ce = fmri_ecovar(e) % Ce = fmri_ecovar(e,VoxId) % % Computes covariance matrix of e. e is typically the % residual temporal error at each voxel. % % e has dimension nRows x nCols x nTP x nRuns. % VoxId - 1D list of subset of voxels to use. % Ce will have dimension nTP x nTP x nRuns. % % $Id: fmri_ecovar.m,v 1.1 1999/03/24 22:11:30 greve Exp $ |
|||
|
fmri_estsignal.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 813 Sz: 859 |
4/23/1999 8:49:21 AM | MatLab script |
function [yest] = fmri_estsignal(X,hest) % % yest = fmri_estsignal(X,hest) % % X: Stim Conv Mtx (nTP x nTotEst x nRuns) % hest: hemodynamic resp est (nRows x nCols x nTotEst) % % yest: estimated fMRI slice (nRows x nCols x nTP x nRuns) % % $Id: fmri_estsignal.m,v 1.1 1999/03/24 22:11:31 greve Exp $ % |
|||
|
fmri_fstem.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 814 Sz: 877 |
4/23/1999 8:49:21 AM | MatLab script |
function fstem = fmri_fstem(varargin) % % fstem = fmri_fstem(BFileName) % % Returns the stem of a file. The stem is % the file name/path up to but not including % the last underscore character '_'. BFileName % can be vertically concatenated list or a % comma-separated list of file names. fstem % is a vertically concatenated list of the % stems. % % $Id: fmri_fstem.m,v 1.1 1999/03/24 22:11:31 greve Exp $ % |
|||
|
fmri_getstem.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 815 Sz: 547 |
2/15/2000 2:41:12 PM | MatLab script |
function [stem, ext] = fmri_getstem(bfilename) % [stem ext] = fmri_getstem(bfilename) |
|||
|
fmri_hankernel.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 816 Sz: 1097 |
4/23/1999 8:49:21 AM | MatLab script |
function HK = fmri_hankernel(HanRadius) % % HK = fmri_hankernel(HanRadius) % % Generates a radially symetric hanning filter. % The filter HK is a nHK x nHK matrix, where % nHK = 2*(floor(HanRadius+.999)) + 1 % The value of the m,n th element is % HK(m,n) = 0.5 + cos(r*pi/2.0); % where r is the distance of m,n from the % center of kernel divided by the Hanning Radius. % If r is > 1, then the component is set to zero. % The coefficients are scaled so that the 2nd % norm = 1. % % $Id: fmri_hankernel.m,v 1.1 1999/03/24 22:11:31 greve Exp $ % |
|||
|
fmri_havg_is.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 817 Sz: 1301 |
4/23/1999 8:49:29 AM | MatLab script |
function h_is = fmri_havg_is(hs,Misa) % % h_is = fmri_havg_is(hs) % h_is = fmri_havg_is(hs,Misa) % % Computes the inter-session HDR average. hs is % the HDR for all the sessions over which to average % (nRows x nCols x Nch x Ns). Misa is the inter-session % averaging matricies (Nch x Nch x Ns). If Misa is not % given, then the inter-session average at each voxel % at each dealy-point is just the average across all % the sessions. h_is will have dimension (nRows x NCols x % Nch). % % See also fmri_avgmtx_is. % % $Id: fmri_havg_is.m,v 1.1 1999/03/26 17:33:05 greve Exp $ |
|||
|
fmri_hcovar.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 818 Sz: 1186 |
4/23/1999 8:49:21 AM | MatLab script |
function Ch = fmri_hcovar(X,Cn) % % Ch = fmri_hcovar(X) % Ch = fmri_hcovar(X,Cn) % % Computes the covariance matrix of the hemodynamic estimates. % X is the stimulus convolution matrix. Cn is the normalized % (ie, diag(Cn)=1) noise covariance matrix. If unspecified, % it is assumed that Cn=I (ie, white noise). % % $Id: fmri_hcovar.m,v 1.1 1999/03/24 22:11:31 greve Exp $ |
|||
|
fmri_hdrdatstruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 819 Sz: 725 |
8/17/2000 3:22:08 PM | MatLab script |
function hdrdat = fmri_hdrdatstruct() % hdrdat = fmri_hdrdatstruct() % $Id: fmri_hdrdatstruct.m,v 1.3 2000/08/17 22:20:21 greve Exp greve $ |
|||
|
fmri_hemodyn.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 820 Sz: 996 |
4/23/1999 8:49:21 AM | MatLab script |
function h = fmri_hemodyn(t, delta, tau) % % function h = fmri_hemodyn(t, delta, tau) % % Simulates the hemodynaimc response using model % from Dale and Buckner, 1997: % % h(t>delta) = ((t-delta)/tau)^2 * exp(-(t-delta)/tau) % h(t<=delta) = 0; % % The HDIR is scaled so that the peak = 1.0 % % Sample parameters: delta = 2.25 sec, tau = 1.25 sec % % $Id: fmri_hemodyn.m,v 1.2 1999/04/01 02:57:27 greve Exp $ % |
|||
|
fmri_idealcbpm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 821 Sz: 1199 |
4/23/1999 8:49:21 AM | MatLab script |
function [CBP, XtX] = IdealCBP(nPerCond, CBOrder) % % [CBP XtX]= IdealCBP(nPerCond, CBOrder) % % Computes Ideal Counterbalancing Probability Matrix % Assumes fixation is condition 0. % % $Id: fmri_idealcbpm.m,v 1.1 1999/03/24 22:11:31 greve Exp $ |
|||
|
fmri_idealxtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 822 Sz: 1520 |
4/23/1999 8:49:22 AM | MatLab script |
function XtX = fmri_idealXtX(nTypesPerSeq, Nh, FixationId) % % XtX = fmri_idealXtX(nTypesPerSeq, Nh, FixationId) % % Computes the ideal (X'*X) where X is the stimulus %' % convolution matrix. % Note that the ideal normalized matrix is independent of the actual % number of stimuli in the sequence. Rather, it is dependent upon % the probability of the stimuli. % % $Id: fmri_idealxtx.m,v 1.1 1999/03/24 22:11:31 greve Exp $ % If there is a fixation stim, remove fixation parameters % and store in variable stps (Stim Types Per Run). |
|||
|
fmri_imresize.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 823 Sz: 1476 |
6/2/1999 2:04:32 PM | MatLab script |
function b = fmri_imresize(a, bdim, method) % b = fmri_imresize(a, bdim) % b = fmri_imresize(a, bdim, method) % % Resize input image a to bdim. % % a is the input image % b is the output image % bdim is the dimensions (rows,cols) of the output % which must be an integral multiple of the input dim. % method - interpoltation method (currently only 'nearest' % is suppored (this is the default). % % $Id: fmri_imresize.m,v 1.1 1999/06/02 17:09:12 greve Exp $ |
|||
|
fmri_indfreqfft.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 824 Sz: 385 |
4/17/2000 11:33:23 AM | MatLab script |
function indfreq = indfreqfft(freq,Ntp,TR) % indfreq = indfreqfft(freq,Ntp,TR) |
|||
|
fmri_isavgstg.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 825 Sz: 4036 |
1/20/2000 11:59:31 AM | MatLab script |
% fmri_isavgstg (Inter-Subject Averaging, Random Effects) % % $Id: fmri_isavgstg.m,v 1.5 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_isavgstruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 826 Sz: 349 |
1/20/2000 11:59:49 AM | MatLab script |
function isas = fmri_isavgstruct() % isas = fmri_isavgstruct() % % Creates a structure for inter-subject averaging. % % $Id: fmri_isavgstruct.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ % |
|||
|
fmri_isconsec.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 827 Sz: 741 |
4/23/1999 8:49:22 AM | MatLab script |
function r = fmri_isconsec(seq,nconsec) % % r = fmri_isconsec(seq,nconsec) % % Returns 1 if any stimulus in seq is consecutively % presented more than nconsec times. Returns 0 if not. % % $Id: fmri_isconsec.m,v 1.1 1999/03/24 22:11:31 greve Exp $ |
|||
|
fmri_isroiavg.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 828 Sz: 2928 |
1/20/2000 11:59:49 AM | MatLab script |
% fmri_isroiavg.m % Takes the output of fmri_roiavg for each subject and computes % inter-subject statistics using a fixed effects model % % $Id: fmri_isroiavg.m,v 1.3 2000/01/20 20:58:30 greve Exp greve $ % % DelaySign, Contrast % |
|||
|
fmri_isxavg_fe.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 829 Sz: 2038 |
3/20/2001 12:21:55 PM | MatLab script |
% Name: fmri_isxavg_fe % Purpose: implements fixed-effects intersession averaging % for output of selxavg % Author: Douglas Greve % Questions or Comments: analysis-bugs@nmr.mgh.harvard.edu % Version: $Id: fmri_isxavg_fe.m,v 1.6 2001/03/07 22:07:18 greve Exp greve $ %%%% These variables must be specified %%%%%%%% % InStemList % FirstSlice % NSlices % OutStem |
|||
|
fmri_isxgrinder.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 830 Sz: 1007 |
4/26/1999 8:00:07 AM | MatLab script |
function [valStat, sigStat, polStat] = fmri_isxgrinder(havg, hstd, DOF, RM, Np) % % [valStat sigStat polStat] = fmri_isxgrinder(havg, hstd, DOF, RM, Np) % |
|||
|
fmri_isxgslice.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 831 Sz: 7107 |
1/20/2000 12:00:20 PM | MatLab script |
% isxgslice % Intersubject Statistical Grinder % % global hAvgFile; % global StatFile; % global ActiveCond, ControlCond; % global TestType, HDelMin, HDelMax; % global OutputFormat % 0 = log(p) (natural log) % 1 = log10(p) % 2 = p % 3 = test value % % global CmpIdeal % global QuitOnError; % % $Id: fmri_isxgslice.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ % |
|||
|
fmri_jackknife.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 832 Sz: 764 |
2/27/2001 12:25:30 PM | MatLab script |
function [vavg, vstd, vjk] = fmri_jackknife(v,blflag) % [vavg vstd] = fmri_jackknife(v,<blflag>) % % Computes the average and stddev of matrix v, where % v is Nsamples x Nvar1 x Nvar2 ... |
|||
|
fmri_ldbfile.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 833 Sz: 2748 |
8/22/2001 3:00:41 PM | MatLab script |
function y = fmri_ldbfile(varargin) % % y = fmri_ldbfile(bfilename) % y = fmri_ldbfile(bfilename1,bfilename2,...,bfilenameN) % % Loads a bshort or bfloat given the full path % and name of the BFile. The type (bshort or % bfloat is determined from the name). % The header is read to get the dimensions, and % the image, y, is reshaped so that it is of the correct % dimensionality. Converts from row-major to matlabs % column-major. If multiple bfiles are specified, then % another dimension is added to y at the end to indicate % the file from which it came. Data from all files must % have the same dimensionality. % % $Id: fmri_ldbfile.m,v 1.5 2000/01/27 19:11:12 greve Exp greve $ % % See also: fmri_svbile() |
|||
|
fmri_ldbheader.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 834 Sz: 646 |
4/11/2000 4:24:30 PM | MatLab script |
function [nrows, ncols, ntp, endian, fs] = fmri_ldbheader(stem) % [nrows ncols ntp endian fs ns] = fmri_ldbheader(stem) |
|||
|
fmri_ldbvolume.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 835 Sz: 2123 |
8/22/2001 3:02:09 PM | MatLab script |
function [vol, ext, endian] = fmri_ldbvolume(stem,ext) % [vol ext endian] = fmri_ldbvolume(stem,<ext>) % % Loads a volume in bfile format and returns a 4D structure % of dimension Nslices X Nrows X Ncols X Ndepth. Automatically % counts the number of slices and determines the extension % (unless extension is specified). % % '$Id: fmri_ldbvolume.m,v 1.4 2000/01/20 20:58:30 greve Exp greve $' |
|||
|
fmri_ldcor.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 836 Sz: 2510 |
1/27/2000 2:40:17 PM | MatLab script |
function cor = fmri_ldcor(subject,arg2,arg3) % % Loads the indicated corronal slices from % $SUBJECTS_DIR/subject/mri/volumeid % % cor = fmri_ldcor(subject) % cor = fmri_ldcor(subject,volumeid) % cor = fmri_ldcor(subject,slices) % cor = fmri_ldcor(subject,volid,slices) % % If unspecified, volumeid defaults to T1. % If unspecified, nslices defaults to [1:256]. % % $Id: fmri_ldcor.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_ldcvm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 837 Sz: 1068 |
9/21/2000 3:16:05 PM | MatLab script |
function cvmstruct = fmri_ldcvm(stem,init) % cvmstruct = fmri_ldcvm(stem, <init>) % If init equals 1 then an empty structure is % returned if the relevant files do not exist. % Otherwise an error is generated. |
|||
|
fmri_lddat.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 838 Sz: 2750 |
5/19/1999 10:15:55 AM | MatLab script |
function [nNNC,nHEst,DOF,TR,nRuns,nTP,nRows,nCols,nSkip,DTOrder,... |
|||
|
fmri_lddat2.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 839 Sz: 3119 |
6/27/2001 9:31:52 AM | MatLab script |
function hdrdat = fmri_lddat2(datfile) % % Load information and parameters from a data file into an hdrdata % structure. To replace fmri_lddat() % % datfile - (string) name of data file % % $Id: fmri_lddat2.m,v 1.3 2000/05/22 19:02:51 greve Exp greve $ |
|||
|
fmri_lddof.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 840 Sz: 1462 |
1/20/2000 12:01:06 PM | MatLab script |
function dof = fmri_lddof(varargin) % % dof = fmri_lddof(BFileName) % % Loads info from the .dof file associated with BFileName. % This is only relevant for back-compatibility with selavg. % % $Id: fmri_lddof.m,v 1.2 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_lddot.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 841 Sz: 299 |
4/27/2000 11:28:46 AM | MatLab script |
function dot = fmri_lddot(dotfile) % dot = fmri_lddot(dotfile) |
|||
|
fmri_ldpar.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 842 Sz: 1402 |
10/1/2001 9:57:35 AM | MatLab script |
function par = fmri_ldpar(varargin) % % Load specified par files for multiple runs. % % par = fmri_ldpar(ParFileList) % par = fmri_ldpar(ParFile1, ParFile2, ...) % % ParFileList is a vertical cat of parfile names (ie, each run's' % parfile name on a different row). % % ParFile format is as follows: % Column 1: stimulus presentation time (float or int) % Column 2: stimulus condition number % Column > 2: ignored % % par dimensionality: nPresentations x 2 x nRuns % % $Id: fmri_ldpar.m,v 1.3 2000/06/06 19:03:31 greve Exp greve $ |
|||
|
fmri_ldsadof.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 843 Sz: 1347 |
4/23/1999 8:49:22 AM | MatLab script |
function dof = fmri_ldsadof(varargin) % % dof = fmri_ldsadof(BFileName) % % % $Id: fmri_ldsadof.m,v 1.1 1999/03/24 22:11:32 greve Exp $ % |
|||
|
fmri_ldsfa.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 844 Sz: 1059 |
4/14/2000 2:17:11 PM | MatLab script |
function sfa = fmri_ldsfa(stem) % sfa = fmri_ldsfa(stem) |
|||
|
fmri_ldslicedelay.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 845 Sz: 534 |
4/17/2000 10:48:45 AM | MatLab script |
function [slc, slcdel] = fmri_ldslicedelay(fname) % [slc slcdel] = |
|||
|
fmri_ldsynch.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 846 Sz: 702 |
11/10/1999 2:06:19 PM | MatLab script |
function synch = fmri_ldsynch(synchfile) % % synch = fmri_ldsynch(synchfile) % % Load specified slice synchronization file % % $Id: fmri_ldsynch.m,v 1.1 1999/11/10 22:00:09 greve Exp $ |
|||
|
fmri_ldtpexcl.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 847 Sz: 444 |
4/23/1999 8:49:22 AM | MatLab script |
function tTPExclude = fmri_ldtpexcl(TPExclFile) % % tTPExclude = ldtpexcl(TPExclFile) % % Reads the TP Exclude File. % % $Id: fmri_ldtpexcl.m,v 1.1 1999/03/24 22:11:32 greve Exp $ % |
|||
|
fmri_lmsfit.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 848 Sz: 965 |
1/27/2000 9:31:52 AM | MatLab script |
function h = fmri_lmsfit(Ch,ss) % % h = fmri_lmsfit(Ch,ss) % % Ch: nTotEst x nTotEst % ss: nRows x nCols x nTotEst % h: nRows x nCols x nTotEst % % $Id: fmri_lmsfit.m,v 1.2 2000/01/27 18:31:09 greve Exp greve $ |
|||
|
fmri_mcorrrestriction.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 849 Sz: 641 |
4/23/1999 8:49:22 AM | MatLab script |
function RMC = fmri_mcorrestriction(RM,TR,nHEst,Delta,Tau) % % RMC = fmri_mcorrestriction(RM,TR,nHEst,Delta,Tau) % % Creates a restriction matrix for correlating with a % hemodynmic response function (HRF). The HRF is % computed using a Gamma function with parameters % Delta and Tau over the estimation time window. % % RM is a restriction matrix created by CreateRM. % % See also: CreateRM(), HemoDyn() % % $Id: fmri_mcorrrestriction.m,v 1.1 1999/03/24 22:11:32 greve Exp $ |
|||
|
fmri_minseqcbe.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 850 Sz: 1137 |
4/23/1999 8:49:22 AM | MatLab script |
function [seqkeep, cbekeep, cbeavg, cbestd] = fmri_minseqcbe(seqseed,Nh,nsearch, nkeep,idealxtx,nswap) % % [seqkeep, cbekeep, cbeavg, cbestd] = % fmri_minseqcbe(seqseed,Nh,nsearch,nkeep,idealxtx,nswap) % % % $Id: fmri_minseqcbe.m,v 1.1 1999/03/24 22:11:32 greve Exp $ % |
|||
|
fmri_minseqtr.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 851 Sz: 1428 |
1/20/2000 12:01:06 PM | MatLab script |
function [seqkeep, trkeep, travg, trstd] = fmri_minseqtr(seqseed,Nh,nsearch,nkeep,nswap,Mss) % % [seqkeep, trkeep, travg, trstd] = fmri_minseqtr(seqseed,Nh,nsearch,nkeep,nswap,<Mss>) % % % $Id: fmri_minseqtr.m,v 1.2 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_minsig.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 852 Sz: 1259 |
4/28/2000 3:23:10 PM | MatLab script |
function [minsig, iminsig, indminsig] = fmri_minsig(sig) % [minsig, iminsig, indminsig] = fmri_minsig(sig) % % sig: - raw (-1,1) significance values (nrows X ncols X nplanes) % minsig - (nrows X ncols), signed, bonferroni corrected % iminsig - (nrows X ncols), plane index of minimum % indminsig - iminsig indexed into sig. % % $Id$ |
|||
|
fmri_mrestriction.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 853 Sz: 3587 |
4/23/1999 8:49:26 AM | MatLab script |
function RM = fmri_mrestriction(TestType,nH, nC, AC, CC, nHTest)
%
% RM = fmri_mrestriction(TestType, nH, nC, AC, CC, <nHTest>)
%
% Creates a restriction matrix
%
% TestType - String (case insensitive) indicating the test to perform:
% t - t-Test, RM will be a row vector
% tm - t-Test, different p for each delay point (RM same as Fc)
% Fm - F-Test, different p for each delay point
% F0 - RM same as t-Test
% Fd - F-test, different row for each delay, all conditions
% for each delay on the same row
% Fc - F-test, different row for each condition, all delays
% for a condition on the same row
% Fcd - F-test, different row for each condition for each delay
% nH - total number of elements in HDIR
% nC - total number of stimulus conditions (including fixation)
% AC - list of active conditions
% CC - list of control conditions
% nHTest - list of HDIR components to test (default: all).
%
% Eg: fmri_mrestriction('t',10, 6, [1 3], [2 5], [3 6:9])
% Generates an RM for testing conditions (1+3)-(2+5) using
% components 3,6,7,8, and 9 in the HDIR. Conditions 0 and 4
% are not tested. There are 10 components in the HDIR, and 5
% stimulus conditions.
%
%
% $Id: fmri_mrestriction.m,v 1.1 1999/03/24 22:11:32 greve Exp $
% Check for the correct number of arguments %
|
|||
|
fmri_mrestriction2.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 854 Sz: 1673 |
11/10/1999 10:36:12 AM | MatLab script |
function RM = fmri_mrestriction2(wcond,wdelay,sumconds,sumdelays) % RM = fmri_mrestriction2(wcond,wdelay,sumconds,sumdelays) % % Creates a restriction matrix given the vector of condition % weights and the vector of delays weights. % % Notes: % 1. wcond is the vector of condition weightings NOT including % the null condition. % 2. The number of rows in RM will be: % 1 for sumconds=1 and sumdelays=1 % nconds for sumdelays=1 % ndelays for sumconds=1 % nc*nd for sumconds=0 and sumdelays=0 % % '$Id: fmri_mrestriction2.m,v 1.1 1999/11/10 17:06:36 greve Exp $' |
|||
|
fmri_nmjackknife.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 855 Sz: 438 |
12/15/1999 1:11:01 PM | MatLab script |
function a = fmri_nmjackknife(v) % Jackknife averaging with normalization % % a = fmri_nmjackknife(v) % % size(v) = (Nh,Nvox,Nsamples) |
|||
|
fmri_norm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 856 Sz: 445 |
1/20/2000 12:01:26 PM | MatLab script |
function u = fmri_norm(v,order) % u = fmri_norm(v, <order>) % % normalizes the columns of v % % '$Id: fmri_norm.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $' |
|||
|
fmri_normcovar.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 857 Sz: 411 |
4/23/1999 8:49:26 AM | MatLab script |
function Cnorm = normcovar(C) % % Cnorm = normcovar(C) % % % $Id: fmri_normcovar.m,v 1.1 1999/03/24 22:11:33 greve Exp $ % |
|||
|
fmri_optseq.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 858 Sz: 2776 |
7/23/2001 10:41:56 AM | MatLab script |
function [paropt,trmin,tsearched,nsearched, optstats] = fmri_optseq(oss) |
|||
|
fmri_optseqstruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 859 Sz: 897 |
7/23/2001 10:41:50 AM | MatLab script |
function oss = fmri_optseqstruct |
|||
|
fmri_par2sam.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 860 Sz: 2371 |
6/3/1999 8:23:26 AM | MatLab script |
function SAM = fmri_par2sam(Par, nTP, TR, nHEst, Baseline) % % SAM = Par2SAM(Par, nTP, TR, nHEst, <Baseline>) % % Computes the Selective Averaging Matrix % % Arguments: % 1. Par - this is a list of time/SimulusId pairs (ie, % the Par file). % 2. nTP - number of time points (ie, number of samples) % 3. TR - Time between samples % 4. nHEst - the number of elements of the hemodynmic impulse % response that will be estimated. % 5. Baseline - compensate for mean. Default is to remove % baseline. Set Baseline = 0 to prevent. % % Returns: % 1. SAM - selective averaging matrix % % Notes: % 1. If presentations do not occur simultanteously with sampling % (ie, the time in the parfile is not an integer multiple of % the TR), the presentation time is rounded to the nearest % sampling time. % 2. It is assumed that the first sample occurs at t=0. % % Douglas N. Greve % 1999-01-07 % Make sure that the number of events is not greater than the % number of samples. |
|||
|
fmri_par2scm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 861 Sz: 4192 |
1/20/2000 12:02:31 PM | MatLab script |
function [SCM, nNNCond, nPerCond] = fmri_par2scm(Par, Nconds, nTP, TR, nHEst, tPreStim, TPExclude) % % [SCM nNNCond nPerCond] = fmri_par2scm(Par, Nconds, nTP, TR, nHEst, tPreStim, % <TPExclude>) % % Computes the Stimuli Convolution Matrix for multiple runs % % Arguments: % 1. Par - this is a list of time/Simulus Id pairs (ie, % the Par file). (nTPx2xnRuns) % 2. Nconds - number of conditions, including null condition. % 3. nTP - number of time points (ie, number of samples) % 4. TR - Time between samples % 5. nHEst - the number of elements of the hemodynmic impulse % response that will be estimated (excluding prestim). % 6. tPreStim - time before stimulus onset to fit; this time comes % out of the total time window. % 7. TPExclude - (optional) nTPxnRuns matrix with ones at locations % of TimePoints (ie, samples or scans) to exclude. If TPExclude % does not appear as an argument, no points are excluded. % % Returns: % 1. SCM - deconvolution matrix (nTP x nHEst x nRuns) % 2. nNNCond - number of non-null (ie, non-fix) conditions. % Notes: % 1. If presentations do not occur simultanteously with sampling % (ie, the time in the parfile is not an integer multiple of % the TR), the presentation time is rounded to the nearest % sampling time. % 2. It is assumed that the first scan event begins at t=0. % 3. Null condition is assumed to be zero. % % $Id: fmri_par2scm.m,v 1.8 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_par2scm0.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 862 Sz: 3717 |
1/20/2000 12:02:35 PM | MatLab script |
function [SCM, nNNCond] = fmri_par2scm(Par, nTP, TR, nHEst, tPreStim, TPExclude) % % [SCM nNNCond] = fmri_par2scm(Par, nTP, TR, nHEst, tPreStim, <TPExclude>) % % Computes the Stimuli Convolution Matrix for multiple runs % % Arguments: % 1. Par - this is a list of time/Simulus Id pairs (ie, % the Par file). (nTPx2xnRuns) % 2. nTP - number of time points (ie, number of samples) % 3. TR - Time between samples % 4. nHEst - the number of elements of the hemodynmic impulse % response that will be estimated (excluding prestim). % 5. tPreStim - time before stimulus onset to fit; this time comes % out of the total time window. % 6. TPExclude - (optional) nTPxnRuns matrix with ones at locations % of TimePoints (ie, samples or scans) to exclude. If TPExclude % does not appear as an argument, no points are excluded. % % Returns: % 1. SCM - deconvolution matrix (nTP x nHEst x nRuns) % 2. nNNCond - number of non-null (ie, non-fix) conditions. % Notes: % 1. If presentations do not occur simultanteously with sampling % (ie, the time in the parfile is not an integer multiple of % the TR), the presentation time is rounded to the nearest % sampling time. % 2. It is assumed that the first scan event begins at t=0. % % $Id: fmri_par2scm0.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_par2scm2.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 863 Sz: 4182 |
1/20/2000 12:02:37 PM | MatLab script |
function [SCM, nNNCond, nPerCond] = fmri_par2scm(Par, Nconds, nTP, TR, nHEst, tPreStim, TPExclude) % % [SCM nNNCond nPerCond] = fmri_par2scm(Par, Nconds, nTP, TR, nHEst, tPreStim, % <TPExclude>) % % Computes the Stimuli Convolution Matrix for multiple runs % % Arguments: % 1. Par - this is a list of time/Simulus Id pairs (ie, % the Par file). (nTPx2xnRuns) % 2. Nconds - number of conditions, including null condition. % 3. nTP - number of time points (ie, number of samples) % 4. TR - Time between samples % 5. nHEst - the number of elements of the hemodynmic impulse % response that will be estimated (excluding prestim). % 6. tPreStim - time before stimulus onset to fit; this time comes % out of the total time window. % 7. TPExclude - (optional) nTPxnRuns matrix with ones at locations % of TimePoints (ie, samples or scans) to exclude. If TPExclude % does not appear as an argument, no points are excluded. % % Returns: % 1. SCM - deconvolution matrix (nTP x nHEst x nRuns) % 2. nNNCond - number of non-null (ie, non-fix) conditions. % Notes: % 1. If presentations do not occur simultanteously with sampling % (ie, the time in the parfile is not an integer multiple of % the TR), the presentation time is rounded to the nearest % sampling time. % 2. It is assumed that the first scan event begins at t=0. % 3. Null condition is assumed to be zero. % % $Id: fmri_par2scm2.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_parsebfilename.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 864 Sz: 651 |
2/15/2000 2:46:18 PM | MatLab script |
function [stem, slice, ext] = fmri_getstem(bfilename) % [stem slice ext] = fmri_getstem(bfilename) % $Id$ |
|||
|
fmri_pcacovmtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 865 Sz: 1307 |
4/23/1999 8:49:26 AM | MatLab script |
function [C, nC] = fmri_pcacovmtx(Q,p) % % [C, nC] = fmri_pcacovmtx(Q,p) % % Computes a new covariance matrix based on the principal components % of the given matrix Q. The number of components used will be % enough to explain at least 100*p percent of the variance. % % % $Id: fmri_pcacovmtx.m,v 1.1 1999/03/24 22:11:33 greve Exp $ % |
|||
|
fmri_pmax.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 866 Sz: 1673 |
4/23/1999 8:49:22 AM | MatLab script |
function [pSigMax, vpSigMax] = fmri_pmax(pSig,vSig) % % [pSigMax vpSigMax] = fmri_pmax(pSig) % [pSigMax vpSigMax] = fmri_pmax(pSig, vSig) % % Returns the maximum significance from a vector of significance % values. pSig may be a 3d matrix in which case the maximum is % searched for over the third dimension. pSigMax would then be % a 2d matrix of maximum significances at each point, corrected % for the number of unplanned comparisons (Bonferoni correction). % % If vSig is included, it must be of the same dimension as pSig. % vpSigMax is a 2d matrix with values from vSig that correspond % to the same locations in pSig from which the values in pSigMax % came. % % $Id: fmri_pmax.m,v 1.1 1999/03/24 22:11:33 greve Exp $ |
|||
|
fmri_pmin.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 867 Sz: 1741 |
3/30/2000 12:01:23 PM | MatLab script |
function [pSigMin, vpSigMin] = fmri_pmin(pSig,vSig) % [pSigMin vpSigMin] = fmri_pmin(pSig) % [pSigMin vpSigMin] = fmri_pmin(pSig, vSig) % % Returns the minimum significance from a vector of significance % values. pSig may be a 3d matrix in which case the minimum is % searched for over the third dimension. pSigMin would then be % a 2d matrix of minimum significances at each point, corrected % for the number of unplanned comparisons (Bonferoni correction). % % If vSig is included, it must be of the same dimension as pSig. % vpSigMin is a 2d matrix with values from vSig that correspond % to the same locations in pSig from which the values in pSigMin % came. % % $Id: fmri_pmin.m,v 1.1 1999/03/24 23:15:17 greve Exp greve $ |
|||
|
fmri_pscavg.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 868 Sz: 767 |
4/23/1999 8:49:26 AM | MatLab script |
% fmri_pscavg.m % Purpose: combines percent signal changes of HDRs across sessions. % Written as a one-shot program for Dr. Capalan's visit. % Variables: InputFiles, OutputFile % % $Id: fmri_pscavg.m,v 1.1 1999/03/24 22:11:33 greve Exp $ |
|||
|
fmri_qrplusc.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 869 Sz: 1706 |
1/20/2000 12:02:48 PM | MatLab script |
function [Urc, Src] = fmri_rplusc(Ur,Sr,Uc,Sc,cutofftype,cutoffthresh) % % [Urc, Src] = fmri_rplusc(Ur,Sr,Uc,Sc,cutofftype,cutoffthresh) % % Computes the (reduced) eigenvectors/values for R+C given the % (reduced) eigenvectors/values for R and C individually. R and % C are symetrical, positive-def matricies. % % Algorithm: Let Q = R+C, for which [A X A'] = svd(Q). Let Ahat % and Xhat be the reduced eigencomponents Q. Then, Urc = Ahat, % and Src = Xhat. However, for R and C with a large number of rows, % computing Q and svd(Q) is not feasible. Ahat and Xhat can still % be determined in a round-about way by first constructing the matrix % P = [Ur*diag(Sr) Uc*diag(Sc)]. This is a matrix whose columns are % the (reduced) eigenvectors of R and C (weighted by the corresponding % eigenvalues). Let Up, Sp be the reduced eigencomponents of P, then % Ahat = P*Up*diag(Sp), and Xhat = Sp; % % $Id: fmri_qrplusc.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_qweiner.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 870 Sz: 1024 |
1/20/2000 12:02:59 PM | MatLab script |
function s = fmri_qweiner(Ur, Sr, Ux, Sx, y) % % s = fmri_qweiner(Ur, Sr, Ux, Sx, y) % % Computes s = R * inv(X) * y using (reduced) eigenvector % representations of R and X. When R is the signal % covariance matrix and X is the signal+noise covariance % matrix, and y is an observable, then s is the weiner % estimate of the signal. % % $Id: fmri_qweiner.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_randc.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 871 Sz: 3256 |
4/23/1999 8:49:26 AM | MatLab script |
function [y, h] = randc(nSeq, Ryy) % % function [y h] = randc(nSeq, Ryy) % % nSeq is the length of the sequence. % Ryy is the desired autocorrelation of the sequence (two-sided) % y is the random sequence % h is the FIR fitler (length(h) = length(Ryy)) % % Produces a zero-mean, unit-variance correlated random sequence % with the given autocorrelation function Ryy. % % Notes: % 1. The length of Ryy must be odd. % % The sequence is generated by constructing % a constant-phase FIR filter: H(f) = sqrt(Syy/Sxx) where % Syy = fft(Ryy) and Sxx = fft(Rxx). Rxx is the autocorrelation % of white noise, ie all zeros except for 1 in the middle. % H(f) is then converted to the time domain, h(t) = ifft(H(f)) % to yeild the coefficients of the FIR filter. A zero-mean, % unity-variance sequence x is generated and filtered by h % to generate y. % % While magnitude of H(f) is determined, the phase is arbitrary. % This makes the computation of H(f) ambiguous, and % many filters will yield the same Ryy. Here, the real and imaginary % parts of H(f) are chosen to be equal. This results in a constant- % phase filter. % % Author: Douglas N. Greve % Date: Aug 17, 1998 % % $Id: fmri_randc.m,v 1.1 1999/03/24 22:11:33 greve Exp $ % % Testing and usage: the code below shows how to use and test this % function. It generates a desired autocorrelation Ryy then uses % this function to generate a random sequence. The matlab xcorr % function is used to generate the emperical autocorrelation function % which is then plotted against the desired. The results show % that the difference between the desired and emperical goes to % zero as the length of the sequence increases. % nSeq = 1024 % nEst = 8; % Ryy = fir1(2*nEst,.25)'; % Ryy = Ryy/max(Ryy); % y = randc(nSeq, Ryy); % nCoeff = length(Ryy); % Ryy2 = xcorr(y,(nCoeff-1)/2, 'biased'); % Ryy2 = Ryy2/max(Ryy2); % nx = [1:nCoeff]; % plot(nx,Ryy,'g', nx,Ryy2,'r'); % Check that the length of Ryy is odd % |
|||
|
fmri_randeff.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 872 Sz: 2272 |
1/20/2000 12:02:59 PM | MatLab script |
function [vSig, pSig] = fmri_randeff(Test, h_is, hs, RM, Ms) % % [vSig, pSig] = fmri_randeff(Test, h_is, hs, RM, Ms) % % Random effects model for inter-session statistical analysis. % Test - test type (t or F) - only t works right now % h_is - average of the HDRs across subjects at each voxel % hs - HDRs for each subject. % RM - restriction matrix % Ms - inter-session averaging matrix (see fmri_avgmtx_is) % % $Id: fmri_randeff.m,v 1.1 1999/03/26 17:31:47 greve Exp $ % |
|||
|
fmri_readreg.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 873 Sz: 996 |
1/20/2000 12:02:59 PM | MatLab script |
function [regmat, subject, inres, betres, intensity] = fmri_readreg(regname) % % [regmat subject inres betres intensity] = fmri_readreg(regname) % % subject - name of subject % inres - in-plane resolution (mm) % betres - between-plane resolution (mm) % ireg - intensity value for register program % regmat - 4x4 matrix which converts a mm location in corronal space % to a mm location in functional space. % % $Id: fmri_readreg.m,v 1.2 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_rescale.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 874 Sz: 1747 |
4/23/1999 8:49:26 AM | MatLab script |
function [ypost, oldmean] = fmri_rescale(ypre,newmean,TPExclude) % [ypost oldmean] = fmri_rescale(ypre,newmean,TPExclude) % % Rescales slices on a run-by-run basis. The scaling factor for each % run is f = newmean/mean(run) where mean(run) is the mean computed % over all voxels at all time-points (ie, the global mean for the run). % This forces the global mean to be the same for all runs. % The oldmean for each slice is returned. % If TPExclude is passed as an argument, data points that correspond % to TPExclude==1 are ignored. They are replaced with newmean in % ypost. The dimensions of TPExclude should be nTP by nRuns. % % Comments or questions: analysis-bugs@nmr.mgh.harvard.edu % % $Id: fmri_rescale.m,v 1.1 1999/03/24 22:11:33 greve Exp $ |
|||
|
fmri_residual.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 875 Sz: 325 |
1/20/2000 12:02:59 PM | MatLab script |
function [eres, sigest] = fmri_residual(y,X,hest) % % [eres sigest] = fmri_residual(y,X,hest) % % Computes the residual error between the actual signal y % and the signal estimate sigest = X*h. % % $Id: fmri_residual.m,v 1.2 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_rhaslice.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 876 Sz: 2996 |
4/23/1999 8:49:27 AM | MatLab script |
% fmri_rhaslice.m % Computes the average HDR of a ROI % % Variables: % tAvgFile, IndexFile, HDRFile, HDRDatFile, OutputFile, Init % % $Id: fmri_rhaslice.m,v 1.1 1999/03/24 22:11:34 greve Exp $ |
|||
|
fmri_roiavg.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 877 Sz: 4208 |
11/5/1999 12:59:32 PM | MatLab script |
% fmri_roiavg % % %---------------------------------------------- % |
|||
|
fmri_sa2sxa.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 878 Sz: 3441 |
1/20/2000 12:02:59 PM | MatLab script |
function [hAvg, eVar, hStd] = fmri_sa2sxa(ySA,nHEst) % % [hAvg eVar hStd] = fmri_sa2sxa(ySA,nHEst) % % Converts from selavg format to selxavg format. In selavg % format, the averages and standard deviations are interleaved % in the same data structure for all conditions, including % fixation. % % -------------- Input Arguments --------------- % 1. ySA - interleaved averages and standard deviations for % all conditions (incl fix) and all delays. % size(ySA) = [nRows nCols 2*nDelays*nCond]. % 2. nHEst - number of coefficients to estimate in the hemodynamic % response. % % ------------- Output Arguments --------------- % 1. hAvg - the average hemodynamic impulse response(s) for % all delays and non-null stimulus conditions % (size(hAvg) = [nRows nCols nHEst*nNNCond]). % 2. eVar - the varaince of the residual errors on a voxel by % voxel basis (size(eVar) = [nRows nCols]). % 1. hStd - the standard deviations of the hemodynamic response(s) for % all delays and non-null stimulus conditions % size(hStd) = [nRows nCols nHEst*nNNCond]). % % $Id: fmri_sa2sxa.m,v 1.3 1999/04/20 17:47:35 greve Exp $ |
|||
|
fmri_saxslice.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 879 Sz: 7142 |
4/23/1999 8:49:27 AM | MatLab script |
% SAXSlice.m % Dec 7, 1998 % % Selective Averaging assuming uncorrelated noise. This uses a % matrix formuluation to solve the problem (as apposed to SelAvg.m % which is simply selective averaging with correlations in the % paradigm assumed to be cancelled by proper counter balancing). % % This is for multiple runs in a single session. % % This differs from SAX in that the inputs and par files % are specified explicitly (not using SubjDir). Also, the % naming conventions are different in that this script requires % a prefix for all names which is prepended to the mnSAX name. % % fmri toolbox functions called: % 1. LdBFile % 2. SvBFile % 3. HanKernel % 4. fMRIPreProc % 5. SelAvgX.m % % See: runSAXSlice % % global TimeWindow, TimeOffset, TR; % global InputFiles, ParFiles; % global hAvgFile, datFile, dofFile; % global HanRadius; % global tTPExclude % global QuitOnError; % % $Id: fmri_saxslice.m,v 1.1 1999/03/24 22:11:34 greve Exp $ |
|||
|
fmri_scm2gcm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 880 Sz: 756 |
5/2/2001 12:26:08 PM | MatLab script |
function gcm = fmri_scm2gcm(X,Nnnc,TR,tPreStim,delta,tau) % % gcm = fmri_scm2gcm(X,delta,tau) % % Produces a Gamma Convolution Matrix from a stimulus % convolution matrix (X) and parameters of the gamma % function (delta, tau). The gamma functions % are interpreted as basis vectors. % % $Id: fmri_scm2gcm.m,v 1.1 1999/04/01 03:03:44 greve Exp greve $ |
|||
|
fmri_segment.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 881 Sz: 1361 |
4/23/1999 8:49:27 AM | MatLab script |
function [ibrain, iair, thresh] = fmri_segment(img) % % [ibrain iair thresh] = fmri_segment(img) % % Segments the brain from the air using a single image. % The algorithm simply measures the mean of the image % and assigns everything over the mean to be brain % and everything below to be air. % % $Id: fmri_segment.m,v 1.3 1999/04/16 20:13:20 greve Exp $ |
|||
|
fmri_selsum.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 882 Sz: 1229 |
1/27/2000 9:31:53 AM | MatLab script |
function ss = fmri_selsum(X,y,Cn) % % ss = fmri_selsum(X,y,<Cn>) % % % $Id: fmri_selsum.m,v 1.2 2000/01/27 18:31:09 greve Exp greve $ % |
|||
|
fmri_seq2scm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 883 Sz: 645 |
4/23/1999 8:49:27 AM | MatLab script |
function scm = fmri_seq2scm(seq, Nh) % % scm = fmri_seq2scm(seq, Nh) % % Converts a sequence of stimuli to a stimulus convolution % matrix assuming that the time between presentations equals % the TR. % % $Id: fmri_seq2scm.m,v 1.1 1999/03/24 22:11:34 greve Exp $ |
|||
|
fmri_seqbase.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 884 Sz: 942 |
4/23/1999 8:49:27 AM | MatLab script |
function base = fmri_seqbase(nTypesPerRun,NoRand) % % base = fmri_seqbase(nTypesPerRun,<NoRand>) % % % $Id: fmri_seqbase.m,v 1.1 1999/03/24 22:11:34 greve Exp $ |
|||
|
fmri_seqmutate.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 885 Sz: 353 |
4/23/1999 8:49:27 AM | MatLab script |
function [seq, nswap] = fmri_seqmutate(oldseq,nswap) % % [seq nswap] = fmri_seqmutate(oldseq, <nswap>) % % % $Id: fmri_seqmutate.m,v 1.1 1999/03/24 22:11:34 greve Exp $ % |
|||
|
fmri_sfastruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 886 Sz: 716 |
4/20/2000 1:29:05 PM | MatLab script |
function sfa = fmri_sfastruct() % sfa = fmri_sfastruct() % $Id$ |
|||
|
fmri_sfaunpack.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 887 Sz: 442 |
4/18/2000 8:49:07 AM | MatLab script |
function [nstd, hr, hi] = fmri_sfaunpack(sfaslice) % [nstd hr hi] = fmri_sfaunpack(sfaslice) % % sfaslice: nrows ncols nplanes % % $Id$ |
|||
|
fmri_shiftcol.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 888 Sz: 1048 |
4/23/1999 8:49:22 AM | MatLab script |
function y = fmri_shiftcol(x,n,wrapflag) % % y = fmri_shiftcol(x,n) % y = fmri_shiftcol(x,n,wrapflag) % % Shift the columns of x by n. If n > 0, then % the shift is to the right (ie, the first column % of x becomes the (n+1)th column of y, the second % column of x becomes the (n+2)th column of y, etc). % If n < 0, the columns are shifted to the left. % If wrapflag = 1 or is not specified, the columns % are wrapped around, otherwise they are filled with % zeros. x must be a 2D array. To shift rows, pass % the transpose of x. % % $Id: fmri_shiftcol.m,v 1.1 1999/04/01 03:04:23 greve Exp $ |
|||
|
fmri_sigmin.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 889 Sz: 667 |
4/28/2000 2:12:32 PM | MatLab script |
function [minsig, iminsig, indminsig] = fmri_minsig(sig) % [minsig, iminsig, indminsig] = fmri_minsig(sig) % % sig: - raw significance values (nrows X ncols X nplanes) |
|||
|
fmri_sobel.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 890 Sz: 128 |
12/15/1999 11:01:08 AM | MatLab script |
function [m, a] = fmri_sobel(img) % % [m, a] = fmri_sobel(img) % |
|||
|
fmri_spatfilter.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 891 Sz: 1390 |
4/23/1999 8:49:27 AM | MatLab script |
function ypost = fmri_spatfil(ypre, SpatialFil) % % ypost = fmri_spatfil(ypre, SpatialFilter) % % Spatially filters a functional slice. % % -------- Input Arguments ------ % 1. ypre - functional slice to be processed. Dimension is % [nRows nCols nTP nRuns]. % 2. SpatialFilter - coefficients of spatial filter (2D). % % -------- Output Arguments ------ % 1. ypost - spatially filtererd slice of the same dimension % as the preprocessed slice, ie, [nRows nCols nTP nRuns]. % % Douglas Greve (greve@nmr.mgh.harvard.edu) % January 25, 1999 % February 12, 1999 % % $Id: fmri_spatfilter.m,v 1.1 1999/03/24 22:11:35 greve Exp $ % % Check that the number of input arguments is correct % |
|||
|
fmri_srchseq.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 892 Sz: 4505 |
1/20/2000 12:03:07 PM | MatLab script |
% fmri_srchseq.m % % Search for an optimum stimulus sequence. % % $Id: fmri_srchseq.m,v 1.4 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_stxgrinder.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 893 Sz: 2633 |
3/21/2001 12:48:32 PM | MatLab script |
function [vSig, pSig] = fmri_stxgrinder(Test, hAvg, VoxVar, Ch, DOF, RM, q) % % [vSig, <pSig>] = fmri_stxgrinder(Test, hAvg, VoxVar, Ch, DOF, RM, q) % % % $Id: fmri_stxgrinder.m,v 1.4 2000/02/21 23:15:53 greve Exp greve $ % |
|||
|
fmri_stxgslice.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 894 Sz: 10016 |
8/28/2001 5:09:32 PM | MatLab script |
% StXGSlice.m % StX Slice Grinder % % global hAvgFile, eVarFile, sumXtXFile, dofFile; % global StatFile; % global ActiveCond, ControlCond; % global TestType, HDelMin, HDelMax; % global OutputFormat % 0 = log(p) (natural log) % 1 = log10(p) % 2 = p % 3 = test value % % global CmpIdeal % global QuitOnError; % % $Id: fmri_stxgslice.m,v 1.16 2000/06/02 22:50:12 greve Exp greve $ % |
|||
|
fmri_subsampmat.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 895 Sz: 511 |
7/22/1999 8:32:57 AM | MatLab script |
function [Mss, Rss] = fmri_subsampmat(TR,Ntp,TS) % [Mss Rss] = fmri_subsampmat(TR,Ntp,TS) % % Creates a subsampling matrix |
|||
|
fmri_svbfile.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 896 Sz: 2124 |
8/22/2001 3:06:19 PM | MatLab script |
function fmri_svbfile(y, BFileName, Endian) % % fmri_svbfile(y,BFileName,Endian) % % Saves a bshort or bfloat given the full path % name of the BFile. The type (bshort or % bfloat) is determined from the name. % The header is written with the dimensions. % Converts from matlab column-major format % to row major. % % Endian is either 0 or 1 (default is 0) % % See also: LdBFile % % $Id: fmri_svbfile.m,v 1.3 2000/09/06 23:00:20 greve Exp greve $ |
|||
|
fmri_svbvolume.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 897 Sz: 801 |
1/27/2000 9:51:34 AM | MatLab script |
function fmri_ldbvolume(vol,stem,voldim,ext) % fmri_ldbvolume(vol,stem,voldim,ext) % % Saves a volume in bfile format where vol is a 4D structure % of dimension Nslices X Nrows X Ncols X Ndepth. % % '$Id: fmri_svbvolume.m,v 1.2 2000/01/27 18:51:10 greve Exp greve $' |
|||
|
fmri_svcvm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 898 Sz: 808 |
9/21/2000 3:14:12 PM | MatLab script |
function fmri_svcvm(cvmstruct,stem) % fmri_svcvm(cvmstruct,stem) |
|||
|
fmri_svdat2.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 899 Sz: 2075 |
11/12/1999 10:51:19 AM | MatLab script |
function fmri_svdat(datfile,hd,format); % % fmri_svdat(datfile,hdrdat,<format>) % % $Id: fmri_svdat2.m,v 1.1 1999/11/12 18:46:47 greve Exp $ |
|||
|
fmri_svpar.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 900 Sz: 1180 |
5/23/2001 4:24:28 PM | MatLab script |
function ok = fmri_svpar(par,parfile,label,trun) % % ok = fmri_svpar(par,parfile,<label>,<trun>) % % Saves time/stimid to pardigm file. If label is included, % it must be a string matrix with a condition name stored % on each row. This name is looked up and appended to each % row of the paradigm file. trun is the duration of the run. % % $Id: fmri_svpar.m,v 1.6 2000/03/31 02:42:29 greve Exp greve $ |
|||
|
fmri_svsfa.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 901 Sz: 2011 |
4/14/2000 2:16:59 PM | MatLab script |
function fmri_svsfa(sfa,stem) % fmri_svsfa(sfa,stem) |
|||
|
fmri_sxa2sa.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 902 Sz: 1975 |
1/20/2000 12:03:28 PM | MatLab script |
function [ySA, dofSA] = fmri_sxa2sa(eVar,Ch,hAvg,hd) % % [ySA dofSA] = fmri_sxa2sa(eVar,Ch,hAvg,hd) % % Converts from selxavg format to selavg format. In selavg % format, the averages and standard deviations are interleaved % in the same data structure for all conditions, including % fixation. In selxavg, the average for the fixation condition % is always zero (by hypothesis) with covariance matrix equal % to eVar*I (ie, the variances are equal across delays, and % the delays are not correlated with each other). % % Note: the information about Ch is lost in that it cannot % be recovered from ySA and/or dofSA, it is saved elsewhere. % % $Id: fmri_sxa2sa.m,v 1.2 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_sxaslice.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 903 Sz: 20072 |
2/8/2001 11:43:53 AM | MatLab script |
% fmri_sxaslice2.m % March 31, 1999 % Modification of fmri_sxaslice to include fitting for the amplitude % of a specified hemodyn response. % Douglas N. Greve, MGH-NMR % % Performs selective averaging using a matrix formulation % (this is the same as deconvolution) assuming white noise. % % This is for multiple runs in a single session. % % % $Id: fmri_sxaslice.m,v 1.28 2000/07/31 23:19:12 greve Exp greve $ % |
|||
|
fmri_sxavol.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 904 Sz: 15647 |
1/26/2000 5:01:40 PM | MatLab script |
% fmri_sxavol.m % Jan 26, 2000 % Modification of fmri_sxaslice to processes an entire volume % % Douglas N. Greve, MGH-NMR % % Performs selective averaging using a matrix formulation % (this is the same as deconvolution) assuming white noise. % % This is for multiple runs in a single session. % % $Id: fmri_sxaslice.m,v 1.22 2000/01/25 23:45:51 greve Exp $ % |
|||
|
fmri_synth_phenc_sig.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 905 Sz: 1628 |
4/19/2000 1:44:31 PM | MatLab script |
function signal = fmri_synth_phenc_sig(fund, TR, Ntp, phase, delay, tau) % % signal = fmri_synth_phenc_sig(fund, TR, Ntp, phase, delay, tau) % % phase in radians % % $Id$ |
|||
|
fmri_synthpar.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 906 Sz: 502 |
4/23/1999 8:49:28 AM | MatLab script |
function Par = fmri_synthpar(nStimPerCond, TR, nRuns) % % Par = fmri_synthpar(nStimPerCond, TR, nRuns) % % % % $Id: fmri_synthpar.m,v 1.1 1999/03/24 22:11:36 greve Exp $ |
|||
|
fmri_synthpar2.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 907 Sz: 658 |
1/20/2000 12:03:33 PM | MatLab script |
function par = fmri_synthpar2(nStimPerCond, TR, Rss, nRuns) % % par = fmri_synthpar2(nStimPerCond, TR, Rss, nRuns) % % $Id: fmri_synthpar2.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
fmri_synthpar3.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 908 Sz: 5484 |
7/25/2000 3:45:41 PM | MatLab script |
function [par,t0avg] = fmri_synthpar3(npercond,tpercond,nruns,trun,tres,tprescan) % [par,t0avg] = fmri_synthpar3(npercond,tpercond,nruns,trun,tres,tprescan) % % npercond - number of presentations per NON-NULL condition, all runs % tpercond - stimulus duration of each NON-NULL condition % nruns - number of runs % trun - duration of each run % tres - temporal resolution (0 for infinite) % tprescan - time of first stimulus prior to scanning (not included % in trun). % % '$Id: fmri_synthpar3.m,v 1.4 2000/05/25 19:49:40 greve Exp greve $' |
|||
|
fmri_synthrun.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 909 Sz: 4146 |
11/10/2000 3:57:03 PM | MatLab script |
function [srs, fSlices] = fmri_synthrun(srs) % % |
|||
|
fmri_synthrunstruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 910 Sz: 735 |
2/23/2000 4:49:07 PM | MatLab script |
function synthrunstruct = fmri_syntrunstruct() |
|||
|
fmri_tavgslice.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 911 Sz: 454 |
4/23/1999 8:49:28 AM | MatLab script |
% fmri_tavgslice % Computes the temporal average at each voxel over multiple runs. % % % $Id: fmri_tavgslice.m,v 1.1 1999/03/24 22:11:36 greve Exp $ |
|||
|
fmri_touch.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 912 Sz: 491 |
4/24/2000 2:48:14 PM | MatLab script |
function r = fmri_touch(fname); % r = fmri_touch(fname); % % Simple function to create a file called fname. This is supposed % to be something like the unix touch, but it has % no effect if fname already exists. % % $Id$ |
|||
|
fmri_untangle.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 913 Sz: 1156 |
9/29/2000 2:03:11 PM | MatLab script |
function [havg, hstd, hdrdat] = fmri_untangle(havgstd, hdrdat, SubtCond0) % % [havg, hstd] = fmri_untangle(havgstd, hdrdat, <SubtCond0>) % % havg: rows cols cond delay % |
|||
|
fmri_untangle2.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 914 Sz: 763 |
9/22/2000 1:15:36 PM | MatLab script |
function [havg, errstd] = fmri_untangle2(havgstd, hdrdat) % % [havg, errstd] = fmri_untangle2(havgstd, hdrdat) % |
|||
|
fmri_voxvar.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 915 Sz: 1836 |
1/25/2000 2:46:22 PM | MatLab script |
function vvar = fmri_voxvar(e,dof,Cn,TPExcl) % % Computes the variance at a voxel given the error % waveform at that voxel. % % vvar = fmri_voxvar(e,dof,<<Cn>,TPExcl>) % % e: nRows x nCols x nTP x nRuns % dof: scalar-int % Cn: nTPxnTP(xnRuns) % TPExcl: nTPxnRuns % % $Id: fmri_voxvar.m,v 1.2 2000/01/25 23:45:51 greve Exp greve $ |
|||
|
fmri_vrestriction.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 916 Sz: 2249 |
4/23/1999 8:49:29 AM | MatLab script |
function RV = fmri_vrestriction(nH, nC, AC, CC, nHTest) % % RV = fmri_vrestriction(nH, nC, AC, CC, nHTest) % % Creates a restriction vector of dimension 1 X nC*nH % % nH - total number of elements in HDIR % nC - total number of stimulus conditions (including fixation) % AC - list of active conditions % CC - list of control conditions % nHTest - list of HDIR components to test (default: all). % % Eg: fmri_vrestriction(10, 6, [1 3], [2 5], [3 6:9]) % Generates an RV for testing conditions (1+3)-(2+5) using % components 3,6,7,8, and 9 in the HDIR. Conditions 0 and 4 % are not tested. There are 10 components in the HDIR, and 5 % stimulus conditions. % % % $Id: fmri_vrestriction.m,v 1.1 1999/03/24 22:11:36 greve Exp $ % Check for the correct number of arguments % |
|||
|
fmri_wisxavg_fe.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 917 Sz: 2381 |
10/13/2000 11:42:10 AM | MatLab script |
% Name: fmri_isxavg_fe % Purpose: implements fixed-effects intersession averaging % for output of selxavg % Author: Douglas Greve % Questions or Comments: analysis-bugs@nmr.mgh.harvard.edu % Version: $Id: fmri_isxavg_fe.m,v 1.4 2000/08/31 18:20:47 greve Exp greve $ %%%% These variables must be specified %%%%%%%% % InStemList % FirstSlice % NSlices % OutStem |
|||
|
fmri_xtx2cbp.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 918 Sz: 613 |
4/23/1999 8:49:28 AM | MatLab script |
function CBP = xtx2cbp(XtX,nNNCond,nTP) % % CBP = xtx2cbp(XtX,nNNCond) % % % % $Id: fmri_xtx2cbp.m,v 1.1 1999/03/24 22:11:36 greve Exp $ |
|||
|
FTest.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 919 Sz: 684 |
3/21/2001 12:36:37 PM | MatLab script |
function p = FTest(dof1, dof2, F, dof2max) % % p = FTest(dof1, dof2, F, <dof2max>) % % Computes p-value given F-value. p and F can be vectors. % dof1 = dof of numerator (Number of Rows in RM) % dof2 = dof of denominator (DOF) % % Ref: Numerical Rec in C, pg 229. % % $Id: FTest.m,v 1.1 1999/03/24 22:11:29 greve Exp greve $ % |
|||
|
gammadist.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 920 Sz: 299 |
6/30/2000 3:45:03 PM | MatLab script |
function y = gammadist(x,avg,stddev) % Gamma Distribution % % y = gammadist(x,avg,stddev) % % This probably does not work. |
|||
|
gaussian.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 921 Sz: 342 |
6/30/2000 3:47:11 PM | MatLab script |
function y = gaussian(x,mean,stddev) % % Gaussian Distribution Function % % y = gaussian(x,mean,stddev) % % y = exp( -((x-mean).^2)/(2*(stddev.^2))) / stddev * sqrt(2*pi); % y = y/sum(y); |
|||
|
gensynthdata.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 922 Sz: 735 |
7/7/1999 6:47:14 AM | MatLab script |
|
hdrview.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 923 Sz: 9982 |
6/10/1999 3:41:48 PM | MatLab script |
function hfig = hdrview(varargin)
%
% hdrview(string,options)
% hfig = hdrview('init',hsa,Nnnc,<TR>,<tPreStim>)
% hdrview('CurPixel',hFig,[r c]);
%
% $Id: hdrview.m,v 1.5 1999/06/10 22:33:33 greve Exp $
|
|||
|
hdrviewlite.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 924 Sz: 13220 |
7/20/2001 1:02:30 PM | MatLab script |
function hdrviewlite(varargin)
%
% hdrview(string,options)
% hdrview('init',hFig,t,dof);
% hdrview('plot',hFig,havg,hstd, CurrPixel);
% hdrview('tmarker',tmarker)
% hdrview('kbd')
% hdrview('wbd')
%
% $Id: hdrviewlite.m,v 1.9 2000/07/18 23:25:05 greve Exp greve $
|
|||
|
hview.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 925 Sz: 1249 |
4/23/1999 8:49:22 AM | MatLab script |
function [t1, hAvg, hStd, hplt] = hview(hsa,Cond,nHEst,TR,tPre,CtrlCond) % % [t, hAvg, hStd, hplt] = hview(hsa,Cond,nHEst,TR,tPre,<CtrlCond>) % % % $Id: hview.m,v 1.1 1999/03/24 22:11:36 greve Exp $ |
|||
|
imagesc1d.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 926 Sz: 729 |
4/23/1999 8:49:28 AM | MatLab script |
function h = imagesc1d(img1d,nRows,nCols) % % h = imagesc1d(img1d,nRows,nCols) % % Produces a 2-D image of a 1-D vector. If nRows or nCols % are unspecified, it attempts to generate a square image. % % $Id: imagesc1d.m,v 1.1 1999/03/24 22:11:36 greve Exp $ % number of pixels in the 1-D image |
|||
|
imgoverlay.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 927 Sz: 2761 |
1/20/2000 12:05:06 PM | MatLab script |
function [imgov,cmap,cscale,ovmax] = imgoverlay(img,overlay,ovmin,ovmax) % % [imgov cmap cscale ovmax] = imgoverlay(img,overlay,ovmin,<ovmax>) % % Creates an overlay given the underlay image (img), % the overlay image (overlay) and the overlay display range % (ovmin, ovmax). This can be used to overlay statistics over % a structural. The img is rescaled to the range of 1:48, and % the overlay image is rescaled to the range of 49:64, afterwhich % the two are added together to create one image returned in % imgov. Set the colormap to cmap to display the underlay in % gray scale and the overlay in color. The overlay image can % contain multiple planes. % % $Id: imgoverlay.m,v 1.3 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
imgoverlaytc.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 928 Sz: 1290 |
1/20/2000 12:05:06 PM | MatLab script |
function [tcimg,cmap,cscale] = imgoverlaytc(img,overlay,ovmin,ovmax,tail,rescale) % % [tcimg,cmap,cscale] = imgoverlaytc(img,overlay,ovmin,ovmax,tail,<rescale>) % % Creates a true-color compositive image with img as a gray-scale % base and overlay as a colored overlay. % % $Id: imgoverlaytc.m,v 1.2 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
imgoverlaytc2.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 929 Sz: 2424 |
11/9/2000 12:47:24 PM | MatLab script |
function [tcimg,cmap,cscale] = imgoverlaytc2(tcimg,overlay,ovmin,ovmax,tail,interp) % % [tcimg,cmap,cscale] = imgoverlaytc(imgtc,overlay,ovmin,ovmax,tail,interp) % % Creates a true-color composite image with img as a gray-scale % base and overlay as a colored overlay. Same as imgoverlaytc() but % the input image (tcimg) is already in true-color format. % % $Id: imgoverlaytc2.m,v 1.3 2000/11/09 19:10:39 greve Exp greve $ |
|||
|
imgto1d.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 930 Sz: 565 |
7/12/2001 9:58:19 AM | MatLab script |
function img1d = imgto1d(img,keeplast) % % img1d = imgto1d(img,keeplast) % % Reshapes the image to 1D matrix. If keeplast=1, % then the image is reshaped to a 2D image with % the first N-1 dimension in the rows and the last % dimension as the columns. % |
|||
|
invillcond.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 931 Sz: 658 |
2/9/2001 10:58:37 AM | MatLab script |
function [im, neigused] = invillcond(m,pvemin) % [im neigused]= invillcond(m,pvemin) |
|||
|
ldstruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 932 Sz: 762 |
4/14/2000 1:17:58 PM | MatLab script |
function s = ldstruct(fid) % s = ldstruct(fid) % % Loads a structure saved with svstruct(). fid is a file % identifier opened for reading. % % $Id$ |
|||
|
linfit.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 933 Sz: 497 |
1/20/2000 2:44:32 PM | MatLab script |
function [slope, offset] = linfit(y,x) % % [slope offset] = linfit(y,x) % % Solves the equation: % y = slope * x + offset % % $Id: linfit.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
load_bhdr.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 934 Sz: 3288 |
9/17/2001 5:57:55 PM | MatLab script |
function [T, VolRes, VolDim] = load_bhdr(bhdrfile); % % [T VolRes VolDim] = load_bhdr(bhdrfile); % % Parses the bhdr header file for bshorts/bfloats % % T is the affine transform that converts col, row, slice to % x, y, z in scanner coordinates, assuming that the count starts % at 0, ie, % % x col % y = T * row % z slice % 1 1 % % VolRes is a 3x1 vector with the col resolution, row % resolution, and slice resolution % % VolDim is a 3x1 vector with the number of columns, rows, and slices. % |
|||
|
load_corinfo.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 935 Sz: 3036 |
9/6/2001 11:17:28 AM | MatLab script |
function [T, VolRes, VolDim, ci] = load_corinfo(corinfofile); % % [T VolRes VolDim ci] = load_corinfo(corinfofile); % % Parses the COR-.info header file for COR volumes. % % T is the affine transform that converts col, row, slice to % x, y, z in scanner coordinates, assuming that the count starts % at 0, ie, % % x col % y = T * row % z slice % 1 1 % % VolRes is a 3x1 vector with the col resolution, row % resolution, and slice resolution % % VolDim is a 3x1 vector with the number of columns, rows, and slices. % % ci is a structure whose components are named after that found in % the COR-.info file. % |
|||
|
mar.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 936 Sz: 224 |
12/18/2000 10:55:46 AM | MatLab script |
function [m, i] = mar(x) % % [m i] = mar(x) % % [m i] = max(abs(reshape1d(x))) % |
|||
|
mkdirp.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 937 Sz: 1031 |
4/30/2001 11:21:25 AM | MatLab script |
function mkdirp(path) % mkdirp(path) % % This is an attempt to recreate the unix "mkdir -p" command % in matlab. It has some problems (following links?). % % $Id$ |
|||
|
mkmosaic.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 938 Sz: 1573 |
3/12/2001 11:11:05 AM | MatLab script |
% mkmosiac.m % % Makes a NxMxnTP mosaic from input slice files. If the % slice files have nTP layers, then the mosaic will have nTP layers. % Used by the csh script mkmosaic. % % $Id: mkmosaic.m,v 1.2 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
mos2vol.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 939 Sz: 1261 |
3/12/2001 11:11:05 AM | MatLab script |
function [vol, tszmos] = mos2vol(mos, szvol, tszmos) % % [vol tszmos] = mos2vol(mos, szvol, <tszmos>) % % Given a mosaic (rows, cols, planes), produces a % volume (rows, cols, slices, planes). If the mosaic has been padded % with blank images, those will be excluded from the volume. % % szvol - size of the volume (rows, cols, slices, <planes>). % % tszmos - size (rows, cols) of the mosaic measured in tiles (optional). % If tszmos is not specified, a default one will be computed using % the function defmossize. % % See also: mos2vol vol2mos mosind2volind mossub2volsub % volind2mosind volsub2mossub defmossize % % $Id$ |
|||
|
mosind2volind.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 940 Sz: 646 |
3/12/2001 11:11:05 AM | MatLab script |
function [iv, im, tszmos] = mosind2volind(im, szvol, tszmos) % [iv tszmos] = mosind2volind(im, szvol, tszmos) |
|||
|
mossub2volsub.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 941 Sz: 1780 |
3/12/2001 11:11:05 AM | MatLab script |
function [rv, cv, sv, im, tszmos] = mossub2volsub(rm, cm, szvol, tszmos) % [rv cv sv tszmos] = mossub2volsub(rm, cm, szvol, tszmos) % % Computes the subscripts in a volume (row, col, slice) that correspond % to a subscript in a mosaic (row, col). Note that when the mosaic has % been padded with blank images, the subscripts in those images do not % have corresponding subscripts in the volume. % % rm - row in the mosaic % cm - column in the mosaic % szvol - size of the volume (Nrows, Ncols, Nslices, ...) % tszmos - size (rows, cols) of the mosaic measured in tiles (optional) % % rv - row in the volume % cv - column in the volume % sv - slice in the volume % % If tszmos is not specified, a default one will be computed using % the function defmossize. % % See also: mos2vol vol2mos mosind2volind mossub2volsub % volind2mosind volsub2mossub defmossize |
|||
|
mstk2mos.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 942 Sz: 968 |
1/14/2000 1:48:04 PM | MatLab script |
function StkMosaic = mstk2mos(MStack,nTileCols) % % StkMosaic = mstk2mos(MStack,nTileCols) % % Converts the multiple image stack into a mosaic. % Eg: if size(MStack) = 128 x 128 x 16 x 10 % and nTileCols = 4, then Mosaic will have % dimension 512 x 512 x 10. The 16 images in % Stack will be tiled in a stack of 10 4x4 mosaics. % % $Id: mstk2mos.m,v 1.2 2000/01/14 22:48:58 greve Exp $ |
|||
|
nmrcolormap.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 943 Sz: 701 |
7/18/2000 3:35:30 PM | MatLab script |
function cmap = nmrcolormap(ncmap,tail) % % cmap = nmrcolormap(ncmap,<tail>) % |
|||
|
ovstruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 944 Sz: 850 |
1/20/2000 2:45:14 PM | MatLab script |
function [ovs] = ovstruct(img,actimg,ovmin,ovmax) % % [ovs] = ovstruct(img,actimg,ovmin,ovmax) % % $Id: ovstruct.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
par2condidmap.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 945 Sz: 613 |
11/12/1999 10:54:22 AM | MatLab script |
function condidmap = par2condidmap(par,nullid) % % condidmap = par2condidmap(par,nullid) % % Extracts and sorts all unique condition numbers in paradigm. % % $Id: par2condidmap.m,v 1.1 1999/11/12 18:50:07 greve Exp $ |
|||
|
pkpulse.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 946 Sz: 1182 |
6/16/2000 9:53:31 AM | MatLab script |
function ipeak = pkpulse(pulse,thresh) % ipeak = pkpulse(pulse,thresh) % % Returns the indices of the peaks in pulse. Algorithm: convert pulse % into a vector of 0s and 1s by thresholding it at thresh. If thresh is % at the right level, this will create boxcar train of 1s and 0s. This is % differentiated so that the begining of the boxcar is 1 and the end is -1. % The peak is between these two limits is returned for each boxcar. % % A plot of just the peaks can be obtained by: % pulsepeaks = zeros(size(pulse)); % pulsepeaks(ipeak) = pulse(ipeak); % % $Id$ |
|||
|
pvecovmtx.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 947 Sz: 228 |
7/26/2000 4:10:43 PM | MatLab script |
function [pve, s] = pvecovmtx(m) % [pve s] = pvecovmtx(m) % % Percent Variance Explained. |
|||
|
qoe.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 948 Sz: 1108 |
10/1/2001 9:57:14 AM | MatLab script |
function qoe(msg) % % qoe(<msg>) % % When there is a global variable defined called QuitOnError % and it is 1, then matlab is quit after printing out the % backtrace. To use, declare "global QuitOnError" and set % to either 0 or 1. % % The main use of this function is when a matlab script is being % executed non-interactively. If the error() function were called % instead, then matlab would hand control back to a non-existent % terminal causing the script to crash very ungracefully. Remember % declare global QuitOnError when starting up. % % $Id: qoe.m,v 1.2 2000/01/07 02:14:03 greve Exp $ |
|||
|
rande.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 949 Sz: 362 |
1/20/2000 2:45:38 PM | MatLab script |
function r = rande(rdim) % % r = rande(dim) % % Generates matrix of given dimension whose elements % are exponentially distributed. The mean and std over % all the elements asymptotically approach one. % % $Id: rande.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
randnorm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 950 Sz: 591 |
11/16/1999 11:58:52 AM | MatLab script |
function [y, H] = randnorm(m, n, Sigma) % % [y H] = randnorm(m, n, Sigma) % % Creates an m-by-n matrix y whose columns are % distributed N(0,Sigma). H is the cholesky % decomposition of Sigma. y = H * randn(m,n). % % $Id: randnorm.m,v 1.1 1999/11/16 19:54:15 greve Exp $ |
|||
|
rcsfmri /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 951 Sz: 597 |
4/23/1999 8:49:22 AM | C shell script text executable |
#!/bin/csh -f #echo $0 |
|||
|
ReadAFNIHead2.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 952 Sz: 3051 |
8/16/2001 12:28:28 PM | MatLab script |
function headinfo = ReadAFNIHead2(hname) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % function: ReadAFNIHead2 % given the name of an AFNI HEAD % file this function reads the % contents and returns information % in a structure where the fields % are arranged as follows: % contents of the structure are: % headinfo.xdim ( x dimension size ) % headinfo.ydim ( y dimension size ) % headinfo.zdim ( z dimension size ) % headinfo.xvox ( x voxel size ) % headinfo.yvox ( y voxel size ) % headinfo.zvox ( z voxel size ) % headinfo.nvols ( number of sub-briks, i.e. for 3D+time ) % headinfo.orient ( orientation code, e.g. 351 ) % the orientation code is 3 numbers and corresponds to the following convention % headinfo.type (type string, eg short, float) % headinfo.byteorder (byte order string: 'b' for big endian, 'l' for little % 0 = R-L % 1 = L-R % 2 = P-A % 3 = A-P % 4 = I-S % 5 = S-I % % Timothy M. Ellmore (tellmore@nih.gov) % Laboratory of Brain and Cognition % National Institute of Mental Health % % Modified by Douglas N. Greve % greve@nmr.mgh.harvard.edu % MGH-NMR Center, Boston Mass % Added byteorder and data type |
|||
|
ReadBRIK2.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 953 Sz: 1611 |
4/4/2001 3:55:08 PM | MatLab script |
function V = ReadBRIK2(fname) % % V = ReadBRIK2(fname) % % ReadBRIK function to read 3D+time AFNI BRIKs % of any type and dimensionality % % Example: % brikfname = 'ASt3avvr+orig.BRIK' % BRIKDATA = ReadBRIK2(brikfname) % BRIKDATA is now a 4D matrix (xdim,ydim,zdim,timepoint) % % Written December 4, 1998 by Timothy M. Ellmore % Laboratory of Brain and Cognition, NIMH % % Modified by Douglas N. Greve % greve@nmr.mgh.harvard.edu % MGH-NMR Center, Boston Mass % Now does not require any info other than the brikname, % ie, automatically detects size, type, endianness, etc |
|||
|
readln.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 954 Sz: 884 |
4/23/1999 8:49:29 AM | MatLab script |
function slines = readln(fid,nl) % % slines = readln(fid,<nlines>) % % % $Id: readln.m,v 1.1 1999/03/24 22:11:37 greve Exp $ |
|||
|
remap_par.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 955 Sz: 729 |
11/12/1999 10:55:23 AM | MatLab script |
function newpar = remap_par(par,condidmap) % % newpar = remap_par(par,condidmap) % % $Id: remap_par.m,v 1.1 1999/11/12 18:51:04 greve Exp $ |
|||
|
reshape1d.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 956 Sz: 196 |
4/23/1999 8:49:29 AM | MatLab script |
function y = reshape1d(x) % y = reshape1d(x) % Reshapes matrix x into 1-D column vector y. % % $Id: reshape1d.m,v 1.1 1999/03/24 22:11:37 greve Exp $ |
|||
|
reshape2d.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 957 Sz: 352 |
2/12/2001 3:38:42 PM | MatLab script |
function m = reshape2d(x) % m = reshape2d(x) % Reshape into a 2d array where % size(m,1) = size(x,1) |
|||
|
roi2ind.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 958 Sz: 845 |
1/20/2000 2:45:55 PM | MatLab script |
function ind = roi2ind(siz,roi) % % ind = roi2ind(siz,roi) % % Converts a Region of Interest into indicies. % % siz = [nrows ncols] % roi = [rowmin colmin rowmax colmax] % % $Id: roi2ind.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
samp2pdf.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 959 Sz: 1257 |
1/4/1999 2:54:07 PM | MatLab script |
function [px, xbin, xdelta] = samp2pdf(x, b) % % [px xbin xdelta] = samp2pdf(x,b) % % Computes the probability distribution function from a sample. % x is the 1-D vector of samples. b is either the number of bins % that the pdf will be divided into or a 3-component vector % [minbin deltabin binmax]. % % xbin is the vector of % bin centers, and px is the vector of probabilities that a % sample will fall into the corresponding bin. If the number % of bins is specified, the bins are % uniformly distributed between the min and max of the sample. % % Author: Douglas N. Greve, MGH-NMR % Date: 12/30/98 |
|||
|
splitstring.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 960 Sz: 528 |
1/20/2000 2:46:30 PM | MatLab script |
function split = splitstring(str) % % split = splitstring(str) % % Split a string into vertically concatenated strings. % % $Id: splitstring.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $ |
|||
|
spm_to_bfloat.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 961 Sz: 1681 |
4/23/1999 10:40:24 AM | MatLab script |
function spm_to_bfloat(iname) % This function reads a single byte SPM image and writes it out % as a series of float slices called actfloat_%d.bfloat % FORMAT spm_to_bfloat(iname); % iname - input image name %______________________________________________________________________ % Writes out transaxially sliced SPM activation images into a series of % slices actfloat_%d.img. % (The actfloat format is for MGH flattening compatibility) %___________________________________________________________________________ % @(#)spm_to_bfloat.m 99/31/03 Chloe Hutton % Use user interface if no input %----------------------------------------------------------------------- |
|||
|
spm_to_bshort.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 962 Sz: 1524 |
4/23/1999 10:40:24 AM | MatLab script |
function spm_to_bshort(iname) % This function reads an SPM image volume xxx.img and writes it out % as a series of bshort slices xxx_num.img xxx_num.hdr. % FORMAT spm_to_bshort(iname); % iname - input image name %______________________________________________________________________ % Writes out transaxially sliced SPM image volume into a series of % slices *.bshort. % (The bshort format is for MGH flattening compatibility) %___________________________________________________________________________ % @(#)spm_to_bshort.m 99/31/03 Chloe Hutton % % Use user interface if no input %----------------------------------------------------------------------- |
|||
|
spm_to_sagbshort.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 963 Sz: 4742 |
4/23/1999 10:40:24 AM | MatLab script |
function spm_to_sagbshort(iname) % Writes out a transaxially sliced image volume into a series of sagittal % slices with the .bshort suffix. % FORMAT spm_to_bshort(iname); % iname - input image filename %___________________________________________________________________________ % Writes out transaxially sliced SPM image xxxx.img into series of sagittal % slices xxxx_num.bshort each with an associated header file xxxx_num.hdr % (The bshort format is for MGH flattening compatibility) %___________________________________________________________________________ % @(#)spm_to_sagbshort.m 99/31/03 Chloe Hutton |
|||
|
stxgpredict.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 964 Sz: 5959 |
7/27/2001 4:28:27 PM | MatLab script |
% stxgpredict.m (see stxpredict) % computes a prediction of the statistical map % given the averages from an already analyzed data set as well % as a list of paradigm files. % These must be previously defined: % hstem % parlist % contrast % tstem % tsigstem % tminsigstem % fstem % fsigstem % ntrs - number of time points per run % firstslice % nslices |
|||
|
svstruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 965 Sz: 1158 |
4/14/2000 1:15:15 PM | MatLab script |
function svstruct(strct, fid) % svstruct(strct, fid) % % Saves a structure as text to file. fid is a file id opened for % writing. The format is: % % fieldname type dim size % value(s) % % type = 0 for numeric, 1 for char % dim is the number of dimensions in the data field (<3) % size is a dim-length vector of the number of elements % in each dimension. % % See also: ldstruct() % % $Id$ |
|||
|
synthcornoise.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 966 Sz: 1488 |
2/9/2001 2:07:29 PM | MatLab script |
function [n, CVM, W2, R1] = synthcornoise(ntrs,ncols,alpha,rho) % [n CVM W2 R1] = synthcornoise(ntrs,ncols,alpha,rho) % % Synthesizes a functional slice of correlated noise using the % alpha-rho model (see fmri_acorrsynth()) to construct the % autocorrelation function. Synthesizes the noise using 2*ntrs % points and then takes the middle half so as to avoid edge effects. % The output data matrix n will have dimension ntrs X ncols. % % The asymptotoic covariance matrix is CVM. This can be compared to % the sampled covariance matrix CVMhat = n*n'/nvoxs; %' % % W2 is the square of the whitening matrix that can be used to remove % the correlation from n, W2 = W * W'; W = chol(W2); %' % % alpha = 1 or rho = 0 will create white noise |
|||
|
synthdrbfile.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 967 Sz: 1083 |
8/6/1999 11:52:34 AM | MatLab script |
%%% synthdrbfile.m %%%%%%%%% |
|||
|
tal_csr2xyz.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 968 Sz: 775 |
9/7/1999 6:50:47 PM | MatLab script |
function [xyz] = tal_csr2xyz(col, slice, row, res, fov) % % [xyz] = tal_csr2xyz(col, slice, row, res, fov) % % Returns Talairach coords x,y,z (mm) given the slice % number and the row and column in the corronal slice. % % res is the voxel resolution in mm (defalut 8mm) % fov is the field of view (default 256mm) |
|||
|
tal_xyz2csr.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 969 Sz: 783 |
10/6/1999 3:54:25 PM | MatLab script |
function [csr] = tal_xyz2csr(x, y, z, res, fov) % % [csr] = tal_xyz2csr(x, y, z, res, fov) % % Returns the corronal slice number and the row and column numbers % in the corronal slice given the Talairach coords x,y,z (mm). % % res is the voxel resolution in mm (defalut 8mm) % fov is the field of view (default 256mm) |
|||
|
tliweights.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 970 Sz: 2002 |
9/11/2000 1:38:16 PM | MatLab script |
function [ind, wind] = tliweights(szmtx, rcs_hat) % [ind wind] = tliweights(szmtx, rcs_hat) % % Weights and indices for trilinear interpolation. % % szmtx is number of rows, columns, and slices in volume (one-based) % rcs_hat - off-grid row, column, and slice to interpolate (N x 3) % % ind (N x 8) -- on-grid indices (row major, one-based) % w (N x 8) -- corresponding weights % % See also: uliweights, bliweights |
|||
|
tTest.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 971 Sz: 877 |
4/23/1999 8:49:29 AM | MatLab script |
function p = tTest(dof, t, dofApprx) % % pSig = tTestB(dof, t, <dofApprx>) % % If dofApprx is not set, tTest() computes the % significance level of t given dof using the % formula: % z = dof./(dof + t .^ 2); % pSig = betainc(z,dof/2,0.5); % When dofApprx is set, an approximation is used % when dof exceeds dofApprx: % p = erfc(abs(t)/sqrt(2.0)); % This can speed the function considerably when % the dof is large. % % Ref: Numerical Rec in C, pg 229. % % % $Id: tTest.m,v 1.1 1999/03/24 22:11:37 greve Exp $ |
|||
|
uliweights.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 972 Sz: 895 |
9/11/2000 1:33:35 PM | MatLab script |
function [ind, wind] = uliweights(szmtx, i_hat) % [ind, wind] = uliweights(szmtx, i_hat) % % Weights and indices for (uni)linear interpolation from a % uniform grid. % % szmtx is number of elements in the grid. % i_hat - off-grid indices to interpolate (N x 1) % % ind (N x 2) % w (N x 2) % % See also: bliweights, tliweights |
|||
|
version.info /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 973 Sz: 4024 |
4/23/1999 8:49:26 AM | ASCII text |
|
vol2mos.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 974 Sz: 1968 |
3/12/2001 11:11:09 AM | MatLab script |
function [mos, tszmos] = vol2mos(vol, tszmos) % [mos tszmos] = vol2mos(vol, tszmos) % % Given a volume (rows, cols, slices, planes), produces a mosaic % (rows, cols, planes). % % tszmos - size (rows, cols) of the mosaic measured in tiles (optional). % If tszmos is not specified, a default one will be computed using % the function defmossize. For example, if there are 16 slices, each % 64X64, then the mosaic will be 4 tiles by 4 tiles which is 256 rows % by 256 columns. % % If the total number of tiles exceeds the number of volume slices, % the mosaic is padded with blank images. % % See also: mos2vol vol2mos mosind2volind mossub2volsub % volind2mosind volsub2mossub defmossize % % $Id$ |
|||
|
volind2mosind.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 975 Sz: 600 |
3/12/2001 11:11:09 AM | MatLab script |
function [im, tszmos] = volind2mosind(iv, szvol, tszmos) % [im tszmos] = volind2mosind(iv, szvol, tszmos) |
|||
|
volsub2mossub.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 976 Sz: 1097 |
3/12/2001 11:11:09 AM | MatLab script |
function [rm, cm, tszmos] = volsub2mossub(rv, cv, sv, szvol, tszmos) % [rm cm tszmos] = volsub2mossub(rv, cv, sv, szvol, tszmos) % % rv - row in the volume % cv - column in the volume % sv - slice in the volume % szvol - size of the volume (Nrows, Ncols, Nslices, ...) % tszmos - size (rows, cols) of the mosaic measured in tiles (optional) % % rm - row in the mosaic % cm - column in the mosaic % % If tszmos is not specified, one will be computed. |
|||
|
vqm.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 977 Sz: 3962 |
10/11/2000 4:38:46 PM | MatLab script |
function Q = vqm(abc,voxsize,voldim,base)
%
% Q = vqm(abc,voxsize,voldim,<base>)
%
% Volume quantization matrix. Q computes the x,y,z of a voxel given
% the subscript of the voxel in the volume.
%
% abc - 3 character string indicating which physical dimension maps to
% the fast (a), medium (b), and slow (c) indicies. The string also
% indicates the sign of the derivative of the physical dimension
% with respect to its index. Valid characters are (case insensitive):
% R - x dimension, dx/di > 0 (index increases Left to Right)
% L - x dimension, dx/di < 0 (index increases Right to Left)
% A - y dimension, dy/di > 0 (index increases Post to Ant)
% P - y dimension, dy/di > 0 (index increases Ant to Post)
% S - z dimension, dz/di > 0 (index increases Infer to Super)
% I - z dimension, dz/di > 0 (index increases Super to Infer)
%
% voxsize - 3 element vector of the (absolute) physical length of
% a voxel side. Each element corresponds to the phyical
% dimension in the abc string.
%
% voxdim - 3 element vector of the number of voxels in each dimension.
% Each element corresponds to the phyical dimension in the abc string.
%
% base - the value of the first index (default is 0).
%
% Example, default for MGH-NMR FreeSsurfer Corronals:
%
% Q = vqm('LIA', [1 1 1], [256 256 256], 0);
%
% Example, default for MGH-NMR FreeSsurfer Functionals
% [R subj inres betres] = fmri_readreg('register.dat');
% Qf = vqm('LIA', [inres inres betres], [64 64 24], 0);
%
% $Id: vqm.m,v 1.1 2000/01/20 20:58:30 greve Exp greve $
|
|||
|
yak.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 978 Sz: 25973 |
3/8/2001 6:18:44 PM | MatLab script |
function yak(varargin)
% a1,underlay,pmin)
%
% yak displays images. It can display a significance
% map over a structural. Multiple images can be viewed
% by hitting the '+' and '-' keys. The sign of the tail
% can be toggled by hitting 't'. Text in the figure gives
% the current status of the image, including number of
% rows, columns, and depth as well as the location and
% pvalue of the mouse. It is assumed that the pvalues
% are ln(p).
%
% yak('init',img)
% yak('init',img,'-A',ActImg)
% yak('init',img,'-h',HsaImg)
%
% yak(cbstring) % for callback functions
%
% $Id: yak.m,v 1.29 2000/12/13 16:59:20 greve Exp greve $
|
|||
|
yakview.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/ |
#: 979 Sz: 5685 |
4/5/2001 10:31:14 AM | MatLab script |
% yakview - views images, stat overlays, and hemodynamic responses. % $Id: yakview.m,v 1.15 2000/09/01 18:33:35 greve Exp greve $ |
|||
| /binfs/freesurfer_alpha/fsfast-20011005/toolbox/trash/ | |||
|
fmri_hdrdatastruct.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/trash/ |
#: 980 Sz: 689 |
6/13/1999 4:15:06 PM | MatLab script |
function hdrdat = fmri_hdrdatstruct() % hdrdat = fmri_hdrdatstruct() % |
|||
|
fmri_isxavg_re.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/trash/ |
#: 981 Sz: 2586 |
10/12/1999 5:24:01 PM | MatLab script |
% Name: fmri_isxavg_re % Purpose: implements random-effects intersession averaging % for output of selxavg % Author: Douglas Greve % Questions or Comments: analysis-bugs@nmr.mgh.harvard.edu % Version: $Id$ %%%% These variables must be specified %%%%%%%% % InStemList % FirstSlice % NSlices % OutStem |
|||
|
fmri_svdat.m /binfs/freesurfer_alpha/fsfast-20011005/toolbox/trash/ |
#: 982 Sz: 2618 |
7/21/1999 3:20:31 PM | MatLab script |
function fmri_svdat(datfile,TR,TW,TPS,nNNC,DOF,nRuns,nTP,... |
|||
| /binfs/freesurfer_alpha/lib/ | |||
|
tkmedit.tcl /binfs/freesurfer_alpha/lib/ |
#: 983 Sz: 42411 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################ # Copyright (c) 1999 CorTechs - All rights reserved ############################################################################ |
|||
| /binfs/freesurfer_alpha/lib/bem/ Skipped directory per survey instructions | |||
| /binfs/freesurfer_alpha/lib/help/ | |||
| /binfs/freesurfer_alpha/lib/help/csurf/ | |||
|
createsurface /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 984 Sz: 1353 |
4/5/2000 12:17:15 PM | ASCII English text |
|
csurf /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 985 Sz: 3293 |
6/4/2000 6:00:30 AM | ASCII English text |
|
editsegmentation /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 986 Sz: 3941 |
4/5/2000 12:17:15 PM | ASCII English text |
|
flattensurface /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 987 Sz: 904 |
6/4/2000 6:00:30 AM | ASCII English text |
|
makefinalsurface /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 988 Sz: 682 |
4/5/2000 12:17:15 PM | ASCII English text |
|
makerelaxationcuts /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 989 Sz: 1885 |
4/5/2000 12:17:15 PM | ASCII English text |
|
medit /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 990 Sz: 2604 |
4/5/2000 12:17:15 PM | ASCII English text |
|
processcreatefixfinal /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 991 Sz: 1302 |
6/4/2000 6:00:30 AM | ASCII English text |
|
processvolume /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 992 Sz: 1446 |
4/5/2000 12:17:15 PM | ASCII English text |
|
register /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 993 Sz: 6717 |
6/4/2000 6:00:30 AM | ASCII English text |
|
spheresurface /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 994 Sz: 679 |
6/8/2000 11:37:49 AM | ASCII English text |
|
surfer /binfs/freesurfer_alpha/lib/help/csurf/ |
#: 995 Sz: 4159 |
4/5/2000 12:17:15 PM | ASCII English text |
| /binfs/freesurfer_alpha/lib/images/ | |||
|
icon_arrow_ccw.gif /binfs/freesurfer_alpha/lib/images/ |
#: 996 Sz: 124 |
4/10/2001 2:07:12 PM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_cw.gif /binfs/freesurfer_alpha/lib/images/ |
#: 997 Sz: 132 |
4/10/2001 2:07:12 PM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_down.gif /binfs/freesurfer_alpha/lib/images/ |
#: 998 Sz: 145 |
4/10/2001 2:07:13 PM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_expand_x.gif /binfs/freesurfer_alpha/lib/images/ |
#: 999 Sz: 120 |
4/10/2001 2:07:13 PM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_expand_y.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1000 Sz: 119 |
4/10/2001 2:07:14 PM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_left.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1001 Sz: 143 |
4/10/2001 2:07:14 PM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_right.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1002 Sz: 143 |
4/10/2001 2:07:15 PM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_rot_x_neg.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1003 Sz: 979 |
5/31/2001 10:05:40 AM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_rot_x_pos.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1004 Sz: 970 |
5/31/2001 10:05:40 AM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_rot_y_neg.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1005 Sz: 958 |
5/31/2001 10:05:42 AM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_rot_y_pos.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1006 Sz: 956 |
5/31/2001 10:05:44 AM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_rot_z_neg /binfs/freesurfer_alpha/lib/images/ |
#: 1007 Sz: 142 |
5/31/2001 10:01:05 AM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_rot_z_neg.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1008 Sz: 957 |
5/31/2001 10:05:45 AM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_rot_z_pos.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1009 Sz: 956 |
5/31/2001 10:05:48 AM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_shrink_x.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1010 Sz: 119 |
4/10/2001 2:07:17 PM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_shrink_y.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1011 Sz: 119 |
4/10/2001 2:07:17 PM | GIF image data, version 89a, 24 x 24 |
|
icon_arrow_up.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1012 Sz: 142 |
4/10/2001 2:07:18 PM | GIF image data, version 89a, 24 x 24 |
|
icon_aux_volume.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1013 Sz: 186 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_brush_3d.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1014 Sz: 730 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_brush_circle.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1015 Sz: 696 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_brush_square.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1016 Sz: 693 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_control_point.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1017 Sz: 104 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_cursor_goto.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1018 Sz: 942 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_cursor_save.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1019 Sz: 936 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_cut_area.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1020 Sz: 155 |
4/10/2001 2:07:10 PM | GIF image data, version 89a, 24 x 24 |
|
icon_cut_clear.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1021 Sz: 117 |
4/10/2001 2:07:10 PM | GIF image data, version 89a, 24 x 24 |
|
icon_cut_closed_line.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1022 Sz: 167 |
4/10/2001 2:07:11 PM | GIF image data, version 89a, 24 x 24 |
|
icon_cut_line.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1023 Sz: 154 |
4/10/2001 2:07:11 PM | GIF image data, version 89a, 24 x 24 |
|
icon_cut_plane.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1024 Sz: 178 |
4/10/2001 2:07:12 PM | GIF image data, version 89a, 24 x 24 |
|
icon_disk.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1025 Sz: 143 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_disk.xjt /binfs/freesurfer_alpha/lib/images/ |
#: 1026 Sz: 10240 |
12/18/2000 3:27:07 PM | GNU tar archive |
|
icon_edit_ctrlpts.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1027 Sz: 970 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_edit_custom.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1028 Sz: 723 |
11/3/2000 1:12:14 PM | GIF image data, version 89a, 24 x 24 |
|
icon_edit_label.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1029 Sz: 991 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_edit_parc.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1030 Sz: 995 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_edit_volume.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1031 Sz: 987 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_folder.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1032 Sz: 146 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_folder.xjt /binfs/freesurfer_alpha/lib/images/ |
#: 1033 Sz: 10240 |
12/18/2000 3:27:07 PM | GNU tar archive |
|
icon_home.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1034 Sz: 176 |
7/9/2001 1:51:28 PM | GIF image data, version 89a, 24 x 24 |
|
icon_linked_cursors.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1035 Sz: 141 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_main_volume.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1036 Sz: 192 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_marker_crosshair.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1037 Sz: 113 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_marker_diamond.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1038 Sz: 123 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_navigate.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1039 Sz: 506 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_orientation_coronal.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1040 Sz: 103 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_orientation_horizontal.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1041 Sz: 137 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_orientation_sagittal.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1042 Sz: 107 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_redraw.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1043 Sz: 275 |
6/8/2001 1:02:50 PM | GIF image data, version 87a, 24 x 24 |
|
icon_snapshot_load.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1044 Sz: 976 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_snapshot_save.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1045 Sz: 971 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_stopwatch.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1046 Sz: 171 |
2/9/2001 1:07:01 PM | GIF image data, version 89a, 24 x 24 |
|
icon_surface_main.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1047 Sz: 987 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_surface_original.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1048 Sz: 985 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_surface_pial.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1049 Sz: 985 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_view_mosaic.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1050 Sz: 132 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_view_multiple.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1051 Sz: 138 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_view_single.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1052 Sz: 135 |
12/18/2000 3:27:07 PM | GIF image data, version 89a, 24 x 24 |
|
icon_zoom_in.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1053 Sz: 168 |
4/10/2001 2:07:18 PM | GIF image data, version 89a, 24 x 24 |
|
icon_zoom_out.gif /binfs/freesurfer_alpha/lib/images/ |
#: 1054 Sz: 163 |
4/10/2001 2:07:19 PM | GIF image data, version 89a, 24 x 24 |
| /binfs/freesurfer_alpha/lib/tcl/ | |||
|
#tkm_functional.tcl# /binfs/freesurfer_alpha/lib/tcl/ |
#: 1055 Sz: 29963 |
4/25/2001 8:55:12 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
check_func_ras_coords.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1056 Sz: 122 |
9/24/2001 7:11:21 AM | ASCII text |
|
curv-flat.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1057 Sz: 1779 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # surfer script: curv-flat [display curvature on flat] ############################################################################## #### file defaults: can resent in csh script with setenv |
|||
|
curv-views.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1058 Sz: 1537 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # surfer script: curv-views [display curvature on requested views] ############################################################################## #### file defaults: can reset in csh script with setenv |
|||
|
dara_data.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1059 Sz: 256 |
9/24/2001 7:11:21 AM | ASCII text |
|
dipmovie-flat.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1060 Sz: 2968 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # tksurfer script: dipmovie-flat [render dipole estimates on flat surface] ############################################################################# # #### file defaults: can reset in csh script with setenv |
|||
|
eccen-flat.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1061 Sz: 3073 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # tksurfer script: eccen-flat [read,smooth,disp phase-encoded data 2D patch] ############################################################################# #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/DALE0308/08798 #### files defaults: can reset in csh script with setenv |
|||
|
eccen-views.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1062 Sz: 3011 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # surfer script: eccen-views [disp phase-encoded data on 3D folded/unfolded] ############################################################################## #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/DALE0308/08798 #### files defaults: can reset in csh script with setenv |
|||
|
fs-flat.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1063 Sz: 2746 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################## # surfer script: fs-flat [display fieldsign on patch] ############################################################################## #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/DALE0308/08798 #### file defaults: can reset in csh script with setenv |
|||
|
fs-make.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1064 Sz: 3763 |
6/22/2000 11:55:48 AM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################## # surfer script: fs-make [calc,write fieldsign using patch--optional disp] ############################################################################## #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/DALE0308/08798 #### set default surface-related files (here for reference) #setfile curv ~/surf/$hemi.curv #setfile patch ~/surf/$hemi.patch #setfile fs */fs/$hemi.fs #setfile fm */fs/$hemi.fm #### file defaults: can reset in csh script with setenv |
|||
|
fs-views.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1065 Sz: 2409 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################## # surfer script: fs-views [read fieldsign, display on folded/unfolded] ############################################################################## #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/DALE0308/08798 #### file defaults: can reset in csh script with setenv |
|||
|
offsetmovie.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1066 Sz: 1156 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################## # surfer script: offsetmovie [save offset movie; interactive or batch] ############################################################################## #### defaults |
|||
|
phasemovie.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1067 Sz: 2821 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # surfer script: phasemovie.tcl [save phase movie; interactive or batch] ############################################################################## #### defaults |
|||
|
polar-flat.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1068 Sz: 3336 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # tksurfer script: polar-flat [read,smooth,disp phase-encoded data 2D patch] ############################################################################# #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/DALE0308/08798 ;# data rootdir usually autoset to $cwd/.. #### file defaults: can reset in csh script with setenv |
|||
|
polar-views.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1069 Sz: 3074 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # surfer script: polar-views [disp phase-encoded data on 3D folded/unfolded] ############################################################################## #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/DALE0308/08798 ;# data rootdir usually autoset to $cwd/.. #### file defaults: can reset in csh script with setenv #set dir 004/image7 ;# usually set in calling script setenv |
|||
|
readenv.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1070 Sz: 1729 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ########################################################################### # read names/values of non-cap setenv vars to override default parms # in csh scripts: # global: setenv parm value # singlerun: setenv $rgbname.parm value # NOTE: # setenv (but not set!) can set varname longer than 20char csh limit # tcl (but not csh!) can read such over-20-char-long env vars # set,setenv (but not tcl set!) create empty var w/o arg (tcl returns err!) ########################################################################### ### first read lower-case global env vars |
|||
|
real-flat.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1071 Sz: 2304 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ################################################################## # tksurfer script: real-flat [read,smooth,disp real data 2D patch] ################################################################## #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/DALE0308/08798 #### file defaults: can reset in csh script with setenv |
|||
|
real-views.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1072 Sz: 2052 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################## # tksurfer script: real-views [disp two-condition data on 3D folded/unfolded] ############################################################################## #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/DALE0308/08798 #### file defaults: can reset in csh script with setenv |
|||
|
saveflat.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1073 Sz: 1207 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # called by flat scripts: saveflat [save flat image, construct filename] ############################################################################## #### make infix for patch rgb name |
|||
|
saveviews.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1074 Sz: 3910 |
6/4/2000 5:59:22 AM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4
#############################################################################
# called by views scripts: saveviews [save requested subset of views]
##############################################################################
#### setenv some subset of: {lat,med,ven,pos,dor,all or custom<transform>}
#### maybe just print defaults
|
|||
|
saveviews.tcl.old /binfs/freesurfer_alpha/lib/tcl/ |
#: 1075 Sz: 3874 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4
#############################################################################
# called by views scripts: saveviews [save requested subset of views]
##############################################################################
#### setenv some subset of: {lat,med,ven,pos,dor,all or custom<transform>}
#### maybe just print defaults
|
|||
|
setdefpatchview.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1076 Sz: 2652 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # tksurfer script: setdefpatchview ############################################################################# # before readenv (just check for patchname; don't blow away aliased patchname) |
|||
|
solmovie-flat.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1077 Sz: 3917 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # tksurfer script: solmovie-flat [render dipole estimates on flat surface] ############################################################################# # NOTE: just setenv inpatch for nomid #setenv flat ;# savergb flag, like med,ven,.. flags in saveviews #setenv flatzrot 105 ;# (nomidzrot still recognized) #setenv flatscale 1.2 #setenv patchname patch-nomid.1000 ;# explicit here (else: patch) #### file defaults: can reset in csh script with setenv |
|||
|
test.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1078 Sz: 192 |
6/28/2001 8:41:17 AM | ASCII text |
|
test.tcl.010601 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1079 Sz: 209 |
6/1/2001 5:40:56 PM | ASCII text |
|
test.tcl.010628 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1080 Sz: 192 |
6/28/2001 8:41:17 AM | ASCII text |
|
testgca.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1081 Sz: 28 |
4/25/2001 9:36:42 AM | ASCII text |
|
tkanalyse.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1082 Sz: 17449 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################ # Copyright (c) 1996 Martin Sereno and Anders Dale ############################################################################ |
|||
|
tkm_common.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1083 Sz: 549 |
6/28/2001 8:41:17 AM | ASCII text |
|
tkm_common.tcl.010503 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1084 Sz: 549 |
5/3/2001 9:41:15 AM | ASCII text |
|
tkm_common.tcl.010515 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1085 Sz: 549 |
5/15/2001 1:23:30 PM | ASCII text |
|
tkm_common.tcl.010516 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1086 Sz: 549 |
5/16/2001 8:33:46 AM | ASCII text |
|
tkm_common.tcl.010601 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1087 Sz: 549 |
6/1/2001 5:40:56 PM | ASCII text |
|
tkm_common.tcl.010628 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1088 Sz: 549 |
6/28/2001 8:41:17 AM | ASCII text |
|
tkm_dialog.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1089 Sz: 970 |
11/21/2000 1:15:16 PM | ASCII text |
|
tkm_functional.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1090 Sz: 31591 |
9/24/2001 7:11:21 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkm_functional.tcl.010503 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1091 Sz: 29914 |
5/3/2001 9:41:15 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkm_functional.tcl.010515 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1092 Sz: 29914 |
5/15/2001 1:23:30 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkm_functional.tcl.010516 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1093 Sz: 30637 |
5/16/2001 8:33:46 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkm_functional.tcl.010601 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1094 Sz: 30637 |
6/1/2001 5:40:56 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkm_functional.tcl.010628 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1095 Sz: 31538 |
6/28/2001 8:41:17 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkm_functional.tcl.010924 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1096 Sz: 31591 |
9/24/2001 7:11:21 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkm_functional.tcl~ /binfs/freesurfer_alpha/lib/tcl/ |
#: 1097 Sz: 29963 |
4/25/2001 8:29:19 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkm_graph.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1098 Sz: 2195 |
2/14/2001 2:19:59 PM | ASCII text |
|
tkm_wrappers.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1099 Sz: 35981 |
9/24/2001 7:11:21 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish
# tkm_MakeBigLabel fwFrame "Label Text"
# tkm_MakeSmallLabel fwFrame "Label Text"
# tkm_MakeNormalLabel fwFrame "Label Text"
# tkm_MakeActiveLabel fwFrame "Left Text" variable [width]
# tkm_MakeCheckboxes fwFrame direction=x|y {checkbox...}
# checkbox = { text "Label" variable {function} ["Tool tip"] }
# checkbox = { image image_name variable {function} ["Tool tip"] }
# tkm_MakeRadioButtons fwFrame direction=x|y "Frame Title" variable {radio button...}
# radio button = { text label value cmd tooltip }
# radio button = { image image_name value cmd tooltip }
# tkm_MakeRadioButton fwFrame "Label Text" variable value [{function}]
# tkm_MakeToolbar fwFrame 0|1=radio variable {function} {button...}
# button = { text name "Label" ["Tool tip"] }
# button = { bitmap name image_name ["Tool tip"] }
# tkm_MakeEntry fwFrame "Left Text" variable [width] [{function}]
# tkm_MakeButtons fwFrame {button...}
# button = { text "Label" {function} "Tool tip" }
# button = { image image_name {function} "Tool tip" }
# tkm_MakeMenu isMenuButton "Menu Name" {item...}
# item = { command "Item Name" command [group_name] }
# item = { radio "Item Name" command variable value [group_name] }
# item = { check "Item Name" command variable [group_name] }
# item = { cascade "Item Name" {item...} [group_name] }
# item = { separator }
# tkm_SetMenuItemGroupStatus group_name 0|1
# tkm_MakeEntryWithIncDecButtons fwFrame "Label" variable {function} step
# tkm_MakeSlider fwFrame {"Left text" "Right text"} variable
# min max length {function} 1|0=include_entry [resolution]
# [horizontal|vertical]
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length
# {function} 1|0=include_entry [resolution] [horizontal|vertical] }
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length {function]
# include_entry=1|0 [resolution] }
# tkm_DoFileDlog { [option arg option arg...] }
# -title string: the title of the dlog box
# -prompt[1..5] string: the prompt for the nth file
# -type[1..5] file|dir: the type of selector (file by default)
# -note[1..5] string: a note to place under the prompt
# -okCmd string: command to execute when okay button is hit.
# %s[1..5] is replaced with the file name entered.
# -cancelCmd string: command to execute when cancel button is hit
# tkm_MakeCancelApplyOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeCloseButton fwFrame wwDlog [{close_function}]
# tkm_MakeApplyCloseButtons fwFrame wwDlog {apply_function} [{close_function}]
# tkm_MakeCancelOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeFileSelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateFileSelectorVariable fwFrame
# tkm_MakeDirectorySelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateDirectorySelectorVariable fwFrame
|
|||
|
tkm_wrappers.tcl.010503 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1100 Sz: 34687 |
5/3/2001 9:41:16 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish
# tkm_MakeBigLabel fwFrame "Label Text"
# tkm_MakeSmallLabel fwFrame "Label Text"
# tkm_MakeNormalLabel fwFrame "Label Text"
# tkm_MakeActiveLabel fwFrame "Left Text" variable [width]
# tkm_MakeCheckboxes fwFrame direction=x|y {checkbox...}
# checkbox = { text "Label" variable {function} ["Tool tip"] }
# checkbox = { image image_name variable {function} ["Tool tip"] }
# tkm_MakeRadioButtons fwFrame direction=x|y "Frame Title" variable {radio button...}
# radio button = { text label value cmd tooltip }
# radio button = { image image_name value cmd tooltip }
# tkm_MakeRadioButton fwFrame "Label Text" variable value [{function}]
# tkm_MakeToolbar fwFrame 0|1=radio variable {function} {button...}
# button = { text name "Label" ["Tool tip"] }
# button = { bitmap name image_name ["Tool tip"] }
# tkm_MakeEntry fwFrame "Left Text" variable [width] [{function}]
# tkm_MakeButtons fwFrame {button...}
# button = { text "Label" {function} "Tool tip" }
# button = { image image_name {function} "Tool tip" }
# tkm_MakeMenu isMenuButton "Menu Name" {item...}
# item = { command "Item Name" command [group_name] }
# item = { radio "Item Name" command variable value [group_name] }
# item = { check "Item Name" command variable [group_name] }
# item = { cascade "Item Name" {item...} [group_name] }
# item = { separator }
# tkm_SetMenuItemGroupStatus group_name 0|1
# tkm_MakeEntryWithIncDecButtons fwFrame "Label" variable {function} step
# tkm_MakeSlider fwFrame {"Left text" "Right text"} variable
# min max length {function} 1|0=include_entry [resolution]
# [horizontal|vertical]
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length
# {function} 1|0=include_entry [resolution] [horizontal|vertical] }
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length {function]
# include_entry=1|0 [resolution] }
# tkm_DoFileDlog { [option arg option arg...] }
# -title string: the title of the dlog box
# -prompt[1..5] string: the prompt for the nth file
# -type[1..5] file|dir: the type of selector (file by default)
# -note[1..5] string: a note to place under the prompt
# -okCmd string: command to execute when okay button is hit.
# %s[1..5] is replaced with the file name entered.
# -cancelCmd string: command to execute when cancel button is hit
# tkm_MakeCancelApplyOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeCloseButton fwFrame wwDlog [{close_function}]
# tkm_MakeApplyCloseButtons fwFrame wwDlog {apply_function} [{close_function}]
# tkm_MakeCancelOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeFileSelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateFileSelectorVariable fwFrame
# tkm_MakeDirectorySelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateDirectorySelectorVariable fwFrame
|
|||
|
tkm_wrappers.tcl.010515 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1101 Sz: 34690 |
5/15/2001 1:23:30 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish
# tkm_MakeBigLabel fwFrame "Label Text"
# tkm_MakeSmallLabel fwFrame "Label Text"
# tkm_MakeNormalLabel fwFrame "Label Text"
# tkm_MakeActiveLabel fwFrame "Left Text" variable [width]
# tkm_MakeCheckboxes fwFrame direction=x|y {checkbox...}
# checkbox = { text "Label" variable {function} ["Tool tip"] }
# checkbox = { image image_name variable {function} ["Tool tip"] }
# tkm_MakeRadioButtons fwFrame direction=x|y "Frame Title" variable {radio button...}
# radio button = { text label value cmd tooltip }
# radio button = { image image_name value cmd tooltip }
# tkm_MakeRadioButton fwFrame "Label Text" variable value [{function}]
# tkm_MakeToolbar fwFrame 0|1=radio variable {function} {button...}
# button = { text name "Label" ["Tool tip"] }
# button = { bitmap name image_name ["Tool tip"] }
# tkm_MakeEntry fwFrame "Left Text" variable [width] [{function}]
# tkm_MakeButtons fwFrame {button...}
# button = { text "Label" {function} "Tool tip" }
# button = { image image_name {function} "Tool tip" }
# tkm_MakeMenu isMenuButton "Menu Name" {item...}
# item = { command "Item Name" command [group_name] }
# item = { radio "Item Name" command variable value [group_name] }
# item = { check "Item Name" command variable [group_name] }
# item = { cascade "Item Name" {item...} [group_name] }
# item = { separator }
# tkm_SetMenuItemGroupStatus group_name 0|1
# tkm_MakeEntryWithIncDecButtons fwFrame "Label" variable {function} step
# tkm_MakeSlider fwFrame {"Left text" "Right text"} variable
# min max length {function} 1|0=include_entry [resolution]
# [horizontal|vertical]
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length
# {function} 1|0=include_entry [resolution] [horizontal|vertical] }
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length {function]
# include_entry=1|0 [resolution] }
# tkm_DoFileDlog { [option arg option arg...] }
# -title string: the title of the dlog box
# -prompt[1..5] string: the prompt for the nth file
# -type[1..5] file|dir: the type of selector (file by default)
# -note[1..5] string: a note to place under the prompt
# -okCmd string: command to execute when okay button is hit.
# %s[1..5] is replaced with the file name entered.
# -cancelCmd string: command to execute when cancel button is hit
# tkm_MakeCancelApplyOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeCloseButton fwFrame wwDlog [{close_function}]
# tkm_MakeApplyCloseButtons fwFrame wwDlog {apply_function} [{close_function}]
# tkm_MakeCancelOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeFileSelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateFileSelectorVariable fwFrame
# tkm_MakeDirectorySelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateDirectorySelectorVariable fwFrame
|
|||
|
tkm_wrappers.tcl.010516 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1102 Sz: 34687 |
5/16/2001 8:33:46 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish
# tkm_MakeBigLabel fwFrame "Label Text"
# tkm_MakeSmallLabel fwFrame "Label Text"
# tkm_MakeNormalLabel fwFrame "Label Text"
# tkm_MakeActiveLabel fwFrame "Left Text" variable [width]
# tkm_MakeCheckboxes fwFrame direction=x|y {checkbox...}
# checkbox = { text "Label" variable {function} ["Tool tip"] }
# checkbox = { image image_name variable {function} ["Tool tip"] }
# tkm_MakeRadioButtons fwFrame direction=x|y "Frame Title" variable {radio button...}
# radio button = { text label value cmd tooltip }
# radio button = { image image_name value cmd tooltip }
# tkm_MakeRadioButton fwFrame "Label Text" variable value [{function}]
# tkm_MakeToolbar fwFrame 0|1=radio variable {function} {button...}
# button = { text name "Label" ["Tool tip"] }
# button = { bitmap name image_name ["Tool tip"] }
# tkm_MakeEntry fwFrame "Left Text" variable [width] [{function}]
# tkm_MakeButtons fwFrame {button...}
# button = { text "Label" {function} "Tool tip" }
# button = { image image_name {function} "Tool tip" }
# tkm_MakeMenu isMenuButton "Menu Name" {item...}
# item = { command "Item Name" command [group_name] }
# item = { radio "Item Name" command variable value [group_name] }
# item = { check "Item Name" command variable [group_name] }
# item = { cascade "Item Name" {item...} [group_name] }
# item = { separator }
# tkm_SetMenuItemGroupStatus group_name 0|1
# tkm_MakeEntryWithIncDecButtons fwFrame "Label" variable {function} step
# tkm_MakeSlider fwFrame {"Left text" "Right text"} variable
# min max length {function} 1|0=include_entry [resolution]
# [horizontal|vertical]
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length
# {function} 1|0=include_entry [resolution] [horizontal|vertical] }
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length {function]
# include_entry=1|0 [resolution] }
# tkm_DoFileDlog { [option arg option arg...] }
# -title string: the title of the dlog box
# -prompt[1..5] string: the prompt for the nth file
# -type[1..5] file|dir: the type of selector (file by default)
# -note[1..5] string: a note to place under the prompt
# -okCmd string: command to execute when okay button is hit.
# %s[1..5] is replaced with the file name entered.
# -cancelCmd string: command to execute when cancel button is hit
# tkm_MakeCancelApplyOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeCloseButton fwFrame wwDlog [{close_function}]
# tkm_MakeApplyCloseButtons fwFrame wwDlog {apply_function} [{close_function}]
# tkm_MakeCancelOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeFileSelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateFileSelectorVariable fwFrame
# tkm_MakeDirectorySelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateDirectorySelectorVariable fwFrame
|
|||
|
tkm_wrappers.tcl.010601 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1103 Sz: 34689 |
6/1/2001 5:40:57 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish
# tkm_MakeBigLabel fwFrame "Label Text"
# tkm_MakeSmallLabel fwFrame "Label Text"
# tkm_MakeNormalLabel fwFrame "Label Text"
# tkm_MakeActiveLabel fwFrame "Left Text" variable [width]
# tkm_MakeCheckboxes fwFrame direction=x|y {checkbox...}
# checkbox = { text "Label" variable {function} ["Tool tip"] }
# checkbox = { image image_name variable {function} ["Tool tip"] }
# tkm_MakeRadioButtons fwFrame direction=x|y "Frame Title" variable {radio button...}
# radio button = { text label value cmd tooltip }
# radio button = { image image_name value cmd tooltip }
# tkm_MakeRadioButton fwFrame "Label Text" variable value [{function}]
# tkm_MakeToolbar fwFrame 0|1=radio variable {function} {button...}
# button = { text name "Label" ["Tool tip"] }
# button = { bitmap name image_name ["Tool tip"] }
# tkm_MakeEntry fwFrame "Left Text" variable [width] [{function}]
# tkm_MakeButtons fwFrame {button...}
# button = { text "Label" {function} "Tool tip" }
# button = { image image_name {function} "Tool tip" }
# tkm_MakeMenu isMenuButton "Menu Name" {item...}
# item = { command "Item Name" command [group_name] }
# item = { radio "Item Name" command variable value [group_name] }
# item = { check "Item Name" command variable [group_name] }
# item = { cascade "Item Name" {item...} [group_name] }
# item = { separator }
# tkm_SetMenuItemGroupStatus group_name 0|1
# tkm_MakeEntryWithIncDecButtons fwFrame "Label" variable {function} step
# tkm_MakeSlider fwFrame {"Left text" "Right text"} variable
# min max length {function} 1|0=include_entry [resolution]
# [horizontal|vertical]
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length
# {function} 1|0=include_entry [resolution] [horizontal|vertical] }
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length {function]
# include_entry=1|0 [resolution] }
# tkm_DoFileDlog { [option arg option arg...] }
# -title string: the title of the dlog box
# -prompt[1..5] string: the prompt for the nth file
# -type[1..5] file|dir: the type of selector (file by default)
# -note[1..5] string: a note to place under the prompt
# -okCmd string: command to execute when okay button is hit.
# %s[1..5] is replaced with the file name entered.
# -cancelCmd string: command to execute when cancel button is hit
# tkm_MakeCancelApplyOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeCloseButton fwFrame wwDlog [{close_function}]
# tkm_MakeApplyCloseButtons fwFrame wwDlog {apply_function} [{close_function}]
# tkm_MakeCancelOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeFileSelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateFileSelectorVariable fwFrame
# tkm_MakeDirectorySelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateDirectorySelectorVariable fwFrame
|
|||
|
tkm_wrappers.tcl.010628 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1104 Sz: 34690 |
6/28/2001 8:41:18 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish
# tkm_MakeBigLabel fwFrame "Label Text"
# tkm_MakeSmallLabel fwFrame "Label Text"
# tkm_MakeNormalLabel fwFrame "Label Text"
# tkm_MakeActiveLabel fwFrame "Left Text" variable [width]
# tkm_MakeCheckboxes fwFrame direction=x|y {checkbox...}
# checkbox = { text "Label" variable {function} ["Tool tip"] }
# checkbox = { image image_name variable {function} ["Tool tip"] }
# tkm_MakeRadioButtons fwFrame direction=x|y "Frame Title" variable {radio button...}
# radio button = { text label value cmd tooltip }
# radio button = { image image_name value cmd tooltip }
# tkm_MakeRadioButton fwFrame "Label Text" variable value [{function}]
# tkm_MakeToolbar fwFrame 0|1=radio variable {function} {button...}
# button = { text name "Label" ["Tool tip"] }
# button = { bitmap name image_name ["Tool tip"] }
# tkm_MakeEntry fwFrame "Left Text" variable [width] [{function}]
# tkm_MakeButtons fwFrame {button...}
# button = { text "Label" {function} "Tool tip" }
# button = { image image_name {function} "Tool tip" }
# tkm_MakeMenu isMenuButton "Menu Name" {item...}
# item = { command "Item Name" command [group_name] }
# item = { radio "Item Name" command variable value [group_name] }
# item = { check "Item Name" command variable [group_name] }
# item = { cascade "Item Name" {item...} [group_name] }
# item = { separator }
# tkm_SetMenuItemGroupStatus group_name 0|1
# tkm_MakeEntryWithIncDecButtons fwFrame "Label" variable {function} step
# tkm_MakeSlider fwFrame {"Left text" "Right text"} variable
# min max length {function} 1|0=include_entry [resolution]
# [horizontal|vertical]
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length
# {function} 1|0=include_entry [resolution] [horizontal|vertical] }
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length {function]
# include_entry=1|0 [resolution] }
# tkm_DoFileDlog { [option arg option arg...] }
# -title string: the title of the dlog box
# -prompt[1..5] string: the prompt for the nth file
# -type[1..5] file|dir: the type of selector (file by default)
# -note[1..5] string: a note to place under the prompt
# -okCmd string: command to execute when okay button is hit.
# %s[1..5] is replaced with the file name entered.
# -cancelCmd string: command to execute when cancel button is hit
# tkm_MakeCancelApplyOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeCloseButton fwFrame wwDlog [{close_function}]
# tkm_MakeApplyCloseButtons fwFrame wwDlog {apply_function} [{close_function}]
# tkm_MakeCancelOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeFileSelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateFileSelectorVariable fwFrame
# tkm_MakeDirectorySelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateDirectorySelectorVariable fwFrame
|
|||
|
tkm_wrappers.tcl.010827 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1105 Sz: 34833 |
8/27/2001 2:41:00 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish
# tkm_MakeBigLabel fwFrame "Label Text"
# tkm_MakeSmallLabel fwFrame "Label Text"
# tkm_MakeNormalLabel fwFrame "Label Text"
# tkm_MakeActiveLabel fwFrame "Left Text" variable [width]
# tkm_MakeCheckboxes fwFrame direction=x|y {checkbox...}
# checkbox = { text "Label" variable {function} ["Tool tip"] }
# checkbox = { image image_name variable {function} ["Tool tip"] }
# tkm_MakeRadioButtons fwFrame direction=x|y "Frame Title" variable {radio button...}
# radio button = { text label value cmd tooltip }
# radio button = { image image_name value cmd tooltip }
# tkm_MakeRadioButton fwFrame "Label Text" variable value [{function}]
# tkm_MakeToolbar fwFrame 0|1=radio variable {function} {button...}
# button = { text name "Label" ["Tool tip"] }
# button = { bitmap name image_name ["Tool tip"] }
# tkm_MakeEntry fwFrame "Left Text" variable [width] [{function}]
# tkm_MakeButtons fwFrame {button...}
# button = { text "Label" {function} "Tool tip" }
# button = { image image_name {function} "Tool tip" }
# tkm_MakeMenu isMenuButton "Menu Name" {item...}
# item = { command "Item Name" command [group_name] }
# item = { radio "Item Name" command variable value [group_name] }
# item = { check "Item Name" command variable [group_name] }
# item = { cascade "Item Name" {item...} [group_name] }
# item = { separator }
# tkm_SetMenuItemGroupStatus group_name 0|1
# tkm_MakeEntryWithIncDecButtons fwFrame "Label" variable {function} step
# tkm_MakeSlider fwFrame {"Left text" "Right text"} variable
# min max length {function} 1|0=include_entry [resolution]
# [horizontal|vertical]
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length
# {function} 1|0=include_entry [resolution] [horizontal|vertical] }
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length {function]
# include_entry=1|0 [resolution] }
# tkm_DoFileDlog { [option arg option arg...] }
# -title string: the title of the dlog box
# -prompt[1..5] string: the prompt for the nth file
# -type[1..5] file|dir: the type of selector (file by default)
# -note[1..5] string: a note to place under the prompt
# -okCmd string: command to execute when okay button is hit.
# %s[1..5] is replaced with the file name entered.
# -cancelCmd string: command to execute when cancel button is hit
# tkm_MakeCancelApplyOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeCloseButton fwFrame wwDlog [{close_function}]
# tkm_MakeApplyCloseButtons fwFrame wwDlog {apply_function} [{close_function}]
# tkm_MakeCancelOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeFileSelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateFileSelectorVariable fwFrame
# tkm_MakeDirectorySelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateDirectorySelectorVariable fwFrame
|
|||
|
tkm_wrappers.tcl.010828 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1106 Sz: 34833 |
8/28/2001 9:21:13 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish
# tkm_MakeBigLabel fwFrame "Label Text"
# tkm_MakeSmallLabel fwFrame "Label Text"
# tkm_MakeNormalLabel fwFrame "Label Text"
# tkm_MakeActiveLabel fwFrame "Left Text" variable [width]
# tkm_MakeCheckboxes fwFrame direction=x|y {checkbox...}
# checkbox = { text "Label" variable {function} ["Tool tip"] }
# checkbox = { image image_name variable {function} ["Tool tip"] }
# tkm_MakeRadioButtons fwFrame direction=x|y "Frame Title" variable {radio button...}
# radio button = { text label value cmd tooltip }
# radio button = { image image_name value cmd tooltip }
# tkm_MakeRadioButton fwFrame "Label Text" variable value [{function}]
# tkm_MakeToolbar fwFrame 0|1=radio variable {function} {button...}
# button = { text name "Label" ["Tool tip"] }
# button = { bitmap name image_name ["Tool tip"] }
# tkm_MakeEntry fwFrame "Left Text" variable [width] [{function}]
# tkm_MakeButtons fwFrame {button...}
# button = { text "Label" {function} "Tool tip" }
# button = { image image_name {function} "Tool tip" }
# tkm_MakeMenu isMenuButton "Menu Name" {item...}
# item = { command "Item Name" command [group_name] }
# item = { radio "Item Name" command variable value [group_name] }
# item = { check "Item Name" command variable [group_name] }
# item = { cascade "Item Name" {item...} [group_name] }
# item = { separator }
# tkm_SetMenuItemGroupStatus group_name 0|1
# tkm_MakeEntryWithIncDecButtons fwFrame "Label" variable {function} step
# tkm_MakeSlider fwFrame {"Left text" "Right text"} variable
# min max length {function} 1|0=include_entry [resolution]
# [horizontal|vertical]
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length
# {function} 1|0=include_entry [resolution] [horizontal|vertical] }
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length {function]
# include_entry=1|0 [resolution] }
# tkm_DoFileDlog { [option arg option arg...] }
# -title string: the title of the dlog box
# -prompt[1..5] string: the prompt for the nth file
# -type[1..5] file|dir: the type of selector (file by default)
# -note[1..5] string: a note to place under the prompt
# -okCmd string: command to execute when okay button is hit.
# %s[1..5] is replaced with the file name entered.
# -cancelCmd string: command to execute when cancel button is hit
# tkm_MakeCancelApplyOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeCloseButton fwFrame wwDlog [{close_function}]
# tkm_MakeApplyCloseButtons fwFrame wwDlog {apply_function} [{close_function}]
# tkm_MakeCancelOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeFileSelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateFileSelectorVariable fwFrame
# tkm_MakeDirectorySelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateDirectorySelectorVariable fwFrame
|
|||
|
tkm_wrappers.tcl.010924 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1107 Sz: 35981 |
9/24/2001 7:11:21 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish
# tkm_MakeBigLabel fwFrame "Label Text"
# tkm_MakeSmallLabel fwFrame "Label Text"
# tkm_MakeNormalLabel fwFrame "Label Text"
# tkm_MakeActiveLabel fwFrame "Left Text" variable [width]
# tkm_MakeCheckboxes fwFrame direction=x|y {checkbox...}
# checkbox = { text "Label" variable {function} ["Tool tip"] }
# checkbox = { image image_name variable {function} ["Tool tip"] }
# tkm_MakeRadioButtons fwFrame direction=x|y "Frame Title" variable {radio button...}
# radio button = { text label value cmd tooltip }
# radio button = { image image_name value cmd tooltip }
# tkm_MakeRadioButton fwFrame "Label Text" variable value [{function}]
# tkm_MakeToolbar fwFrame 0|1=radio variable {function} {button...}
# button = { text name "Label" ["Tool tip"] }
# button = { bitmap name image_name ["Tool tip"] }
# tkm_MakeEntry fwFrame "Left Text" variable [width] [{function}]
# tkm_MakeButtons fwFrame {button...}
# button = { text "Label" {function} "Tool tip" }
# button = { image image_name {function} "Tool tip" }
# tkm_MakeMenu isMenuButton "Menu Name" {item...}
# item = { command "Item Name" command [group_name] }
# item = { radio "Item Name" command variable value [group_name] }
# item = { check "Item Name" command variable [group_name] }
# item = { cascade "Item Name" {item...} [group_name] }
# item = { separator }
# tkm_SetMenuItemGroupStatus group_name 0|1
# tkm_MakeEntryWithIncDecButtons fwFrame "Label" variable {function} step
# tkm_MakeSlider fwFrame {"Left text" "Right text"} variable
# min max length {function} 1|0=include_entry [resolution]
# [horizontal|vertical]
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length
# {function} 1|0=include_entry [resolution] [horizontal|vertical] }
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length {function]
# include_entry=1|0 [resolution] }
# tkm_DoFileDlog { [option arg option arg...] }
# -title string: the title of the dlog box
# -prompt[1..5] string: the prompt for the nth file
# -type[1..5] file|dir: the type of selector (file by default)
# -note[1..5] string: a note to place under the prompt
# -okCmd string: command to execute when okay button is hit.
# %s[1..5] is replaced with the file name entered.
# -cancelCmd string: command to execute when cancel button is hit
# tkm_MakeCancelApplyOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeCloseButton fwFrame wwDlog [{close_function}]
# tkm_MakeApplyCloseButtons fwFrame wwDlog {apply_function} [{close_function}]
# tkm_MakeCancelOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeFileSelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateFileSelectorVariable fwFrame
# tkm_MakeDirectorySelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateDirectorySelectorVariable fwFrame
|
|||
|
tkm_wrappers.tcl~ /binfs/freesurfer_alpha/lib/tcl/ |
#: 1108 Sz: 34833 |
6/28/2001 8:41:18 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish
# tkm_MakeBigLabel fwFrame "Label Text"
# tkm_MakeSmallLabel fwFrame "Label Text"
# tkm_MakeNormalLabel fwFrame "Label Text"
# tkm_MakeActiveLabel fwFrame "Left Text" variable [width]
# tkm_MakeCheckboxes fwFrame direction=x|y {checkbox...}
# checkbox = { text "Label" variable {function} ["Tool tip"] }
# checkbox = { image image_name variable {function} ["Tool tip"] }
# tkm_MakeRadioButtons fwFrame direction=x|y "Frame Title" variable {radio button...}
# radio button = { text label value cmd tooltip }
# radio button = { image image_name value cmd tooltip }
# tkm_MakeRadioButton fwFrame "Label Text" variable value [{function}]
# tkm_MakeToolbar fwFrame 0|1=radio variable {function} {button...}
# button = { text name "Label" ["Tool tip"] }
# button = { bitmap name image_name ["Tool tip"] }
# tkm_MakeEntry fwFrame "Left Text" variable [width] [{function}]
# tkm_MakeButtons fwFrame {button...}
# button = { text "Label" {function} "Tool tip" }
# button = { image image_name {function} "Tool tip" }
# tkm_MakeMenu isMenuButton "Menu Name" {item...}
# item = { command "Item Name" command [group_name] }
# item = { radio "Item Name" command variable value [group_name] }
# item = { check "Item Name" command variable [group_name] }
# item = { cascade "Item Name" {item...} [group_name] }
# item = { separator }
# tkm_SetMenuItemGroupStatus group_name 0|1
# tkm_MakeEntryWithIncDecButtons fwFrame "Label" variable {function} step
# tkm_MakeSlider fwFrame {"Left text" "Right text"} variable
# min max length {function} 1|0=include_entry [resolution]
# [horizontal|vertical]
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length
# {function} 1|0=include_entry [resolution] [horizontal|vertical] }
# tkm_MakeSliders fwFrame {slider...}
# slider = { {"Left text" "Right text"} variable min max length {function]
# include_entry=1|0 [resolution] }
# tkm_DoFileDlog { [option arg option arg...] }
# -title string: the title of the dlog box
# -prompt[1..5] string: the prompt for the nth file
# -type[1..5] file|dir: the type of selector (file by default)
# -note[1..5] string: a note to place under the prompt
# -okCmd string: command to execute when okay button is hit.
# %s[1..5] is replaced with the file name entered.
# -cancelCmd string: command to execute when cancel button is hit
# tkm_MakeCancelApplyOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeCloseButton fwFrame wwDlog [{close_function}]
# tkm_MakeApplyCloseButtons fwFrame wwDlog {apply_function} [{close_function}]
# tkm_MakeCancelOKButtons fwFrame wwDlog {ok_fuction} [{cancel_function}]
# tkm_MakeFileSelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateFileSelectorVariable fwFrame
# tkm_MakeDirectorySelector fwFrame "Prompt:" variable default_lcoation_func
# tkm_UpdateDirectorySelectorVariable fwFrame
|
|||
|
tkmedit.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1109 Sz: 87533 |
9/24/2001 7:11:21 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkmedit.tcl.010503 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1110 Sz: 78244 |
5/3/2001 9:41:16 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkmedit.tcl.010515 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1111 Sz: 80216 |
5/15/2001 1:23:31 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkmedit.tcl.010516 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1112 Sz: 79632 |
5/16/2001 8:33:47 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkmedit.tcl.010601 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1113 Sz: 79651 |
6/1/2001 5:40:57 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkmedit.tcl.010628 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1114 Sz: 81658 |
6/28/2001 8:41:18 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkmedit.tcl.010827 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1115 Sz: 87510 |
8/27/2001 2:41:00 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkmedit.tcl.010828 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1116 Sz: 87533 |
8/28/2001 9:21:14 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkmedit.tcl.010924 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1117 Sz: 87533 |
9/24/2001 7:11:21 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkmedit.tcl.old /binfs/freesurfer_alpha/lib/tcl/ |
#: 1118 Sz: 85100 |
8/22/2001 1:10:02 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkmedit.tcl~ /binfs/freesurfer_alpha/lib/tcl/ |
#: 1119 Sz: 74400 |
4/6/2001 11:55:57 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tkregister.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1120 Sz: 27415 |
6/7/2000 10:01:57 AM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################ # Copyright (c) 1996 Martin Sereno and Anders Dale ############################################################################ |
|||
|
tkregister.tcl.old /binfs/freesurfer_alpha/lib/tcl/ |
#: 1121 Sz: 24183 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################ # Copyright (c) 1996 Martin Sereno and Anders Dale ############################################################################ |
|||
|
tksurfer.new.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1122 Sz: 91839 |
10/1/2001 2:14:37 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tksurfer.new.tcl.010711 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1123 Sz: 86437 |
7/11/2001 11:48:39 AM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tksurfer.new.tcl.010716 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1124 Sz: 88341 |
7/16/2001 2:42:58 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tksurfer.new.tcl.010816 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1125 Sz: 88898 |
8/16/2001 1:19:31 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tksurfer.new.tcl.010828 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1126 Sz: 88898 |
8/28/2001 1:42:41 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tksurfer.new.tcl.010914 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1127 Sz: 91832 |
9/14/2001 1:10:22 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tksurfer.new.tcl.011001 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1128 Sz: 91834 |
10/1/2001 2:14:36 PM | a /usr/bin/tixwish script text executable |
#! /usr/bin/tixwish |
|||
|
tksurfer.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1129 Sz: 63590 |
8/28/2001 1:33:34 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################ # Copyright (c) 1999 CorTechs - All rights reserved ############################################################################ |
|||
|
tksurfer.tcl.010500 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1130 Sz: 55787 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################ # Copyright (c) 1999 CorTechs - All rights reserved ############################################################################ |
|||
|
tksurfer.tcl.120400 /binfs/freesurfer_alpha/lib/tcl/ |
#: 1131 Sz: 63625 |
12/4/2000 12:31:16 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################ # Copyright (c) 1999 CorTechs - All rights reserved ############################################################################ |
|||
|
tksurfer.tcl.old /binfs/freesurfer_alpha/lib/tcl/ |
#: 1132 Sz: 56887 |
6/7/2000 11:55:20 AM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################ # Copyright (c) 1999 CorTechs - All rights reserved ############################################################################ |
|||
|
twocond-flat.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1133 Sz: 3737 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################# # tksurfer script: twocond-flat [read,smooth,disp phase-encoded data 2D patch] ############################################################################# # NOTE: to get effect of nomid scripts #setenv flatzrot 105 ;# nomidzrot still recognized, too #setenv flatscale 1.2 #setenv patchname patch-nomid.1000 ;# else default patch #tksurfer -$name $hemi 1000a -tcl polar-flat.tcl #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/MARTY0928/10138 #### file defaults: can reset in csh script with setenv |
|||
|
twocond-masked-views.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1134 Sz: 146 |
10/12/2000 9:23:16 AM | ASCII text |
|
twocond-views.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1135 Sz: 3426 |
10/3/2000 10:15:05 AM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################## # surfer script: twocond-views [disp two-condition data on 3D folded/unfolded] ############################################################################## #### session dir autoset to $cwd/.. when cwd=scripts #setsession ~/fmri/MARTY0928/10138 #### file defaults: can reset in csh script with setenv |
|||
|
wrappers.tcl /binfs/freesurfer_alpha/lib/tcl/ |
#: 1136 Sz: 15360 |
6/4/2000 5:59:26 AM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################ # Copyright (c) 1996-1999 Martin Sereno and Anders Dale ############################################################################ ### standard widget wrappers |
|||
|
wrappers.tcl.old /binfs/freesurfer_alpha/lib/tcl/ |
#: 1137 Sz: 15626 |
4/5/2000 12:17:15 PM | a /usr/local/bin/tclsh7.4 script text executable |
#! /usr/local/bin/tclsh7.4 ############################################################################ # Copyright (c) 1996-1999 Martin Sereno and Anders Dale ############################################################################ ### standard widget wrappers |
|||
| /binfs/freesurfer_alpha/local/ Skipped directory per survey instructions | |||
| /binfs/freesurfer_alpha/sessions/ | |||
| /binfs/freesurfer_alpha/subjects/ Skipped directory per survey instructions | |||
| /binfs/freesurfer_alpha/talairach/ Skipped directory per survey instructions | |||
| /usr/pubsw/packages/mni/1.0.4/ | |||
| /usr/pubsw/packages/mni/1.0.4/bin/ | |||
|
ana2mnc /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1138 Sz: 5859 |
8/9/2001 8:22:16 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w # Script to convert analyze files to minc format |
|||
|
autocrop /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1139 Sz: 39092 |
8/9/2001 8:22:19 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w # autocrop - a program for extracting and manipulating the bounds of a # MINC volume, with the capability to output parameters for mincresample # or mincreshape, or a whole new (cropped) MINC volume. # -------------------------------------------------------------------- # Copyright (c) 1994-96 Greg Ward, McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. Permission to # use, copy, modify, and distribute this software and its # documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies. The # author and McGill University make no representations about the # suitability of this software for any purpose. It is provided "as # is" without express or implied warranty. # # Note that the programs mincinfo, mincreshape, and mincresample are # written & copyrighted by Peter Neelin, McConnell Brain Imaging # Centre, with the same copyright as above. # -------------------------------------------------------------------- # By Greg Ward 94/9/22 # $Id: autocrop.in,v 1.3 2000/01/30 18:15:35 stever Exp $ |
|||
|
change_volume_sampling.pl /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1140 Sz: 1498 |
8/9/2001 8:22:23 AM | Perl script |
#! /usr/pubsw/bin/perl -w |
|||
|
check_scale /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1141 Sz: 454044 |
11/21/2002 7:13:59 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: <input.xfm> <result.xfm> [<file.mnc>] |
|||
|
conglomerate /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1142 Sz: 2037616 |
11/21/2002 7:13:59 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Skipped per survey instructions. Probably a program that expects console input |
|||
|
Display /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1143 Sz: 2471556 |
11/21/2002 7:13:59 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Skipped per survey instructions. Probably a program that expects console input |
|||
|
evaluate_field /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1144 Sz: 1333112 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: Symbol `__vt_3ios' has different size in shared object, consider re-linking
: Symbol `__vt_7istream.3ios' has different size in shared object, consider re-linking
: Symbol `__vt_8ofstream.3ios' has different size in shared object, consider re-linking
: Symbol `__vt_7ostream.3ios' has different size in shared object, consider re-linking
: Symbol `__vt_8ifstream.3ios' has different size in shared object, consider re-linking
Command-specific options:
General options:
-clobber: Overwrite existing file.
-noclobber: Do not overwrite existing file (default).
-verbose: Print out log messages as processing is being done (default).
-quiet: Do not print out any log messages.
-version: Print out version info and exit.
Output options:
-like: Specify volume that field is to be like.
-mask: Specify region on which field is evaluated.
-byte: Write out byte data.
-short: Write out short integer data.
-long: Write out long integer data.
-float: Write out single-precision floating-point data.
-double: Write out double-precision floating-point data.
-signed: Write signed integer data.
-unsigned: Write unsigned integer data.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] -like <volume.mnc> <infile.fld> <outfile.mnc>
[-help]
|
|||
|
extracttag /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1145 Sz: 417124 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-verbose: Show progress
-clobber: Overwrite output file - if it exists.
-debug: Show debugging information, depending on level specified
Default value: 0
-volume: Generate a tag volume out of the qualifying tag points
-tag: Generate a tag file out of the qualifying tag points
-mintags: Set the minimum number of tag points to be chosen - threshold adjusted
Default value: 0
-maxtags: Set the max number of tag points to be chosen - zero for all
Default value: -1
-threshold: Set the threshold of selection criterion (probability level)
Default value: -1 -1
-top_thres: Set the upper threshold for minimum number of tagpoint selection
Default value: 1.001
-label: Specify the voxel label of the extracted tag points
-mask: Specify a mask volume, to limit seatch space.
-user_mask_value: Specify the mask value, used in the mask volume to limit search
Default value: 1
-world: Specify that the mask be traversed in world coordinate space.
-random: Specify that qualified tag points be traversed in random stepsizes.
-comment: Specify a comment to be included in the tag file.
-append: Append to an existing tagfile or tagvolume (thus clobbering).
-version: Print out version info and exit.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: <options> <prob_mask_filename>
[-help]
|
|||
|
field2imp /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1146 Sz: 6453 |
8/9/2001 8:22:26 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w #--------------------------------------------------------------------------- #@COPYRIGHT : # Copyright 1996, John G. Sled, # McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this # software and its documentation for any purpose and without # fee is hereby granted, provided that the above copyright # notice appear in all copies. The author and McGill University # make no representations about the suitability of this # software for any purpose. It is provided "as is" without # express or implied warranty. #---------------------------------------------------------------------------- #$RCSfile: field2imp.in,v $ #$Revision: 1.13 $ #$Author: jgsled $ #$Date: 1997/09/29 19:14:49 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header ---------------------------------- #@NAME : field2imp #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: create a compact representation of the given field #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : August 28, 1996 J.G.Sled #@MODIFIED : # $Id: field2imp.in,v 1.13 1997/09/29 19:14:49 jgsled Exp $ #----------------------------------------------------------------------------- |
|||
|
imp2field /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1147 Sz: 9302 |
8/9/2001 8:22:29 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w #--------------------------------------------------------------------------- #@COPYRIGHT : # Copyright 1996, John G. Sled, # McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this # software and its documentation for any purpose and without # fee is hereby granted, provided that the above copyright # notice appear in all copies. The author and McGill University # make no representations about the suitability of this # software for any purpose. It is provided "as is" without # express or implied warranty. #---------------------------------------------------------------------------- #$RCSfile: imp2field.in,v $ #$Revision: 1.13 $ #$Author: jgsled $ #$Date: 1997/09/29 19:14:50 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header ---------------------------------- #@NAME : imp2field #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : August 28, 1996 J.G.Sled #@MODIFIED : # $Id: imp2field.in,v 1.13 1997/09/29 19:14:50 jgsled Exp $ #----------------------------------------------------------------------------- |
|||
|
invert_raw_image /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1148 Sz: 4400 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage : xsize ysize <bytesperpixel> |
|||
|
make_model /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1149 Sz: 3320 |
8/9/2001 7:28:44 AM | C shell script text executable |
#!/bin/csh -f # This script is used to create the blurred intensity and gradient # volumes needed to make up the volumetric features for a general # set of model files needed for fitting with mritotal and nlfit. # # All model files MUST be voxel-matched to _mask.mnc volume # # Before running this script, the mni_reg package should be # installed. # |
|||
|
make_phantom /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1150 Sz: 409464 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
Object definition options.
-rectangle: Build rectangular object (default).
-ellipse: Build ellipsoid object.
-center: Center point of object (in world coords x y z).
Default value: 128 128 128
-xcenter: Center of object in X dimension
Default value: 128
-ycenter: Center of object in Y dimension
Default value: 128
-zcenter: Center of object in Z dimension
Default value: 128
-width: Width of object (in world mm along X Y Z).
Default value: 60 80 30
-xwidth: Width of object in X dimension
Default value: 60
-ywidth: Width of object in Y dimension
Default value: 80
-zwidth: Width of object in Z dimension
Default value: 30
-fill_value: Real value used to fill object
Default value: 1
-edge_value: Real value used to fill object
Default value: 1
-background: Real value used to fill background
Default value: 0
-no_partial: Do not account for partial volume effects.
Volume definition options.
-nelements: Number of elements along each dimension (X, Y, Z)
Default value: 128 128 128
-xnelements: Number of elements along the X dimension
Default value: 128
-ynelements: Number of elements along the Y dimension
Default value: 128
-znelements: Number of elements along the Z dimension
Default value: 128
-step: Step size along each dimension (X, Y, Z)
Default value: 2 2 2
-xstep: Step size along the X dimension
Default value: 2
-ystep: Step size along the Y dimension
Default value: 2
-zstep: Step size along the Z dimension
Default value: 2
-start: Start point along each dimension (X, Y, Z)
Default value: 0 0 0
-xstart: Start point along the X dimension
Default value: 0
-ystart: Start point along the Y dimension
Default value: 0
-zstart: Start point along the Z dimension
Default value: 0
-byte: Write out byte data (default)
-short: Write out short integer data
-long: Write out long integer data
-float: Write out single-precision floating-point data
-double: Write out double-precision floating-point data
-signed: Write signed integer data
-unsigned: Write unsigned integer data (default)
-voxel_range: Valid voxel range for output data
Default value: 1 255
-real_range: Valid real range for output data
Default value: 0 1
-no_clobber: Do not overwrite output file (default).
-clobber: Overwrite output file.
Options for logging progress. Default = -verbose.
-verbose: Write messages indicating progress
-quiet: Do not write log messages
-debug: Print out debug info.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] output.mnc
[-help]
|
|||
|
make_template /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1151 Sz: 8543 |
8/9/2001 8:22:33 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w #--------------------------------------------------------------------------- #@COPYRIGHT : # Copyright 1996, John G. Sled, # McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this # software and its documentation for any purpose and without # fee is hereby granted, provided that the above copyright # notice appear in all copies. The author and McGill University # make no representations about the suitability of this # software for any purpose. It is provided "as is" without # express or implied warranty. #---------------------------------------------------------------------------- #$RCSfile: make_template.in,v $ #$Revision: 1.14 $ #$Author: jgsled $ #$Date: 1997/10/24 21:02:45 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header ---------------------------------- #@NAME : make_template #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: #@ #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : August 15, 1996 J.G.Sled #@MODIFIED : # $Id: make_template.in,v 1.14 1997/10/24 21:02:45 jgsled Exp $ #----------------------------------------------------------------------------- |
|||
|
micreateimage /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1152 Sz: 96308 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options: -parent: MINC file to inherit attributes from -size: lengths of the four image dimensions Default value: -1 -1 -1 -1 -type: type of the image variable: byte, short, long, float, or double "byte" -valid_range: valid range of image data to be stored in the MINC file Default value: 0 0 -orientation: orientation of the image dimensions: transverse, coronal, or sagittal "transverse" -value: value with which to fill the image Default value: 1.79769e+308 -clobber: overwrite child file if it already exists Generic options for all commands: -help: Print summary of command-line options and abort Usage: micreateimage <MINC file> [option] [option] ... options may come in any order; micreateimage -help for descriptions |
|||
|
minc_modify_header /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1153 Sz: 70936 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
Options for specifying attribute values by name.
-sinsert: Insert string attribute (<var>:<attr>=<value>).
-dinsert: Insert a double precision attribute (<var>:<attr>=<value>(,...)).
-delete: Delete an attribute (<var>:<attr>).
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <file.mnc>
[-help]
|
|||
|
mincaverage /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1154 Sz: 155980 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-clobber: Overwrite existing file.
-noclobber: Don't overwrite existing file (default).
-no_clobber: Synonym for -noclobber.
-verbose: Print out log messages (default).
-quiet: Do not print out log messages.
-debug: Print out debugging messages.
-check_dimensions: Check that dimension info matches across files (default).
-nocheck_dimensions: Do not check dimension info.
-max_buffer_size_in_kb: Specify the maximum size of the internal buffers (in kbytes).
Default value: 4096
-filetype: Use data type of first file (default).
-byte: Write out byte data.
-short: Write out short integer data.
-long: Write out long integer data.
-float: Write out single-precision floating-point data.
-double: Write out double-precision floating-point data.
-signed: Write signed integer data.
-unsigned: Write unsigned integer data (default if type specified).
-range: Valid range for output data.
Default value: 0 0
-normalize: Normalize data sets for mean intensity.
-nonormalize: Do not normalize data sets (default).
-sdfile: Specify an output sd file (default=none).
-copy_header: Copy all of the header from the first file (default for one file).
-nocopy_header: Do not copy all of the header from the first file (defa
ult for many files)).
-avgdim: Specify a dimension along which we wish to average.
-binarize: Binarize the volume by looking for values in a given range.
-binrange: Specify a range for binarization.
Default value: 1.79769e+308 -1.79769e+308
-binvalue: Specify a target value (+/- 0.5) for binarization.
Default value: -1.79769e+308
-weights: Specify weights for averaging ("<w1>,<w2>,...").
-width_weighted: Weight by dimension widths when -avgdim is used.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [options] <in1.mnc> [...] <out.mnc>
-help
|
|||
|
mincbbox /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1155 Sz: 397528 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-threshold: Real value threshold for bounding box.
Default value: 0
-one_line: Output on one line (default): start_x y z width_x y z
-two_lines: Output on two lines: start_x y z \n width_x y z
-mincresample: Output format for mincresample: (-step x y z -start x y z -nelements x y z
-mincreshape: Output format for mincreshape: (-start x,y,z -count dx,dy,dz
-minccrop: Output format for minccrop: (-xlim x1 x2 -ylim y1 y2 -zlim z1 z2
Options for logging progress. Default = -verbose.
-verbose: Write messages indicating progress
-quiet: Do not write log messages
-debug: Print out debug info.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <inputfile>
[-help]
|
|||
|
mincblur /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1156 Sz: 467216 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-fwhm: Full-width-half-maximum of gaussian kernel
Default value: 0
-standarddev: Standard deviation of gaussian kernel
Default value: 0
-3dfwhm: Full-width-half-maximum of gaussian kernel
Default value: -1.79769e+308 -1.79769e+308 -1.79769e+308
-dimensions: Number of dimensions to blur (either 1,2 or 3).
Default value: 3
Program flags.
-gaussian: Use a gaussian smoothing kernel (default).
-rect: Use a rect (box) smoothing kernel.
-gradient: Create the gradient magnitude volume as well.
-partial: Create the partial derivative and gradient magnitude volumes as well.
-no_apodize: Do not apodize the data before blurring.
-no_clobber: Do not overwrite output file (default).
-clobber: Overwrite output file.
Options for logging progress. Default = -verbose.
-verbose: Write messages indicating progress
-quiet: Do not write log messages
-debug: Print out debug info.
-version: Print out version info and exit.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <inputfile> <output_basename>
[-help]
|
|||
|
mincchamfer /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1157 Sz: 411980 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-first: Number of initial background structure dilations
Default value: 0
Options for logging progress. Default = -verbose.
-verbose: Write messages indicating progress
-quiet: Do not write log messages
-debug: Print out debug info.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <inputfile> <outputfile>
[-help]
|
|||
|
mincconcat /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1158 Sz: 161452 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
General options:
-clobber: Overwrite existing file.
-noclobber: Do not overwrite existing file (default).
-verbose: Print out log messages as processing is being done (default).
-quiet: Do not print out any log messages.
-max_chunk_size_in_kb: Specify the maximum size of the copy buffer (in kbytes).
Default value: 4096
Output type options:
-filetype: Don't do any type conversion (default).
-byte: Convert to byte data
-short: Convert to short integer data
-long: Convert to long integer data
-float: Convert to single-precision floating-point data
-double: Convert to double-precision floating-point data
-signed: Convert to signed integer data
-unsigned: Convert to unsigned integer data
-valid_range: Valid range for output data (pixel values)
Default value: 0 0
Concatenation options:
-concat_dimension: Concatenate along a given dimension.
-start: Starting coordinate for new dimension.
Default value: 1.79769e+308
-step: Step size for new dimension.
Default value: 1.79769e+308
-width: Sample width for new dimension.
Default value: 1.79769e+308
-coordlist: Specify the dimension coordinates ("<c1>,<c2>,...").
-widthlist: Specify the dimension widths ("<w1>,<w2>,...").
-check_dimensions: Check that files have matching dimensions (default).
-nocheck_dimensions: Do not check that files have matching dimensions.
-ascending: Sort coordinates in ascending order (default).
-descending: Sort coordinates in descending order.
-interleaved: Sort coordinates in coordinate order, interleaving if necessary (default).
-sequential: Sort coordinates in sequential file order.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <infile1> [<infile2>...] <outfile>
[-help]
|
|||
|
minccopy /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1159 Sz: 104840 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-pixel_values: Copy pixel values as is.
-real_values: Copy real pixel intensities (default).
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <infile> <outfile>
-help
|
|||
|
mincdiff /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1160 Sz: 3047 |
8/9/2001 7:12:48 AM | C shell script text executable |
#! /bin/csh -f # # Script to find differences between minc files # # Usage: mincdiff [-l] <file1.mnc> <file2.mnc> # # Modifications: # $Log: mincdiff,v $ # Revision 6.1 1999/10/19 14:45:20 neelin # Fixed Log subsitutions for CVS # # Revision 6.0 1997/09/12 13:23:46 neelin # Release of minc version 0.6 # # Revision 5.0 1997/08/21 13:24:47 neelin # Release of minc version 0.5 # # Revision 4.0 1997/05/07 20:01:01 neelin # Release of minc version 0.4 # # Revision 3.0 1995/05/15 19:31:40 neelin # Release of minc version 0.3 # # Revision 2.1 1995/01/24 09:12:29 neelin # Added support for compressed minc files. # # Revision 2.0 94/09/28 10:34:46 neelin # Release of minc version 0.2 # # Revision 1.4 94/09/28 10:34:44 neelin # Pre-release # # Revision 1.3 94/07/18 10:41:26 neelin # Added -nonormalize option to mincextract for comparing image data. # # Revision 1.2 93/11/01 16:50:03 neelin # Some fixes. # # # Copyright 1993 Peter Neelin, McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this # software and its documentation for any purpose and without # fee is hereby granted, provided that the above copyright # notice appear in all copies. The author and McGill University # make no representations about the suitability of this # software for any purpose. It is provided "as is" without # express or implied warranty. # Constants |
|||
|
mincedit /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1161 Sz: 3431 |
8/9/2001 7:12:48 AM | C shell script text executable |
#! /bin/csh -f # # Script to allow editing of minc files # # Usage: mincedit <minc file> [<editor>] # # Modifications: # $Log: mincedit,v $ # Revision 6.1 1999/10/19 14:45:21 neelin # Fixed Log subsitutions for CVS # # Revision 6.0 1997/09/12 13:23:34 neelin # Release of minc version 0.6 # # Revision 5.0 1997/08/21 13:24:35 neelin # Release of minc version 0.5 # # Revision 4.0 1997/05/07 20:00:36 neelin # Release of minc version 0.4 # # Revision 3.0 1995/05/15 19:31:09 neelin # Release of minc version 0.3 # # Revision 2.0 1994/09/28 10:33:58 neelin # Release of minc version 0.2 # # Revision 1.6 94/09/28 10:33:55 neelin # Pre-release # # Revision 1.5 93/08/25 11:24:48 neelin # Added checking for -h or -help options. # # Revision 1.4 93/08/11 15:19:09 neelin # Added RCS logging in source. # # # # Copyright 1993 Peter Neelin, McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this # software and its documentation for any purpose and without # fee is hereby granted, provided that the above copyright # notice appear in all copies. The author and McGill University # make no representations about the suitability of this # software for any purpose. It is provided "as is" without # express or implied warranty. # Constants |
|||
|
mincexample1 /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1162 Sz: 114584 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: <infile.mnc> <outfile.mnc> |
|||
|
mincexample2 /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1163 Sz: 115224 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: <infile.mnc> <outfile.mnc> |
|||
|
mincexpand /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1164 Sz: 56808 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-header_only: Expand only enough file to get the header.
-all_data: Expand the whole file (default).
-name_only: Print out only the file name.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <infile> [<outfile>]
-help
|
|||
|
mincextract /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1165 Sz: 111880 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Skipped per survey instructions. Probably a program that expects console input |
|||
|
mincheader /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1166 Sz: 2407 |
8/9/2001 7:12:49 AM | C shell script text executable |
#! /bin/csh -f # Modifications: # $Log: mincheader,v $ # Revision 6.1 1999/10/19 14:45:23 neelin # Fixed Log subsitutions for CVS # # Revision 6.0 1997/09/12 13:23:37 neelin # Release of minc version 0.6 # # Revision 5.0 1997/08/21 13:24:37 neelin # Release of minc version 0.5 # # Revision 4.0 1997/05/07 20:00:42 neelin # Release of minc version 0.4 # # Revision 3.0 1995/05/15 19:31:32 neelin # Release of minc version 0.3 # # Revision 2.2 1995/01/25 08:04:41 neelin # Added check for failure to read minc file. # # Revision 2.1 95/01/24 10:19:09 neelin # Added support for compressed files. # # Revision 2.0 94/09/28 10:34:10 neelin # Release of minc version 0.2 # # Revision 1.6 94/09/28 10:34:06 neelin # Pre-release # # Revision 1.5 93/10/14 10:09:35 neelin # Fixed usage error message. # # Revision 1.4 93/08/25 11:24:20 neelin # Added checking for -h or -help options. # # Revision 1.3 93/08/11 15:20:55 neelin # Added RCS logging in source. # # # Set defaults |
|||
|
mincinfo /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1167 Sz: 63912 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-image_info: Print out the default information about the images.
-dimnames: Print the names of the dimensions in the file.
-varnames: Print the names of the variables in the file.
-dimlength: Print the length of the specified dimension.
-vartype: Print the type of the specified variable.
-vardims: Print the dimension names for the specified variable.
-varatts: Print the attribute names for the specified variable.
-varvalues: Print the values for the specified variable.
-atttype: Print the type of the specified attribute (variable:attribute).
-attvalue: Print the value(s) of the specified attribute (variable:attribute).
-error_string: Error to print on stdout (default = exit with error status).
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <mincfile>
-help
|
|||
|
minclookup /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1168 Sz: 154188 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-clobber: Overwrite existing file.
-noclobber: Don't overwrite existing file (default).
-verbose: Print out log messages (default).
-quiet: Do not print out log messages.
-buffer_size: Set the internal buffer size (in kb).
Default value: 10240
-filetype: Use data type of first file (default).
-byte: Write out byte data.
-short: Write out short integer data.
-long: Write out long integer data.
-float: Write out single-precision floating-point data.
-double: Write out double-precision floating-point data.
-signed: Write signed integer data.
-unsigned: Write unsigned integer data (default if type specified).
-valid_range: Valid range for output data.
Default value: 0 0
-gray: Use a grayscale lookup table (default).
-grey: Use a grayscale lookup table.
-hotmetal: Use a hot metal lookup table.
-spectral: Use a spectral lookup table.
-invert: Invert the lookup table (only applies to -continuous).
-noinvert: Don't invert the lookup table.
-range: Min and max for lookup table (default from file).
Default value: 1.79769e+308 1.79769e+308
-minimum: Minimum for continuous lookup table.
Default value: 1.79769e+308
-maximum: Maximum for continuous lookup table.
Default value: 1.79769e+308
-lookup_table: File containing the lookup table (use - for stdin).
-lut_string: String containing the lookup table, with ";" to separate lines.
-discrete: Lookup table has discrete (integer) entries - range is ignored.
-continuous: Lookup table is continuous from 0 to 1 (default).
-null_value: Specify a vector value for entries missing from a discrete lookup.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [options] <in.mnc> <out.mnc>
-help
|
|||
|
mincmakescalar /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1169 Sz: 147628 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-clobber: Overwrite existing file.
-noclobber: Don't overwrite existing file (default).
-verbose: Print out log messages (default).
-quiet: Do not print out log messages.
-buffer_size: Set the internal buffer size (in kb).
Default value: 10240
-filetype: Use data type of first file (default).
-byte: Write out byte data.
-short: Write out short integer data.
-long: Write out long integer data.
-float: Write out single-precision floating-point data.
-double: Write out double-precision floating-point data.
-signed: Write signed integer data.
-unsigned: Write unsigned integer data (default if type specified).
-valid_range: Valid range for output data.
Default value: 0 0
-magnitude: Compute magnitude of vectors (default).
-average: Average components of vectors.
-rgbtogrey: Convert RGB to greyscale.
-rgbtogray: Synonym for rgbtogrey.
-linear: Specify comma-separated list of coefficients for linear combination.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [options] <in.mnc> <out.mnc>
-help
|
|||
|
mincmakevector /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1170 Sz: 145484 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-clobber: Overwrite existing file.
-noclobber: Don't overwrite existing file (default).
-verbose: Print out log messages (default).
-quiet: Do not print out log messages.
-buffer_size: Set the internal buffer size (in kb).
Default value: 10240
-filetype: Use data type of first file (default).
-byte: Write out byte data.
-short: Write out short integer data.
-long: Write out long integer data.
-float: Write out single-precision floating-point data.
-double: Write out double-precision floating-point data.
-signed: Write signed integer data.
-unsigned: Write unsigned integer data (default if type specified).
-valid_range: Valid range for output data.
Default value: 0 0
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [options] <in1.mnc> [...] <out.mnc>
-help
|
|||
|
mincmath /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1171 Sz: 155724 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
General options:
-clobber: Overwrite existing file.
-noclobber: Don't overwrite existing file (default).
-no_clobber: Synonym for -noclobber.
-verbose: Print out log messages (default).
-quiet: Do not print out log messages.
-debug: Print out debugging messages.
-copy_header: Copy all of the header from the first file.
-nocopy_header: Do not copy all of the header from the first file.
-filetype: Use data type of first file (default).
-byte: Write out byte data.
-short: Write out short integer data.
-long: Write out long integer data.
-float: Write out single-precision floating-point data.
-double: Write out double-precision floating-point data.
-signed: Write signed integer data.
-unsigned: Write unsigned integer data (default if type specified).
-range: Valid range for output data.
Default value: 0 0
-max_buffer_size_in_kb: Specify the maximum size of the internal buffers (in kbytes).
Default value: 4096
-dimension: Specify a dimension along which we wish to perform a calculation.
-check_dimensions: Check that files have matching dimensions (default).
-nocheck_dimensions: Do not check that files have matching dimensions.
-ignore_nan: Ignore invalid data (NaN) for accumulations.
-propagate_nan: Invalid data in any file at a voxel produces a NaN (default).
-nan: Output NaN when an illegal operation is done (default).
-zero: Output zero when an illegal operation is done.
-illegal_value: Value to write out when an illegal operation is done.
Default value: 1.79769e+308
Options for specifying constants:
-constant: Specify a constant argument.
Default value: 1.79769e+308
-const: Synonym for -constant.
Default value: 1.79769e+308
-const2: Specify two constant arguments.
Default value: 1.79769e+308 1.79769e+308
Operations:
-add: Add N volumes or volume + constant.
-sub: Subtract 2 volumes or volume - constant.
-mult: Multiply N volumes or volume * constant.
-div: Divide 2 volumes or volume / constant.
-invert: Calculate 1/x at each voxel (use -constant for c/x).
-sqrt: Take square root of a volume.
-square: Take square of a volume.
-abs: Take absolute value of a volume.
-max: Synonym for -maximum.
-maximum: Find maximum of N volumes.
-minimum: Find minimum of N volumes.
-exp: Calculate c2*exp(c1*x). The constants c1 and c2 default to 1.
-log: Calculate log(x/c2)/c1. The constants c1 and c2 default to 1.
-scale: Scale a volume: volume * c1 + c2.
-clamp: Clamp a volume to lie between two values.
-segment: Segment a volume: within range = 1, outside range = 0.
-nsegment: Opposite of -segment: within range = 0, outside range = 1.
-percentdiff: Percent difference between 2 volumes, thresholded (const def=0.0).
-pd: Synonym for -percentdiff.
-eq: Test for integer vol1 == vol2 or vol1 == const.
-ne: Test for integer vol1 != vol2 or vol1 != const.
-gt: Test for vol1 > vol2 or vol1 > const.
-ge: Test for vol1 >= vol2 or vol1 >= const.
-lt: Test for vol1 < vol2 or vol1 < const.
-le: Test for vol1 <= vol2 or vol1 <= const.
-and: Calculate vol1 && vol2 (&& ...).
-or: Calculate vol1 || vol2 (|| ...).
-not: Calculate !vol1.
-isnan: Test for NaN values in vol1.
-nisnan: Negation of -isnan.
-count_valid: Count the number of valid values in N volumes.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [options] <in1.mnc> [...] <out.mnc>
-help
|
|||
|
mincresample /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1172 Sz: 459036 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-clobber: Overwrite existing file.
-noclobber: Do not overwrite existing file (default).
-verbose: Print out log messages as processing is being done (default).
-quiet: Do not print out any log messages.
-transformation: File giving world transformation. (Default = identity).
-invert_transformation: Invert the transformation before using it.
-noinvert_transformation: Do not invert the transformation (default).
-tfm_input_sampling: Transform the input sampling with the transform (default).
-use_input_sampling: Use the input sampling without transforming (old behaviour).
-like: Specifies a model file for the resampling.
-standard_sampling: Set the sampling to standard values (step, start and dircos).
-spacetype: Set the spacetype attribute to a specified string.
-talairach: Output is in Talairach space.
-units: Specify the units of the output sampling.
-nelements: Number of elements along each dimension (X, Y, Z)
Default value: 0 0 0
-xnelements: Number of elements along the X dimension
Default value: 0
-ynelements: Number of elements along the Y dimension
Default value: 0
-znelements: Number of elements along the Z dimension
Default value: 0
-step: Step size along each dimension (X, Y, Z)
Default value: 0 0 0
-xstep: Step size along the X dimension
Default value: 0
-ystep: Step size along the Y dimension
Default value: 0
-zstep: Step size along the Z dimension
Default value: 0
-start: Start point along each dimension (X, Y, Z)
Default value: 1.79769e+308 1.79769e+308 1.79769e+308
-xstart: Start point along the X dimension
Default value: 1.79769e+308
-ystart: Start point along the Y dimension
Default value: 1.79769e+308
-zstart: Start point along the Z dimension
Default value: 1.79769e+308
-dircos: Direction cosines along each dimension (X, Y, Z)
Default value: 1.79769e+308 1.79769e+308 1.79769e+308 1.79769e+308 1.79769e+30
8 1.79769e+308 1.79769e+308 1.79769e+308 1.79769e+308
-xdircos: Direction cosines along the X dimension
Default value: 1.79769e+308 1.79769e+308 1.79769e+308
-ydircos: Direction cosines along the Y dimension
Default value: 1.79769e+308 1.79769e+308 1.79769e+308
-zdircos: Direction cosines along the Z dimension
Default value: 1.79769e+308 1.79769e+308 1.79769e+308
-origin: Origin of first pixel in 3D space
Default value: 1.79769e+308 1.79769e+308 1.79769e+308
-transverse: Write out transverse slices
-sagittal: Write out sagittal slices
-coronal: Write out coronal slices
-byte: Write out byte data
-short: Write out short integer data
-long: Write out long integer data
-float: Write out single-precision floating-point data
-double: Write out double-precision floating-point data
-signed: Write signed integer data
-unsigned: Write unsigned integer data
-range: Valid range for output data
Default value: -1.79769e+308 -1.79769e+308
-nofill: Use value zero for points outside of input volume
-fill: Use a fill value for points outside of input volume
-fillvalue: Specify a fill value for points outside of input volume
Default value: 1.79769e+308
-trilinear: Do trilinear interpolation
-tricubic: Do tricubic interpolation
-nearest_neighbour: Do nearest neighbour interpolation
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <infile> <outfile>
[-help]
|
|||
|
mincreshape /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1173 Sz: 149660 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
General options:
-clobber: Overwrite existing file.
-noclobber: Do not overwrite existing file (default).
-verbose: Print out log messages as processing is being done (default).
-quiet: Do not print out any log messages.
-max_chunk_size_in_kb: Specify the maximum size of the copy buffer (in kbytes).
Default value: 4096
Image conversion options (pixel type and range):
-filetype: Don't do any type conversion (default).
-byte: Convert to byte data
-short: Convert to short integer data
-long: Convert to long integer data
-float: Convert to single-precision floating-point data
-double: Convert to double-precision floating-point data
-signed: Convert to signed integer data
-unsigned: Convert to unsigned integer data
-valid_range: Valid range for output data (pixel values)
Default value: 1.79769e+308 1.79769e+308
-image_range: Normalize images to a given minimum and maximum
Default value: 1.79769e+308 1.79769e+308
-normalize: Normalize images to file minimum and maximum.
-nonormalize: Do not normalize images (default).
-nopixfill: Do not convert out-of-range values in input file.
-pixfill: Replace out-of-range values in input file by smallest value (default).
-pixfillvalue: Specify new value to replace out-of-range values in input file.
Default value: -1.79769e+308
Image conversion options (dimension direction and size):
-scalar: Convert vector images to scalar images.
-noscalar: Do not convert vector images to scalar images (default).
+direction: Flip images to give positive step value for spatial axes.
-direction: Flip images to give negative step value for spatial axes.
-anydirection: Don't flip images along spatial axes (default).
+xdirection: Flip images to give positive xspace:step value (left-to-right).
-xdirection: Flip images to give negative xspace:step value (right-to-left).
-xanydirection: Don't flip images along x-axis.
+ydirection: Flip images to give positive yspace:step value (post-to-ant).
-ydirection: Flip images to give negative yspace:step value (ant-to-post).
-yanydirection: Don't flip images along y-axis.
+zdirection: Flip images to give positive zspace:step value (inf-to-sup).
-zdirection: Flip images to give negative zspace:step value (sup-to-inf).
-zanydirection: Don't flip images along z-axis.
-keepaspect: Preserve aspect ratio when resizing images.
-nokeepaspect: Do not preserve aspect ratio when resizing images (default).
-imgsize: Specify the desired image size.
Default value: -1
-rowsize: Specify the desired number of rows in the image.
Default value: -1
-colsize: Specify the desired number of columns in the image.
Default value: -1
-dimsize: Specify the size of a named dimension (<dimension>=<size>).
Reshaping options:
-transverse: Write out transverse slices
-sagittal: Write out sagittal slices
-coronal: Write out coronal slices
-dimorder: Specify dimension order (<dim1>,<dim2>,<dim3>,...).
-dimrange: Specify range of dimension subscripts (<dim>=<start>[,<count>]).
-start: Specifies corner of hyperslab (C conventions for indices)
-count: Specifies edge lengths of hyperslab to read
Missing data options:
-nofill: Use value zero for points outside of input volume (default)
-fill: Use a fill value for points outside of input volume
-fillvalue: Specify a fill value for points outside of input volume
Default value: 1.79769e+308
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <infile> <outfile>
[-help]
|
|||
|
minctoraw /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1174 Sz: 107144 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
-byte: Write out data as bytes
-short: Write out data as short integers
-long: Write out data as long integers
-float: Write out data as single precision floating-point values
-double: Write out data as double precision floating-point values
-signed: Write out signed data
-unsigned: Write out unsigned data
-range: Specify the range of output values
Default value: 1.79769e+308 1.79769e+308
-normalize: Normalize integer pixel values to file max and min
-nonormalize: Turn off pixel normalization (Default)
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <mincfile>
-help
|
|||
|
minctracc /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1175 Sz: 962024 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Parameters left:
-help
Command-specific options:
---Transformation maps one to volume two---
Initial transformation information.
-no_clobber: Do not overwrite output file (default).
-clobber: Overwrite output file.
-transformation: Initial world transformation. (Default = PAT).
-identity: Use identity transformation for starting point.
-est_center: use center estimated from Principal axis trans.
-est_scales: use scales estimated from Principal axis trans.
-est_rotations: use rotations estimated from Principal axis trans.
-est_translations: use translations estimated from Principal axis trans.
-center: Force center of rotation and scale.
Default value: -1.79769e+308 -1.79769e+308 -1.79769e+308
Output transformation type. Default = -procrustes.
-pat: principal axis transformation matrix (input matrix ignored).
-lsq3: 3 parameter transformation (3 translations only).
-lsq6: 6 parameter transformation (3 translation, 3 rotation, scale=1.0).
-lsq7: 7 parameter transformation (lsq6 + 1 global scale, same as -procrustes).
-lsq9: 9 parameter transformation (lsq6 + 3 scales).
-lsq10: 10 parameter transformation (lsq9 + 1 shear).
-lsq12: full 12 parameter transformation (lsq9 + 3 shears).
-lsq: full 12 parameter transformation (same as -lsq12).
-procrustes: procrustes transformation (3 trans, 3 rots, 1 scale), same as -lsq7.
-forward: Recover forward transformation (source -> model, default).
-invert: Recover inverted transformation (model -> source).
Options for feature volumes.
-feature_vol: Specify extra featurs <f1.mnc> <f2.mnc> [obj_func] [weight].
Options for mask volumes.
-model_mask: Specifies a binary mask file for the target.
-source_mask: Specifies a binary mask file for the source.
Interpolation options.
-trilinear: Do trilinear interpolation
-tricubic: Do tricubic interpolation
-nearest_neighbour: Do nearest neighbour interpolation
Linear optimization objective functions. (default = -xcorr)
-xcorr: Use cross correlation.
-zscore: Use normalized difference.
-ssc: Use stochastic sign change (Minoshima).
-vr: Use variance of ratio vol1/vol2 (Woods).
-mi: Use mutual information similarity measure (Collignon)
-groups: Number of groups for -vr and -mi.
Default value: 256
-blur_pdf: Size of pdf and jpdf blurring kernel for -mi.
Default value: 3
-threshold: Lower limit for voxel real value threshold
Default value: 0 0
-speckle: percent speckle noise to add to source
Default value: 5
Options for linear optimization.
-tol: Stopping criteria tolerance
Default value: 0.005
-simplex: Radius of simplex volume.
Default value: 20
-w_translations: Optimization weight of translation in x, y, z.
Default value: 1 1 1
-w_rotations: Optimization weight of rotations around x, y, z.
Default value: 0.0174533 0.0174533 0.0174533
-w_scales: Optimization weight of scaling along x, y, z.
Default value: 0.02 0.02 0.02
-w_shear: Optimization weight of shears a,b and c.
Default value: 0.02 0.02 0.02
Options for measurement comparison.
-matlab: Output curves for selected objective function vs parameter. ""
-num_steps: Number of steps at which to measure obj fn for matlab output.
Default value: 15
-measure: Output value of each obj. func. for given x-form. ""
Options for 3D lattice.
-source_lattice: Force lattice on source volume (def=auto selected).
-model_lattice: Force lattice on model volume (def=auto selected).
-step: Step size along each dimension (X, Y, Z)
Default value: 4 4 4
-xstep: Step size along the column dimension
Default value: 4
-ystep: Step size along the row dimension
Default value: 4
-zstep: Step size along the slice dimension
Default value: 4
Non-linear transformation information:
-nonlinear: recover nonlinear deformation field.
-2D-non-lin: Estimate the non-lin fit on a 2D slice only.
-3D-non-lin: Estimate the non-lin fit on a 3D volume (default).
-sub_lattice: Diameter (in number of nodes) of local sub-lattice.
Default value: 5
-use_magnitude: use magnitude data local deformation (default).
-optical_flow: use optical flow to compute deformation.
-use_simplex: use 3D simplex optimization for local deformation (default).
-quadratic: use quadratic fit for local deformation.
-use_local: Turn on local smoothing (default = global smoothing).
-use_nonisotropic: Turn on directionally sensitive smoothing (def=isotropic smoothing).
-super: super sample deformation field during optimization (default).
Default value: 2
-no_super: do not super sample deformation field during optimization.
-iterations: Number of iterations for non-linear optimization
Default value: 4
-weight: Weighting factor for each iteration in nl optimization
Default value: 0.6
-stiffness: Weighting factor for smoothing between nl iterations
Default value: 0.5
-similarity_cost_ratio: Weighting factor for r=similarity*w + cost(1*w)
Default value: 0.5
Options for logging progress. Default = -verbose 1.
-verbose: Write messages indicating progress
Default value: 1
-quiet: Do not write log messages
-debug: Print out debug info.
-version: Print out version info and exit.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <sourcefile> <targetfile> <output transfile>
[-help]
|
|||
|
mincview /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1176 Sz: 3885 |
8/9/2001 7:12:50 AM | C shell script text executable |
#! /bin/csh -f # Script for viewing a minc file. # Requires a pnm file viewer such as xv or display from ImageMagick, # as wells as the filter invert_raw_image. # # Displays images with patient left on left side of the screen. # Constants |
|||
|
mincwindow /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1177 Sz: 144908 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options: -clobber: Overwrite existing file. -noclobber: Don't overwrite existing file (default). -verbose: Print out log messages (default). -quiet: Do not print out log messages. Generic options for all commands: -help: Print summary of command-line options and abort Usage: [options] <in.mnc> <out.mnc> <min> <max> [<newvalue>] Usage: -help |
|||
|
miwriteimages /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1178 Sz: 83788 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Error: Incorrect number of arguments Usage: miwriteimages <file name> <slices> <frames> <raw file> where the raw file consists of doubles, with height*width values per image (height and width are determined from the MINC file). |
|||
|
mritoself /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1179 Sz: 23288 |
8/9/2001 8:22:37 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w # ------------------------------ MNI Header ---------------------------------- #@NAME : mritoself #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: register MRI data within modality, within subject #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : originally: April 1995, Greg Ward # rewrite #1: July 1995, GW # rewrite #2: December 1995-February 1996, GW #@MODIFIED : April-May 1996, Louis Collins: modifications to make an # official mritoself for ICBM and AI data #@VERSION : $Id: mritoself.in,v 1.3 2000/01/30 18:15:35 stever Exp $ #@COMMENTS : # possible additions: # figure out the thresholding stuff # add the dilation code back in (add to findprogram list, and # change default from 0 to 1 or 2. # figure out how to have automatically defined step sizes that # do not align with either volume voxel sizes. #----------------------------------------------------------------------------- # usage: mritoself [options] source_vol target_vol transform |
|||
|
mritotal /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1180 Sz: 87070 |
8/9/2001 8:22:41 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w # mritotal (new and improved) # # All-new version of Louis Collins' mritotal script. Embodies pretty # much the same algorithm, but rewritten almost entirely from scratch # by Greg Ward, August 1995. The changes to the algorithm are: # * volume is subsampled before any blurring takes place (old version # blurred to 2mm, then subsampled, then blurred to 8mm and 16mm -- # this is more correct, but very memory intensive) # * volume may be cropped at the same time as it's subsampled # (this is very data-specific -- for ICBM data, we crop off 25% # of the data at the low z, ie. at the bottom of the head # * volume is zero-padded before blurring instead of cropped after # blurring # * COG of source volume is computed only once (by a separate program, # volume_cog) rather than by a PAT on every fitting step; in fact, # the PAT is only used once, to estimate the translations of the first # fit step # # The changes to the user interface are extensive. Most importantly, # you can specify which preprocessing steps to take using either # a protocol file or with command-line overrides. See the man # page for full details. # # Here is Louis' original copyright notice # (with a slight revision ;-): # # -------------------------------------------------------------------- # Copyright (c) 1993-97 Louis Collins and Greg Ward, McConnell Brain # Imaging Centre, Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this software and # its documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies. The # author and McGill University make no representations about the # suitability of this software for any purpose. It is provided "as # is" without express or implied warranty. # # Developed by Louis Collins under the direction of Dr. Alan Evans and # Dr. Terry Peters at the NeuroImaging Laboratory at the Montreal # Neurological Institute. # # Note that the programs mincinfo and mincresample are written & # copyrighted by Peter Neelin, McConnell Brain Imaging Centre, with # the same copyright as above. # -------------------------------------------------------------------- # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ |
|||
|
ncdump /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1181 Sz: 44212 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: invalid option -- e [-c|-h] [-v ...] [[-b|-f] [c|f]] [-l len] [-n name] [-d n[,n]] file [-c] Coordinate variable data and header information [-h] Header information only, no data [-v var1[,...]] Data for variable(s) <var1>,... only [-b [c|f]] Brief annotations for C or Fortran indices in data [-f [c|f]] Full annotations for C or Fortran indices in data [-l len] Line length maximum in data section (default 80) [-n name] Name for netCDF (default derived from file name) [-d n[,n]] Approximate floating-point values with less precision file File name of input netCDF file |
|||
|
ncgen /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1182 Sz: 73272 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: invalid option -- h : -: Usage: [ -b ] [ -c ] [ -f ] [ -o outfile] [ file ... ] |
|||
|
nu_correct /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1183 Sz: 20332 |
8/9/2001 8:22:44 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w #--------------------------------------------------------------------------- #@COPYRIGHT : # Copyright 1996, John G. Sled, # McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this # software and its documentation for any purpose and without # fee is hereby granted, provided that the above copyright # notice appear in all copies. The author and McGill University # make no representations about the suitability of this # software for any purpose. It is provided "as is" without # express or implied warranty. #---------------------------------------------------------------------------- #$RCSfile: nu_estimate.in,v $ #$Revision: 1.15 $ #$Author: jgsled $ #$Date: 1999/08/10 18:05:42 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header ---------------------------------- #@NAME : nu_estimate or nu_correct #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: estimate intensity non-uniformity artifacts from given volume #@ or #@ estimate and correct intensity non-uniformity artifact #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : August 7, 1996 J.G.Sled #@MODIFIED : # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ #----------------------------------------------------------------------------- |
|||
|
nu_estimate /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1184 Sz: 20332 |
8/9/2001 8:22:47 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w #--------------------------------------------------------------------------- #@COPYRIGHT : # Copyright 1996, John G. Sled, # McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this # software and its documentation for any purpose and without # fee is hereby granted, provided that the above copyright # notice appear in all copies. The author and McGill University # make no representations about the suitability of this # software for any purpose. It is provided "as is" without # express or implied warranty. #---------------------------------------------------------------------------- #$RCSfile: nu_estimate.in,v $ #$Revision: 1.15 $ #$Author: jgsled $ #$Date: 1999/08/10 18:05:42 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header ---------------------------------- #@NAME : nu_estimate or nu_correct #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: estimate intensity non-uniformity artifacts from given volume #@ or #@ estimate and correct intensity non-uniformity artifact #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : August 7, 1996 J.G.Sled #@MODIFIED : # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ #----------------------------------------------------------------------------- |
|||
|
nu_estimate_np_and_em /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1185 Sz: 61502 |
8/9/2001 8:22:51 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w #--------------------------------------------------------------------------- #@COPYRIGHT : # Copyright 1996, John G. Sled, # McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this # software and its documentation for any purpose and without # fee is hereby granted, provided that the above copyright # notice appear in all copies. The author and McGill University # make no representations about the suitability of this # software for any purpose. It is provided "as is" without # express or implied warranty. #---------------------------------------------------------------------------- #$RCSfile: nu_estimate_np_and_em.in,v $ #$Revision: 1.19 $ #$Author: jgsled $ #$Date: 1999/08/11 17:33:05 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header ---------------------------------- #@NAME : NUestimate_np_and_em #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: iteratively estimates intensity non-uniformity artifacts #@ in MRI volumes #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : January 15, 1996 J.G.Sled #@MODIFIED : # $Id: nu_estimate_np_and_em.in,v 1.19 1999/08/11 17:33:05 jgsled Exp $ #----------------------------------------------------------------------------- |
|||
|
nu_evaluate /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1186 Sz: 11399 |
8/9/2001 8:22:54 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w #--------------------------------------------------------------------------- #@COPYRIGHT : # Copyright 1996, John G. Sled, # McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this # software and its documentation for any purpose and without # fee is hereby granted, provided that the above copyright # notice appear in all copies. The author and McGill University # make no representations about the suitability of this # software for any purpose. It is provided "as is" without # express or implied warranty. #---------------------------------------------------------------------------- #$RCSfile: nu_evaluate.in,v $ #$Revision: 1.14 $ #$Author: jgsled $ #$Date: 1997/10/24 21:02:46 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header ---------------------------------- #@NAME : NUevaluate #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: correct a volume for intensity non-uniformity artifacts #@ using supplied (.imp) field #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : August 7, 1996 J.G.Sled #@MODIFIED : # $Id: nu_evaluate.in,v 1.14 1997/10/24 21:02:46 jgsled Exp $ #----------------------------------------------------------------------------- |
|||
|
param2xfm /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1187 Sz: 437344 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options: -center: Force center of rotation and scale. Default value: 0 0 0 -translation: Translation x,y,z. Default value: 0 0 0 -rotations: Rotation angle (in degrees). Default value: 0 0 0 -scales: Scaling factors. Default value: 1 1 1 -shears: Scaling factors. Default value: 0 0 0 -clobber: Overwrite existing file (default = no clobber). -version: Print out version info and exit. Generic options for all commands: -help: Print summary of command-line options and abort Usage: [options] <result.xfm> |
|||
|
rand_param /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1188 Sz: 14576 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options: -translation: Translation x,y,z. Default value: 0 -rotations: Rotation angle (in degrees). Default value: 0 -scales: Scaling factors. Default value: 0 -shears: Scaling factors. Default value: 0 -version: Print out version info and exit. Generic options for all commands: -help: Print summary of command-line options and abort Usage: [options] |
|||
|
rawtominc /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1189 Sz: 134460 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options:
Options to specify input dimension order (from slowest to fastest).
Default = -transverse.
-transverse: Transverse images : [[time] z] y x
-sagittal: Sagittal images : [[time] x] z y
-coronal: Coronal images : [[time] y] z x
-time: Time ordered images : [[z] time] y x
-xyz: Dimension order : [[time] x] y z
-xzy: Dimension order : [[time] x] z y
-yxz: Dimension order : [[time] y] x z
-yzx: Dimension order : [[time] y] z x
-zxy: Dimension order : [[time] z] x y
-zyx: Dimension order : [[time] z] y x
-vector: Specifies the size of a vector dimension
Default value: -1
Options to specify input data type. Default = -byte.
-byte: Byte values
-short: Short integer values
-long: Long integer values
-float: Single-precision floating point values
-double: Double-precision floating point values
Options for sign of input data. Default = -signed (-unsigned for byte).
-signed: Signed values
-unsigned: Unsigned values
Other input value options.
-range: Valid range of input values (default = full range).
Default value: 0 -1
-real_range: Real range of input values (ignored for floating-point types).
Default value: 1.79769e+308 1.79769e+308
Options for type of output minc data. Default = input data type
-obyte: Byte values
-oshort: Short integer values
-olong: Long integer values
-ofloat: Single-precision floating point values
-odouble: Double precision floating point values
Options for sign of output minc data.
Default = -signed (-unsigned for byte data)
-osigned: Signed values
-ounsigned: Unsigned values
Other output value options.
-orange: Valid range of output minc values.
Default value: 0 -1
Options to specify whether integers are scanned for min and max.
-scan_range: Scan input for min and max.
-noscan_range: Do not scan input for min and max (default).
Options for writing output file. Default = -noclobber.
-clobber: Overwrite existing file
-noclobber: Don't overwrite existing file
Option for specifying input raw data file.
-input: Name of input file (default=stdin).
Options for specifying spatial dimension coordinates.
-xstep: Step size for x dimension.
Default value: 1.79769e+308
-ystep: Step size for y dimension.
Default value: 1.79769e+308
-zstep: Step size for z dimension.
Default value: 1.79769e+308
-xstart: Starting coordinate for x dimension.
Default value: 1.79769e+308
-ystart: Starting coordinate for y dimension.
Default value: 1.79769e+308
-zstart: Starting coordinate for z dimension.
Default value: 1.79769e+308
-xdircos: Direction cosines for x dimension.
Default value: 1.79769e+308 1.79769e+308 1.79769e+308
-ydircos: Direction cosines for y dimension.
Default value: 1.79769e+308 1.79769e+308 1.79769e+308
-zdircos: Direction cosines for z dimension.
Default value: 1.79769e+308 1.79769e+308 1.79769e+308
-origin: Coordinate of first pixel.
Default value: 1.79769e+308 1.79769e+308 1.79769e+308
Options for specifying imaging modality. Default = -nomodality.
-nomodality: Do not store modality type in file.
-pet: PET data.
-mri: MRI data.
-spect: SPECT data.
-gamma: Data from a gamma camera.
-mrs: MR spectroscopy data.
-mra: MR angiography data.
-ct: CT data.
-dsa: DSA data
-dr: Digital radiography data.
Options for specifying attribute values by name.
-sattribute: Set a string attribute (<var>:<attr>=<value>).
-dattribute: Set a double precision attribute (<var>:<attr>=<value>).
-attribute: Set an attribute, guessing the type (<var>:<attr>=<value>).
Options for specifying time dimension coordinates.
-frame_times: Specify the frame starting times ("<t1>,<t2>,<t3>,...").
-frame_widths: Specify the frame lengths ("<w1>,<w2>,<w3>,...").
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <output.mnc> [[<size4>] <size3>] <size2> <size1>
[-help]
|
|||
|
register /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1190 Sz: 1883264 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: [-help] [-rgb] [-cmap] [-single] [-double] [volume1.mnc]
[volume2.mnc] [tags.tag]
-help: Prints this message.
-rgb: Starts program in RGB mode.
-cmap: Starts program in colour map mode.
-single: Starts program in single buffer mode.
-double: Starts program in double buffer mode.
-global variable value:
Sets a global variable that changes configuration of program.
-version: Displays the version number of the program.
|
|||
|
resample_labels /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1191 Sz: 21401 |
8/9/2001 8:22:57 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w # ------------------------------ MNI Header ---------------------------------- #@NAME : resample_labels #@INPUT : $InVolume - a label volume in some sampling grid and space #@OUTPUT : $OutVolume - a new label volume, with a different sampling # grid and/or space from $InVolume, but hopefully # with volume and shape nearly preserved #@RETURNS : #@DESCRIPTION: Resamples a label volume using the following algorithm: # * split multi-label volume into several binary volumes # * use trilinear interpolation to create a fuzzy label # volume from each # * apply a mask to restrict the labels so they only cover # voxels that fall within the thresholds used when painting # (the mask is determined from the MRI volume resampled # to the same target space as the label volume) # * threshold it (0.5? 0.4? 0.49?) # * recombine into a new multi-label volume #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : January 1996, Greg Ward #@MODIFIED : Sept 1997, John Sled. Configuration for use with N3 release. #@VERSION : $Id: resample_labels.in,v 1.12 1997/09/10 22:40:28 jgsled Exp $ #----------------------------------------------------------------------------- |
|||
|
sharpen_hist /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1192 Sz: 851780 |
11/21/2002 7:14:00 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: Symbol `__vt_3ios' has different size in shared object, consider re-linking
: Symbol `__vt_7istream.3ios' has different size in shared object, consider re-linking
: Symbol `__vt_8ofstream.3ios' has different size in shared object, consider re-linking
: Symbol `__vt_7ostream.3ios' has different size in shared object, consider re-linking
: Symbol `__vt_8ifstream.3ios' has different size in shared object, consider re-linking
Command-specific options:
General options:
-clobber: Overwrite existing file.
-noclobber: Do not overwrite existing file (default).
-verbose: Print out log messages as processing is being done (default).
-quiet: Do not print out any log messages.
-version: Print out version info and exit.
options:
-fwhm: Width of deconvolution kernel.
Default value: 1
-noise: Noise level for Weiner filter.
Default value: 0.1
-blur: Skip deblurring step.
-min: Bin value mapped to zero in lookup table.
Default value: -1.79769e+308
-max: Bin value mapped to one in lookup table.
Default value: 1.79769e+308
-range: Range of bin values mapped from zero to one in lookup table.
Default value: -1.79769e+308 1.79769e+308
-debug: Save intermediate steps as matlab files.
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <infile> <outfile>
-help
|
|||
|
sharpen_volume /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1193 Sz: 5743 |
8/9/2001 8:23:00 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w #--------------------------------------------------------------------------- #@COPYRIGHT : # Copyright 1996, John G. Sled, # McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. # Permission to use, copy, modify, and distribute this # software and its documentation for any purpose and without # fee is hereby granted, provided that the above copyright # notice appear in all copies. The author and McGill University # make no representations about the suitability of this # software for any purpose. It is provided "as is" without # express or implied warranty. #---------------------------------------------------------------------------- #$RCSfile: sharpen_volume.in,v $ #$Revision: 1.13 $ #$Author: jgsled $ #$Date: 1997/09/29 19:14:54 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header ---------------------------------- #@NAME : sharpen_volume #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: modifies intensities so as to produce a sharper histogram #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : February 28, 1996 #@MODIFIED : #----------------------------------------------------------------------------- |
|||
|
spline_smooth /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1194 Sz: 1339928 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: Symbol `__vt_3ios' has different size in shared object, consider re-linking
: Symbol `__vt_7istream.3ios' has different size in shared object, consider re-linking
: Symbol `__vt_8ofstream.3ios' has different size in shared object, consider re-linking
: Symbol `__vt_7ostream.3ios' has different size in shared object, consider re-linking
: Symbol `__vt_8ifstream.3ios' has different size in shared object, consider re-linking
Command-specific options:
General options:
-clobber: Overwrite existing file.
-noclobber: Do not overwrite existing file (default).
-verbose: Print out log messages as processing is being done (default).
-quiet: Do not print out any log messages.
-version: Print out version info and exit.
Options:
-lambda: Scale invariant smoothing parameter. The default is chosen
to provide minimal smoothing except in regions of missing data.
Default value: 0.01
-distance: Distance between basis functions in mm. This parameter
determines the overall smoothness.
Default value: 60
-b_spline: Basis functions are tensor B splines (default).
-tp_spline: Basis functions are thin plate splines.
-mask: Specify data region to which splines are fit.
-output_mask: Specify region on which to evaluate smoothed function.
-extrapolate: Extrapolate to region outside mask (implies full_support).
-noextrapolate: Do not extrapolate to region outside mask. (default)
-full_support: Cover region outside mask with basis functions.
-subsample: Only fit to every nth data point.
Default value: 1
-compact: Specify file in which to store compact field representation.
-novolume: Do not produce smoothed minc volume
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <infile> <outfile>
[-help]
|
|||
|
transformtags /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1195 Sz: 412792 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options: -vol1: Transform tags for volume 1. -vol2: Transform tags for volume 2 (default). -transformation: Name of transformation file (default = identity). Generic options for all commands: -help: Print summary of command-line options and abort Usage: [<options>] infile.tag outfile.tag |
|||
|
volume_cog /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1196 Sz: 406952 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Skipped per survey instructions. Probably a program that expects console input |
|||
|
volume_hist /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1197 Sz: 800636 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
: Symbol `__vt_3ios' has different size in shared object, consider re-linking
: Symbol `__vt_7istream.3ios' has different size in shared object, consider re-linking
: Symbol `__vt_8ifstream.3ios' has different size in shared object, consider re-linking
Command-specific options:
General options:
-clobber: Overwrite existing file.
-noclobber: Do not overwrite existing file (default).
-verbose: Print out log messages as processing is being done (default).
-quiet: Do not print out any log messages.
-version: Print out version info and exit.
Options:
-bins: Number of bins in each histogram.
Default value: 200
-mask: <mask.mnc> Use mask volume to make one or more histograms.
-classes: <number> Limit number of histograms to make.
Default value: -1
-select: <class> Only compute histogram for selected class.
Default value: -1
-auto_range: Compute histogram range for each class.
-window: Use triangular Parzen window.
-text: Produce files in text format. (default)
-matlab: Produce files in matlab format. (not available)
Generic options for all commands:
-help: Print summary of command-line options and abort
Usage: [<options>] <infile> <outfile>
[-help]
|
|||
|
volume_stats /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1198 Sz: 850492 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Skipped per survey instructions. Probably a program that expects console input |
|||
|
voxeltoworld /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1199 Sz: 389908 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: <image file> <voxel index 1 (slowest)> <index 2> <index 3> |
|||
|
worldtovoxel /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1200 Sz: 389876 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: <image file> <world x coord> <y coord> <z coord> |
|||
|
xcorr_vol /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1201 Sz: 394516 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: xcorr_vol vol1.mnc vol2.mnc [mask.mnc] |
|||
|
xdisp /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1202 Sz: 1588232 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
xdisp (v4.3.5, June 20, 2000): An image display utility for X systems.
Usage: xdisp filename [options]
Options:
-w width
-width width -> image width in pixels (default=256)
-h height
-h height -> image height in pixels (256)
-o byte_offset
-offset offset -> offset in bytes to image data (0)
-skip offset -> offset in bytes between image elements (0)
-u upper
-upper upper -> initial colormap upper value (image max)
-l lower
-lower lower -> initial colormap lower value (image min)
-wl -> always display window/level (False)
-all -> load all images from file upon startup
-byte -> data is signed byte
-ubyte -> data is unsigned byte
-short -> data is signed short integer (default)
-ushort -> data is unsigned short integer
-int -> data is signed integer
-uint -> data is unsigned integer
-long -> data is signed long integer
-ulong -> data is unsigned long integer
-float -> data is float
-double -> data is double
-nc num_colors -> number of colors to allocate
-cmi -> image is in CMI format
-color_bar -> display a color_scale at the side of the image
-bilinear -> use bilinear interpolation for all resizes (default)
-nearest_neighbour
-nn -> use nearest neighbour interpolation for resizes
-rescale -> always rescale image (False)
-v
-verbose -> verbose mode (False)
-z factor
-zoom factor -> initial zoom factor (1.0)
-gamma gamma -> initial Gamma correction factor (1.0)
-grc color -> graphics overlay color
-grey -> use a grey scale color table (default)
-hot -> use a hot metal color table
-spectral -> use spectral color table
-image num -> initial image to display
-name window_name -> name of windows and icons
-noiconify -> initial command window state
-fg color
-foreground color -> foreground color
-bg color
-background color -> background color
-geom WxH+x+y
-geometry WxH+x+y -> main window geometry
-private -> install a private color map
-roi filename -> ROI file name
-swap -> swap bytes of image data
-PseudoColor -> attempt to use a PseudoColor visual (default)
-DirectColor -> attempt to use a DirectColor visual
-TrueColor -> attempt to use a TrueColor visual
-version -> display the version number
-help -> this help message
-- -> read from standard in
Within the image window moving the mouse with the middle button
depressed changes the window/level. Hold down the left button
to draw ROIs. The right button (de)iconifies the command window.
Type 'h' within the image window for a complete help listing.
Example 1: display a 512x512 byte image and skip a 2048 byte header
xdisp my_image.byte -width 512 -height 512 -offset 2048 -byte -noiconify
Example 2: display a minc file, load the entire volume at startup and
use a TrueColor visual, spectral colormap and show the colorbar
xdisp cool_stuff.mnc -all -TrueColor -spectral -color_bar
|
|||
|
xfm2param /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1203 Sz: 457404 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Command-specific options: -center: Force center of rotation and scale. Default value: 0 0 0 -version: Print out version info and exit. Generic options for all commands: -help: Print summary of command-line options and abort Usage: file.xfm [file.mnc] [options] |
|||
|
xfmconcat /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1204 Sz: 401848 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: <input1.xfm> [<input2.xfm> ...] <result.xfm> |
|||
|
xfminvert /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1205 Sz: 401592 |
11/21/2002 7:14:01 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: <input.xfm> <result.xfm> |
|||
|
xfmri /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1206 Sz: 6906076 |
11/21/2002 7:14:02 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
Usage: [-h] [-v] [-a <filename>] [-f <filename>]
-a <filename> Name of anatomic data file.
-f <filename> Name of functional data file (time series).
-mc <filename> Name of correlation t map file.
-p <filename> Name of paradigm file.
-o <filename> Name of output map file (default: <input>_tmap.mnc)
-cmdln Run program in commandline mode.
-spearman Calculate spearman statistics (default).
-lm Calculate linear model statistics.
-spc Calculate percent signal change map.
-silent Supress any messages.
-verbose Be very loquacious (debug).
-h: Prints this message.
-v: Displays the version number of the program.
|
|||
|
xfmtool /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1207 Sz: 9565 |
8/9/2001 8:23:03 AM | a /usr/pubsw/bin/perl -w script text executable |
#! /usr/pubsw/bin/perl -w # ------------------------------ MNI Header ---------------------------------- #@NAME : xfmtool #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: Tool to perform various operations on xfm files. Currently # just inverts and concatenates any number of xfm's, but # I could probably extend it to more operations pretty easily. #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : 1996/06/07, Greg Ward #@MODIFIED : #@VERSION : $Id: xfmtool.in,v 1.1 2000/02/10 15:06:22 stever Exp $ #----------------------------------------------------------------------------- |
|||
|
zscore_vol /usr/pubsw/packages/mni/1.0.4/bin/ |
#: 1208 Sz: 412968 |
11/21/2002 7:14:02 AM | ELF 32-bit LSB executable, Intel 80386, version 1 |
usage: xcorr_vol.c vol1.mnc vol2.mnc threshold [mask.mnc] |
|||
| /usr/pubsw/packages/mni/1.0.4/data/ | |||
| /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ | |||
|
average_305.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1209 Sz: 5909296 |
3/10/2000 2:38:26 PM | data |
|
average_305_16_blur.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1210 Sz: 553820 |
8/9/2001 7:44:39 AM | data |
|
average_305_16_mask.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1211 Sz: 552780 |
8/9/2001 7:44:40 AM | data |
|
average_305_2_blur.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1212 Sz: 5335180 |
8/9/2001 7:49:57 AM | data |
|
average_305_2_dxyz.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1213 Sz: 5335540 |
8/9/2001 7:50:03 AM | data |
|
average_305_2_mask.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1214 Sz: 5334168 |
8/9/2001 7:50:13 AM | data |
|
average_305_4_blur.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1215 Sz: 4973436 |
8/9/2001 7:47:25 AM | data |
|
average_305_4_dxyz.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1216 Sz: 4973796 |
8/9/2001 7:47:34 AM | data |
|
average_305_4_mask.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1217 Sz: 4972424 |
8/9/2001 7:47:42 AM | data |
|
average_305_8_blur.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1218 Sz: 648588 |
8/9/2001 7:45:02 AM | data |
|
average_305_8_dxyz.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1219 Sz: 648944 |
8/9/2001 7:45:03 AM | data |
|
average_305_8_mask.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1220 Sz: 647536 |
8/9/2001 7:45:04 AM | data |
|
average_305_headmask.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1221 Sz: 758068 |
3/10/2000 3:41:24 PM | data |
|
average_305_mask.mnc /usr/pubsw/packages/mni/1.0.4/data/mni_autoreg/ |
#: 1222 Sz: 5906088 |
3/10/2000 2:38:28 PM | data |
| /usr/pubsw/packages/mni/1.0.4/data/N3/ | |||
|
average_305_mask_1mm.mnc.gz /usr/pubsw/packages/mni/1.0.4/data/N3/ |
#: 1223 Sz: 64270 |
8/9/2001 7:55:19 AM | gzip compressed data, was "average_305_mask_1mm.mn |
| /usr/pubsw/packages/mni/1.0.4/etc/ | |||
| /usr/pubsw/packages/mni/1.0.4/etc/mni_autoreg/ | |||
|
mritotal.cfg /usr/pubsw/packages/mni/1.0.4/etc/mni_autoreg/ |
#: 1224 Sz: 1716 |
8/9/2001 7:28:44 AM | ASCII English text |
|
mritotal.default.cfg /usr/pubsw/packages/mni/1.0.4/etc/mni_autoreg/ |
#: 1225 Sz: 4759 |
8/9/2001 7:29:23 AM | ASCII English text |
|
mritotal.default.cfg.orig /usr/pubsw/packages/mni/1.0.4/etc/mni_autoreg/ |
#: 1226 Sz: 4741 |
8/9/2001 7:28:44 AM | ASCII English text |
|
mritotal.icbm.cfg /usr/pubsw/packages/mni/1.0.4/etc/mni_autoreg/ |
#: 1227 Sz: 1386 |
8/9/2001 7:28:44 AM | ASCII English text |
| /usr/pubsw/packages/mni/1.0.4/include/ | |||
|
minc.h /usr/pubsw/packages/mni/1.0.4/include/ |
#: 1228 Sz: 18152 |
11/9/2001 5:24:16 AM | ASCII C program text |
|
netcdf.h /usr/pubsw/packages/mni/1.0.4/include/ |
#: 1229 Sz: 15049 |
8/9/2001 7:10:16 AM | ASCII C program text |
|
netcdf.inc /usr/pubsw/packages/mni/1.0.4/include/ |
#: 1230 Sz: 4323 |
8/9/2001 7:10:16 AM | ASCII fortran program text |
|
volume_io.h /usr/pubsw/packages/mni/1.0.4/include/ |
#: 1231 Sz: 1818 |
11/9/2001 5:24:19 AM | ASCII C program text |
| /usr/pubsw/packages/mni/1.0.4/include/Acr_nema/ | |||
|
acr_io.h /usr/pubsw/packages/mni/1.0.4/include/Acr_nema/ |
#: 1232 Sz: 7298 |
8/10/2001 8:29:06 AM | ASCII C program text |
|
acr_nema.h /usr/pubsw/packages/mni/1.0.4/include/Acr_nema/ |
#: 1233 Sz: 2478 |
8/10/2001 8:29:06 AM | ASCII C program text |
|
dicom_client_routines.h /usr/pubsw/packages/mni/1.0.4/include/Acr_nema/ |
#: 1234 Sz: 3755 |
8/10/2001 8:29:06 AM | ASCII C program text |
|
dicom_network.h /usr/pubsw/packages/mni/1.0.4/include/Acr_nema/ |
#: 1235 Sz: 5885 |
8/10/2001 8:29:06 AM | ASCII C program text |
|
element.h /usr/pubsw/packages/mni/1.0.4/include/Acr_nema/ |
#: 1236 Sz: 8426 |
8/10/2001 8:29:06 AM | ASCII C program text |
|
file_io.h /usr/pubsw/packages/mni/1.0.4/include/Acr_nema/ |
#: 1237 Sz: 5262 |
8/10/2001 8:29:06 AM | ASCII C program text |
|
group.h /usr/pubsw/packages/mni/1.0.4/include/Acr_nema/ |
#: 1238 Sz: 5512 |
8/10/2001 8:29:06 AM | ASCII C program text |
|
message.h /usr/pubsw/packages/mni/1.0.4/include/Acr_nema/ |
#: 1239 Sz: 2984 |
8/10/2001 8:29:06 AM | ASCII C program text |
|
value_repr.h /usr/pubsw/packages/mni/1.0.4/include/Acr_nema/ |
#: 1240 Sz: 2519 |
8/10/2001 8:29:06 AM | ASCII C program text |
| /usr/pubsw/packages/mni/1.0.4/include/volume_io/ | |||
|
alloc.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1241 Sz: 10797 |
11/9/2001 5:23:13 AM | ASCII C program text |
|
arrays.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1242 Sz: 6613 |
11/9/2001 5:23:19 AM | ASCII C program text |
|
basic.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1243 Sz: 5310 |
11/14/2001 3:31:52 PM | ASCII C program text |
|
def_math.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1244 Sz: 1123 |
11/9/2001 5:23:28 AM | ASCII C program text |
|
files.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1245 Sz: 1461 |
11/9/2001 5:23:32 AM | ASCII C program text |
|
geom_structs.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1246 Sz: 7722 |
11/9/2001 5:23:37 AM | ASCII C program text |
|
geometry.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1247 Sz: 8226 |
11/14/2001 3:32:19 PM | ASCII C program text |
|
internal_volume_io.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1248 Sz: 1000 |
8/9/2001 7:12:48 AM | ASCII C program text |
|
multidim.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1249 Sz: 11315 |
11/9/2001 5:23:45 AM | ASCII C program text |
|
progress.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1250 Sz: 1787 |
11/9/2001 5:23:49 AM | ASCII C program text |
|
string_funcs.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1251 Sz: 1589 |
11/9/2001 5:23:52 AM | ASCII C program text |
|
system_dependent.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1252 Sz: 1405 |
8/9/2001 7:12:48 AM | ASCII C program text |
|
transforms.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1253 Sz: 2996 |
11/9/2001 5:23:55 AM | ASCII C program text |
|
vol_io_prototypes.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1254 Sz: 49718 |
8/9/2001 7:12:48 AM | ASCII C program text |
|
volume.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1255 Sz: 17110 |
11/9/2001 5:23:59 AM | ASCII C program text |
|
volume_cache.h /usr/pubsw/packages/mni/1.0.4/include/volume_io/ |
#: 1256 Sz: 3635 |
11/9/2001 5:24:03 AM | ASCII C program text |
| /usr/pubsw/packages/mni/1.0.4/lib/ | |||
|
libacrnema.a /usr/pubsw/packages/mni/1.0.4/lib/ |
#: 1257 Sz: 94358 |
9/12/2001 1:12:31 PM | current ar archive |
|
libminc.a /usr/pubsw/packages/mni/1.0.4/lib/ |
#: 1258 Sz: 109670 |
8/9/2001 7:12:47 AM | current ar archive |
|
libnetcdf.a /usr/pubsw/packages/mni/1.0.4/lib/ |
#: 1259 Sz: 68462 |
8/9/2001 7:10:16 AM | current ar archive |
|
libvolume_io.a /usr/pubsw/packages/mni/1.0.4/lib/ |
#: 1260 Sz: 442148 |
8/9/2001 7:12:48 AM | current ar archive |
| /usr/pubsw/packages/mni/1.0.4/lib/mni_autoreg/ | |||
|
file_utilities.pl /usr/pubsw/packages/mni/1.0.4/lib/mni_autoreg/ |
#: 1261 Sz: 22195 |
8/9/2001 7:28:44 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : file_utilities.pl #@DESCRIPTION: Functions to manipulate/check/validate/search files and # directories. #@GLOBALS : #@CREATED : 1995/08/07, Greg Ward (from gpw_utilities.pl) #@MODIFIED : #@VERSION : $Id: file_utilities.pl,v 1.1.1.1 2000/01/19 14:10:31 louis Exp $ #----------------------------------------------------------------------------- # -------------------------------------------------------------------- # Copyright (c) 1995 Greg Ward, McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. Permission to # use, copy, modify, and distribute this software and its # documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies. The # author and McGill University make no representations about the # suitability of this software for any purpose. It is provided "as # is" without express or implied warranty. # -------------------------------------------------------------------- |
|||
|
JobControl.pm /usr/pubsw/packages/mni/1.0.4/lib/mni_autoreg/ |
#: 1262 Sz: 49031 |
8/9/2001 7:28:44 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : JobControl.pm #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: A module for doing process and job stuff -- spawning # children and waiting for them (or detaching them to the # background), detaching ourself to the background, running # stuff remotely -- that sort of thing. #@METHOD : #@GLOBALS : %Options - package options: # Verbose print commands as we execute them? # Execute actually execute commands? # MergeErrors merge stderr with stdout? # ErrorAction what to do when a command fails # Batch submit commands to batch system? # Clobber overwrite output files (instead of append) # LogHandle filehandle to write commands to # Notify should &Obituary actually send mail? # %Programs - known programs and their full paths # %PreOptions - options to come at the start of the command line # for a given program # %PostOptions- options for the end of the command line #@CALLS : #@CREATED : 1995/03/03, Greg Ward #@MODIFIED : 1995/11/14, GW: made into a package # 1996/04/11, GW: made into a Perl 5 module # 1996/12/10, GW: thorough overhaul to allow commands as lists, # default options for commands, and a priori # searching for required programs; also major # code reorg and cleanup #@VERSION : $Id: JobControl.pm,v 1.1.1.1 2000/01/19 14:10:31 louis Exp $ #----------------------------------------------------------------------------- # -------------------------------------------------------------------- # Copyright (c) 1995 Greg Ward, McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. Permission to # use, copy, modify, and distribute this software and its # documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies. The # author and McGill University make no representations about the # suitability of this software for any purpose. It is provided "as # is" without express or implied warranty. # -------------------------------------------------------------------- |
|||
|
minc_utilities.pl /usr/pubsw/packages/mni/1.0.4/lib/mni_autoreg/ |
#: 1263 Sz: 19722 |
8/9/2001 7:28:44 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : minc_utilities.pl #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: Interfaces to a various MINC utilities for common # image- and volume-processing tasks. Uses &Spawn to run # the commands, so be sure you have set the error action # to something reasonable (using &SetSpawnOptions). # Also, requires the following global variables to give # the full location and standard options for the # programs: # $MincInfo # $VolumeStats # $VolumeCOG #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : Greg Ward, July 95 #@MODIFIED : considerably #@VERSION : $Id: minc_utilities.pl,v 1.1.1.1 2000/01/19 14:10:31 louis Exp $ #----------------------------------------------------------------------------- # -------------------------------------------------------------------- # Copyright (c) 1995 Greg Ward, McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. Permission to # use, copy, modify, and distribute this software and its # documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies. The # author and McGill University make no representations about the # suitability of this software for any purpose. It is provided "as # is" without express or implied warranty. # -------------------------------------------------------------------- |
|||
|
misc_utilities.pl /usr/pubsw/packages/mni/1.0.4/lib/mni_autoreg/ |
#: 1264 Sz: 7458 |
8/9/2001 7:28:44 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : misc_utilities.pl #@DESCRIPTION: Miscellaneous and unclassifiable (but otherwise useful!) # utility routines: # ×tamp # &userstamp # &comp_num_lists # &print_banner #@GLOBALS : #@CREATED : 95/08/07, Greg Ward (from gpw_utilities.pl) #@MODIFIED : #@VERSION : $Id: misc_utilities.pl,v 1.1.1.1 2000/01/19 14:10:32 louis Exp $ #----------------------------------------------------------------------------- # -------------------------------------------------------------------- # Copyright (c) 1995 Greg Ward, McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. Permission to # use, copy, modify, and distribute this software and its # documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies. The # author and McGill University make no representations about the # suitability of this software for any purpose. It is provided "as # is" without express or implied warranty. # -------------------------------------------------------------------- |
|||
|
numeric_utilities.pl /usr/pubsw/packages/mni/1.0.4/lib/mni_autoreg/ |
#: 1265 Sz: 5675 |
8/9/2001 7:28:44 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : numeric_utilities.pl #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: Short routines for doing common numeric tasks, including # &in_range, &labs (list absolute value), &round, ... #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : 95/08/07, Greg Ward - broke off from gpw_utilties.pl #@MODIFIED : #@VERSION : $Id: numeric_utilities.pl,v 1.1.1.1 2000/01/19 14:10:32 louis Exp $ #----------------------------------------------------------------------------- # -------------------------------------------------------------------- # Copyright (c) 1995 Greg Ward, McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. Permission to # use, copy, modify, and distribute this software and its # documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies. The # author and McGill University make no representations about the # suitability of this software for any purpose. It is provided "as # is" without express or implied warranty. # -------------------------------------------------------------------- |
|||
|
path_utilities.pl /usr/pubsw/packages/mni/1.0.4/lib/mni_autoreg/ |
#: 1266 Sz: 7884 |
8/9/2001 7:28:44 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : path_utilities.pl #@DESCRIPTION: Functions for recognizing, parsing, and tweaking Unix # filenames and paths: # &replace_dir # &replace_ext # &split_path #@GLOBALS : #@CREATED : 1995/08/07, Greg Ward (from gpw_utilities.pl) #@MODIFIED : #@VERSION : $Id: path_utilities.pl,v 1.1.1.1 2000/01/19 14:10:32 louis Exp $ #----------------------------------------------------------------------------- # -------------------------------------------------------------------- # Copyright (c) 1995 Greg Ward, McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. Permission to # use, copy, modify, and distribute this software and its # documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies. The # author and McGill University make no representations about the # suitability of this software for any purpose. It is provided "as # is" without express or implied warranty. # -------------------------------------------------------------------- |
|||
|
Startup.pm /usr/pubsw/packages/mni/1.0.4/lib/mni_autoreg/ |
#: 1267 Sz: 14773 |
8/14/2001 9:21:44 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : Startup.pm #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: Code that should be executed in all "serious" (long-running, # usually) Perl scripts. # # Please read all comments here before using! #@METHOD : #@GLOBALS : The following subroutines are exported into the namespace # of your main program: # &Startup # &SelfAnnounce # &Shutdown # &Cleanup # &Fatal # Also, the following variables are exported by tha package, # but only set when you call &Startup: # $ProgramPath, $ProgramName - the two components of $0 # $TmpDir - a (hopefully) uniquely named temporary directory # $StartDir - the working directory at startup # $StartDirName - the final component of the directory from # which we were run (eg. if pwd = "/usr/local/poobah" on # startup, then $StartDirName will be "poobah") # # @DefaultArgs - a basic argument table (for use with my # ParseArgs package) for setting common globals # ($Verbose, $Execute, $Debug, $Clobber, $Debug, $TmpDir, # and $KeepTmp) via common options (-verbose, -execute, # -debug, etc) # $KeepTmp - set to 0; change this to 1 to prevent deleting # the temporary directory and everything in it. # # These flags aren't actually used by anything in startup.pl, # but are frequently useful and can be changed by the # arguments in @DefaultArgs: # # $Verbose - a commonly-used flag that controls whether # your program should be noisy or quiet; set to 1 # $Execute - a commonly-used flag that controls whether # subprograms are actually run (and various other # outside-world-interaction stuff, depending on the # application; set to 1 # $Clobber - flag denoting whether your program should # overwrite existing files (and tell subprograms to # do the same) # $Debug - turns on even more verbosity (and tell # subprograms to do the same) # # Also, &Startup modifies the %SIG builtin hash to install # a handler for various signals. (The handler just prints # out what signal was received, calls &Cleanup [to # nuke the contents of $TmpDir], and exits with non-zero # return status.) # #@CALLS : #@CREATED : 95/05/16, Greg Ward: from code in mritotal, do_mritopet, and # autocrop #@MODIFIED : 95/07/07, GW: renamed from gpw_common.pl to startup.pl, # moved the actual startup code into &Startup, # added tons of comments # 95/08/22, GW: removed $PrintTimes from list of needed globals # (now it's just a parameter to &Cleanup); cosmetic # and doc changes # 96/03/21, GW: rearranged shutdown sequence, added/edited # tons of comments #@COMMENTS : #@VERSION : $Id: Startup.pm,v 1.1.1.1 2000/01/19 14:10:31 louis Exp $ #---------------------------------------------------------------------------- # -------------------------------------------------------------------- # Copyright (c) 1995 Greg Ward, McConnell Brain Imaging Centre, # Montreal Neurological Institute, McGill University. Permission to # use, copy, modify, and distribute this software and its # documentation for any purpose and without fee is hereby granted, # provided that the above copyright notice appear in all copies. The # author and McGill University make no representations about the # suitability of this software for any purpose. It is provided "as # is" without express or implied warranty. # -------------------------------------------------------------------- # To use startup.pl, you should (obviously) have `require "startup.pl"' # in your code. Then, before any serious work (eg. creating # directories, processing files, etc.) is done, call &Startup. See # &Startup for a complete list of everything it does. # # Then, once serious processing has begun (ie. if there might be files # in $TmpDir), you should call &Fatal instead of die for any errors; # this will properly clean up and leave a non-zero exit status for the # caller.) (Note: calling die will also result in $TmpDir being cleanup # up, but you have to worry about putting a newline at the end of the # error string in order to prevent the "in xxx line yyy" message. # However, you don't have to worry about any modules calling die (or # croak) -- your program will still clean up correctly, thanks to the # "die handler" set by &Startup.) # # When everything finishes normally, call &Shutdown as one of the last # things you do. (It doesn't have to be the last, as it doesn't exit -- # it just prints out some timing stats and nukes the temporary # directory.) # ------------------------------------------------------------------ # |
|||
|
string_utilities.pl /usr/pubsw/packages/mni/1.0.4/lib/mni_autoreg/ |
#: 1268 Sz: 1497 |
8/9/2001 7:28:44 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : string_utilities.pl #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: String utilties (duh!). #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : 1996/06/11, Greg Ward #@MODIFIED : #@VERSION : $Id: string_utilities.pl,v 1.1 2000/02/28 16:38:25 stever Exp $ #----------------------------------------------------------------------------- # ------------------------------ MNI Header ---------------------------------- #@NAME : &parse_num_list #@INPUT : $list - a string containing a "list" of numbers, something # like "1-3,4,6,9-11" #@OUTPUT : #@RETURNS : a real Perl list with the string expanded as you'd expect # (e.g. (1,2,3,4,6,9,10,11)) # OR empty list if your string is bogus (and prints a warning) #@DESCRIPTION: #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : January 1996, Greg Ward #@MODIFIED : #----------------------------------------------------------------------------- |
|||
|
volume_heuristics.pl /usr/pubsw/packages/mni/1.0.4/lib/mni_autoreg/ |
#: 1269 Sz: 3322 |
8/9/2001 7:28:44 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : volume_heuristics.pl #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: Routines that make some guesses about the nature of volumetric # data sets of the human brain, generally in order to reduce the # amount of data in a consistent way. You should # `require "numeric_utilities.pl"' before calling any of # the routines in this file. #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : 95/10/27, Greg Ward (from code in mritotal) #@MODIFIED : #----------------------------------------------------------------------------- |
|||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/ | |||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/ | |||
|
MNI.pm /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/ |
#: 1270 Sz: 913 |
10/3/1997 1:21:00 PM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : MNI #@DESCRIPTION: Dummy module used to give the whole MNI Perl Library a # version number. #@EXPORT : #@EXPORT_OK : #@EXPORT_TAGS: #@USES : #@REQUIRES : #@CREATED : 1997/05/13, Greg Ward #@MODIFIED : #@VERSION : $Id: MNI.pm,v 1.2 1997/10/03 20:20:35 greg Exp $ #@COPYRIGHT : Copyright (c) 1997 by Gregory P. Ward, McConnell Brain Imaging # Centre, Montreal Neurological Institute, McGill University. # # This file is part of the MNI Perl Library. It is free # software, and may be distributed under the same terms # as Perl itself. #----------------------------------------------------------------------------- |
|||
|
mni_perllib.pod /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/ |
#: 1271 Sz: 2750 |
8/6/1997 3:27:16 PM | ASCII English text |
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/ | |||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/ | |||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ | |||
|
autosplit.ix /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1272 Sz: 349 |
8/9/2001 7:18:06 AM | ASCII text |
|
check_files.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1273 Sz: 3138 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/FileUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
check_input_dirs.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1274 Sz: 1555 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/FileUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
check_output_dirs.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1275 Sz: 1888 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/FileUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
check_output_path.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1276 Sz: 4630 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/FileUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
find_program.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1277 Sz: 1663 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/FileUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
find_programs.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1278 Sz: 1553 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/FileUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
generate_numbered_filename.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1279 Sz: 2535 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/FileUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
search_directories.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1280 Sz: 1964 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/FileUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
statfs.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1281 Sz: 2781 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/FileUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
test_file.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/FileUtilities/ |
#: 1282 Sz: 3442 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/FileUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ | |||
|
auto_threshold.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1283 Sz: 591 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
autosplit.ix /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1284 Sz: 411 |
8/9/2001 7:18:05 AM | ASCII text |
|
compute_resample_args.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1285 Sz: 2046 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
compute_reshape_args.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1286 Sz: 2889 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
get_dimension_order.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1287 Sz: 2492 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
get_history.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1288 Sz: 1212 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
percent_threshold.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1289 Sz: 431 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
put_history.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1290 Sz: 1272 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
update_history.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1291 Sz: 3668 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
volume_cog.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1292 Sz: 557 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
volume_max.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1293 Sz: 626 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
volume_min.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1294 Sz: 625 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
volume_minmax.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1295 Sz: 440 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
volume_params.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MincUtilities/ |
#: 1296 Sz: 3078 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MincUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MiscUtilities/ | |||
|
autosplit.ix /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MiscUtilities/ |
#: 1297 Sz: 230 |
8/9/2001 7:18:05 AM | ASCII text |
|
lcompare.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MiscUtilities/ |
#: 1298 Sz: 2762 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MiscUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
make_banner.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MiscUtilities/ |
#: 1299 Sz: 1389 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MiscUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
nlist_equal.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MiscUtilities/ |
#: 1300 Sz: 890 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MiscUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
shellquote.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MiscUtilities/ |
#: 1301 Sz: 2550 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MiscUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
timestamp.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MiscUtilities/ |
#: 1302 Sz: 1380 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MiscUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
userstamp.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/MiscUtilities/ |
#: 1303 Sz: 1388 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/MiscUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/NumericUtilities/ | |||
|
autosplit.ix /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/NumericUtilities/ |
#: 1304 Sz: 171 |
8/9/2001 7:18:05 AM | ASCII text |
|
in_range.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/NumericUtilities/ |
#: 1305 Sz: 1150 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/NumericUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
labs.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/NumericUtilities/ |
#: 1306 Sz: 1311 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/NumericUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
round.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/NumericUtilities/ |
#: 1307 Sz: 1860 |
8/9/2001 7:18:05 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/NumericUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/PathUtilities/ | |||
|
autosplit.ix /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/PathUtilities/ |
#: 1308 Sz: 240 |
8/9/2001 7:18:06 AM | ASCII text |
|
expand_path.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/PathUtilities/ |
#: 1309 Sz: 1740 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/PathUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
merge_paths.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/PathUtilities/ |
#: 1310 Sz: 1269 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/PathUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
normalize_dirs.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/PathUtilities/ |
#: 1311 Sz: 1053 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/PathUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
replace_dir.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/PathUtilities/ |
#: 1312 Sz: 1371 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/PathUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
replace_ext.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/PathUtilities/ |
#: 1313 Sz: 1246 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/PathUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
|
split_path.al /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/auto/MNI/PathUtilities/ |
#: 1314 Sz: 3137 |
8/9/2001 7:18:06 AM | Perl script |
# NOTE: Derived from blib/lib/MNI/PathUtilities.pm. # Changes made here will be lost when autosplit again. # See AutoSplit.pm. |
|||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/Getopt/ | |||
|
Tabular.pm /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/Getopt/ |
#: 1315 Sz: 24179 |
9/11/1997 2:20:21 PM | Perl script |
package Getopt::Tabular; # Getopt/Tabular.pm # # Perl5 package for table-driven argument parsing, somewhat like Tk's # ParseArgv. To use the package, you just have to set up an argument table # (a list of array references), and call &GetOptions (the name is exported # from the module). &GetOptions takes two or three arguments; a reference # to your argument table (which is not modified), a reference to the list # of command line arguments, e.g. @ARGV (or a copy of it), and (optionally) # a reference to a new empty array. In the two argument form, the second # argument is modified in place to remove all options and their arguments. # In the three argument form, the second argument is unmodified, and the # third argument is set to a copy of it with options removed. # # The argument table consists of one element per valid command-line option; # each element should be a reference to a list of the form: # # ( option_name, type, num_values, option_data, help_string, arg_desc ) # # See Getopt/Tabular.pod for complete information. # # originally by Greg Ward 1995/07/06-07/09 as ParseArgs.pm # renamed to Getopt::Tabular and somewhat reorganized/reworked, # 1996/11/08-11/10 # # $Id: Tabular.pm,v 1.5 1997/09/11 21:20:21 greg Exp $ # Copyright (c) 1995-96 Greg Ward. All rights reserved. This package is # free software; you can redistribute it and/or modify it under the same # terms as Perl itself. |
|||
|
Tabular.pod /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/Getopt/ |
#: 1316 Sz: 40206 |
8/27/1997 1:14:17 PM | ASCII English text |
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/i686-linux/ | |||
|
perllocal.pod /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/i686-linux/ |
#: 1317 Sz: 233 |
8/9/2001 7:19:19 AM | ASCII text |
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/i686-linux/auto/ | |||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/i686-linux/auto/mni_perllib/ | |||
| /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/MNI/ | |||
|
DataDir.pm /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/MNI/ |
#: 1318 Sz: 7303 |
8/9/2001 7:18:05 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : MNI::DataDir #@DESCRIPTION: #@EXPORT : #@EXPORT_OK : #@EXPORT_TAGS: #@USES : #@REQUIRES : Common way for MNI packages to find a directory containing # static data (eg. model files). #@CREATED : #@MODIFIED : #@VERSION : $Id: DataDir.pm.in,v 1.6 1997/09/30 21:12:27 greg Exp $ #@COPYRIGHT : Copyright (c) 1997 by Gregory P. Ward, McConnell Brain Imaging # Centre, Montreal Neurological Institute, McGill University. # # This file is part of the MNI Perl Library. It is free # software, and may be distributed under the same terms # as Perl itself. #----------------------------------------------------------------------------- |
|||
|
FileUtilities.pm /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/MNI/ |
#: 1319 Sz: 43348 |
10/3/1997 6:34:03 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : MNI::FileUtilities #@DESCRIPTION: Functions to manipulate/check/validate/search files and # directories on POSIX systems. #@EXPORT : check_output_dirs # check_output_path # check_input_dirs # check_files # test_file #@EXPORT_OK : search_directories # find_program # find_programs # generate_numbered_filename # statfs #@EXPORT_TAGS: all, check, search, misc #@USES : POSIX, MNI::PathUtilities #@REQUIRES : Exporter #@CREATED : 1997/04/25, Greg Ward (from file_utilities.pl, revision 1.16) #@MODIFIED : #@VERSION : $Id: FileUtilities.pm,v 1.12 1997/10/03 13:31:57 greg Exp $ #@COPYRIGHT : Copyright (c) 1997 by Gregory P. Ward, McConnell Brain Imaging # Centre, Montreal Neurological Institute, McGill University. # # This file is part of the MNI Perl Library. It is free # software, and may be distributed under the same terms # as Perl itself. #----------------------------------------------------------------------------- |
|||
|
MincUtilities.pm /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/MNI/ |
#: 1320 Sz: 34853 |
10/3/1997 6:36:41 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : MNI::MincUtilities #@DESCRIPTION: various MINC hacks, most using external programs #@EXPORT : #@EXPORT_OK : volume_min volume_max volume_minmax # percent_threshold auto_threshold volume_cog # get_history put_history update_history # volume_params get_dimension_order # compute_resample_args compute_reshape_args #@EXPORT_TAGS: range, threshold, history, geometry, args, all #@USES : MNI::Spawn, MNI::NumericUtilities, MNI::MiscUtilities #@REQUIRES : Exporter #@CREATED : 1997/08/07, Greg Ward (from minc_utilities.pl, revision 1.16) #@MODIFIED : #@VERSION : $Id: MincUtilities.pm,v 1.8 1997/10/03 13:35:25 greg Exp $ #@COPYRIGHT : Copyright (c) 1997 by Gregory P. Ward, McConnell Brain Imaging # Centre, Montreal Neurological Institute, McGill University. # # This file is part of the MNI Perl Library. It is free # software, and may be distributed under the same terms # as Perl itself. #----------------------------------------------------------------------------- |
|||
|
MiscUtilities.pm /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/MNI/ |
#: 1321 Sz: 15725 |
10/3/1997 6:37:09 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : MNI::MiscUtilities #@DESCRIPTION: Miscellaneous and unclassifiable (but otherwise useful!) # utility routines #@EXPORT : timestamp # userstamp # lcompare # nlist_equal # make_banner # shellquote #@EXPORT_OK : #@EXPORT_TAGS: #@USES : POSIX, Sys::Hostname, Cwd #@REQUIRES : Exporter #@CREATED : 1997/04/24, Greg Ward (from misc_utilities.pl) #@MODIFIED : #@VERSION : $Id: MiscUtilities.pm,v 1.7 1997/10/03 13:37:04 greg Exp $ #@COPYRIGHT : Copyright (c) 1997 by Gregory P. Ward, McConnell Brain Imaging # Centre, Montreal Neurological Institute, McGill University. # # This file is part of the MNI Perl Library. It is free # software, and may be distributed under the same terms # as Perl itself. #----------------------------------------------------------------------------- |
|||
|
NumericUtilities.pm /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/MNI/ |
#: 1322 Sz: 6761 |
10/3/1997 6:37:27 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : MNI::NumericUtilities #@DESCRIPTION: Short routines for doing common numeric tasks. #@EXPORT : #@EXPORT_OK : in_range # labs # round # min # max #@EXPORT_TAGS: all #@USES : #@REQUIRES : Exporter #@CREATED : 1997/06/06, Greg Ward (from numeric_utilities.pl, revision 1.9) #@MODIFIED : #@VERSION : $Id: NumericUtilities.pm,v 1.3 1997/10/03 13:37:23 greg Exp $ #@COPYRIGHT : Copyright (c) 1997 by Gregory P. Ward, McConnell Brain Imaging # Centre, Montreal Neurological Institute, McGill University. # # This file is part of the MNI Perl Library. It is free # software, and may be distributed under the same terms # as Perl itself. #----------------------------------------------------------------------------- |
|||
|
PathUtilities.pm /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/MNI/ |
#: 1323 Sz: 21653 |
10/3/1997 6:26:19 AM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : MNI::PathUtilities #@DESCRIPTION: Subroutines for recognizing, parsing, and tweaking POSIX # filenames and paths: # split_path # replace_dir # replace_ext #@EXPORT : #@EXPORT_OK : normalize_dirs # split_path # replace_dir # replace_ext # merge_paths # expand_path #@EXPORT_TAGS: all #@USES : #@REQUIRES : Exporter # AutoLoader #@CREATED : 1997/05/13, Greg Ward (from path_utilities.pl, revision 1.10) #@MODIFIED : #@VERSION : $Id: PathUtilities.pm,v 1.10 1997/10/03 13:25:57 greg Exp $ #@COPYRIGHT : Copyright (c) 1997 by Gregory P. Ward, McConnell Brain Imaging # Centre, Montreal Neurological Institute, McGill University. # # This file is part of the MNI Perl Library. It is free # software, and may be distributed under the same terms # as Perl itself. #----------------------------------------------------------------------------- |
|||
|
Spawn.pm /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/MNI/ |
#: 1324 Sz: 47599 |
10/1/1997 1:53:19 PM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : MNI::Spawn #@DESCRIPTION: All-singing, all-dancing program runner (includes path # searching, default arguments, verbose command logging, # interface to UCSF Batch, output redirect/capture, and # error checking). #@EXPORT : SetOptions, RegisterPrograms # AddDefaultArgs, ClearDefaultArgs, Spawn, # UNTOUCHED, REDIRECT, CAPTURE, MERGE #@EXPORT_OK : #@EXPORT_TAGS: all, const, subs #@USES : Carp, Cwd, # MNI::FileUtilities, MNI::PathUtilities, MNI::MiscUtilities #@REQUIRES : Exporter #@CREATED : 1997/07/07, Greg Ward (loosely based on JobControl.pm, rev 2.8) #@MODIFIED : #@VERSION : $Id: Spawn.pm,v 1.11 1997/10/01 20:18:46 greg Exp $ #@COPYRIGHT : Copyright (c) 1997 by Gregory P. Ward, McConnell Brain Imaging # Centre, Montreal Neurological Institute, McGill University. # # This file is part of the MNI Perl Library. It is free # software, and may be distributed under the same terms # as Perl itself. #----------------------------------------------------------------------------- |
|||
|
Spawn.pod /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/MNI/ |
#: 1325 Sz: 47213 |
10/1/1997 1:49:14 PM | ASCII English text |
|
Startup.pm /usr/pubsw/packages/mni/1.0.4/lib/perl5/5.6.0/MNI/ |
#: 1326 Sz: 37830 |
9/30/1997 2:02:22 PM | Perl script |
# ------------------------------ MNI Header ---------------------------------- #@NAME : MNI::Startup #@DESCRIPTION: Perform common startup/shutdown tasks. #@EXPORT : (read the docs for how exports work with this module) #@EXPORT_OK : #@EXPORT_TAGS: #@USES : Carp, Cwd, MNI::MiscUtilities #@REQUIRES : Exporter #@CREATED : 1997/07/25, Greg Ward (from old Startup.pm, rev. 1.23) #@MODIFIED : #@VERSION : $Id: Startup.pm,v 1.10 1997/09/30 20:37:37 greg Exp $ #@COPYRIGHT : Copyright (c) 1997 by Gregory P. Ward, McConnell Brain Imaging # Centre, Montreal Neurological Institute, McGill University. # # This file is part of the MNI Perl Library. It is free # software, and may be distributed under the same terms # as Perl itself. #----------------------------------------------------------------------------- |
|||
| /usr/pubsw/packages/mni/1.0.4/man/ | |||
| /usr/pubsw/packages/mni/1.0.4/man/cat1/ | |||
|
minc_modify_header.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1327 Sz: 3441 |
8/9/2001 7:12:48 AM | ASCII English text, with overstriking |
|
mincaverage.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1328 Sz: 5747 |
8/9/2001 7:12:48 AM | ASCII English text, with overstriking |
|
mincconcat.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1329 Sz: 5863 |
8/9/2001 7:12:48 AM | ASCII English text, with overstriking |
|
mincexpand.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1330 Sz: 1392 |
8/9/2001 7:12:49 AM | ASCII English text, with overstriking |
|
mincheader.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1331 Sz: 965 |
8/9/2001 7:12:49 AM | ASCII English text, with overstriking |
|
mincinfo.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1332 Sz: 4120 |
8/9/2001 7:12:49 AM | ASCII English text, with overstriking |
|
minclookup.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1333 Sz: 10167 |
8/9/2001 7:12:49 AM | ASCII English text, with overstriking |
|
mincmakescalar.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1334 Sz: 5468 |
8/9/2001 7:12:49 AM | ASCII English text, with overstriking |
|
mincmakevector.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1335 Sz: 3416 |
8/9/2001 7:12:49 AM | ASCII English text, with overstriking |
|
mincmath.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1336 Sz: 10582 |
8/9/2001 7:12:49 AM | ASCII English text, with overstriking |
|
mincresample.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1337 Sz: 14922 |
8/9/2001 7:12:49 AM | ASCII English text, with overstriking |
|
mincreshape.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1338 Sz: 16043 |
8/9/2001 7:12:49 AM | ASCII English text, with overstriking |
|
rawtominc.1 /usr/pubsw/packages/mni/1.0.4/man/cat1/ |
#: 1339 Sz: 14708 |
8/9/2001 7:12:50 AM | ASCII C program text, with overstriking |
| /usr/pubsw/packages/mni/1.0.4/man/cat3/ | |||
| /usr/pubsw/packages/mni/1.0.4/man/man1/ | |||
|
autocrop.1 /usr/pubsw/packages/mni/1.0.4/man/man1/ |
#: 1340 Sz: 25977 |
8/9/2001 7:28:44 AM | ASCII troff or preprocessor input text |
|
mincblur.1 /usr/pubsw/packages/mni/1.0.4/man/man1/ |
#: 1341 Sz: 4604 |
8/9/2001 7:28:42 AM | troff or preprocessor input text |
|
minctracc.1 /usr/pubsw/packages/mni/1.0.4/man/man1/ |
#: 1342 Sz: 12898 |
8/9/2001 7:28:44 AM | troff or preprocessor input text |
|
mritoself.1 /usr/pubsw/packages/mni/1.0.4/man/man1/ |
#: 1343 Sz: 2539 |
8/9/2001 7:28:44 AM | troff or preprocessor input text |
|
mritotal.1 /usr/pubsw/packages/mni/1.0.4/man/man1/ |
#: 1344 Sz: 19500 |
8/9/2001 7:28:44 AM | troff or preprocessor input text |
|
ncdump.1 /usr/pubsw/packages/mni/1.0.4/man/man1/ |
#: 1345 Sz: 8322 |
8/9/2001 7:10:17 AM | ASCII troff or preprocessor input text |
|
ncgen.1 /usr/pubsw/packages/mni/1.0.4/man/man1/ |
#: 1346 Sz: 14621 |
8/9/2001 7:10:17 AM | ASCII troff or preprocessor input text |
| /usr/pubsw/packages/mni/1.0.4/man/man3/ | |||
|
Getopt::Tabular.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1347 Sz: 50139 |
8/9/2001 7:18:07 AM | troff or preprocessor input text |
|
MNI::DataDir.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1348 Sz: 9154 |
8/9/2001 7:18:11 AM | troff or preprocessor input text |
|
MNI::FileUtilities.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1349 Sz: 26520 |
8/9/2001 7:18:11 AM | troff or preprocessor input text |
|
MNI::MincUtilities.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1350 Sz: 23771 |
8/9/2001 7:18:06 AM | troff or preprocessor input text |
|
MNI::MiscUtilities.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1351 Sz: 10934 |
8/9/2001 7:18:09 AM | troff or preprocessor input text |
|
MNI::NumericUtilities.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1352 Sz: 6462 |
8/9/2001 7:18:08 AM | troff or preprocessor input text |
|
MNI::PathUtilities.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1353 Sz: 18324 |
8/9/2001 7:18:10 AM | troff or preprocessor input text |
|
MNI::Spawn.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1354 Sz: 61222 |
8/9/2001 7:18:10 AM | troff or preprocessor input text |
|
MNI::Startup.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1355 Sz: 29169 |
8/9/2001 7:18:08 AM | troff or preprocessor input text |
|
mni_perllib.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1356 Sz: 6865 |
8/9/2001 7:18:08 AM | troff or preprocessor input text |
|
netcdf.3 /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1357 Sz: 29565 |
8/9/2001 7:10:18 AM | ASCII troff or preprocessor input text |
|
netcdf.3f /usr/pubsw/packages/mni/1.0.4/man/man3/ |
#: 1358 Sz: 26244 |
8/9/2001 7:10:18 AM | ASCII troff or preprocessor input text |
Go to: