This page is an entry point into a collection of articles of potential interest to fellow FreeSurfer users.

Understanding FreeSurfer, Its Process and Data

Some introductory and overview information about the FreeSurfer process, and the programs and data files involved. Useful if you are newly encountering FreeSurfer, or if you need some material to present to colleagues to bring them up to speed quickly.

Topic and Link Description
FreeSurfer Process Diagram An overview (circa 2003) of the FreeSurfer process, illustrated with miniature pictorial versions of the files produced and consumed at each stage.
FreeSurfer 3.0.3 (2006) Process vs Data Files A table concisely presenting FreeSurfer’s main processing steps, with cross-reference to data files consumed and produced at each stage.
FreeSurfer (2001)Process and Data files Ditto for FS 2001.
Data File Sample Images: (400K) Larger-sized look at the files involved at each step of the process. Again, view in conjunction with the pages above.
Surfaces vs MRI Images: Sample images showing FS-generated surfaces intersected with the MRI data that produced them.

Installing FreeSurfer and Initial Validation

  • Installation/Validation Notes: I used to have  a lot to say about the FS 2001 installation. My experience with the FS 2006 installation and validation was very smooth, and the online docs much better… so start here:FreeSurfer Wiki – DownloadAndInstall

Program and File Technical Documentation

Documentation on miscellaneous FreeSurfer programs and files.