- recon-all for each subject
- check brainmask, if changed re-run recon-all from that step
- check gray matter/white matter boundaries, if changed re-run recon-all from that step
- create a FreeSurfer Group Descriptor File (FSGDF)
This page describes the FreeSurfer Group Descriptor File (FSGDF)
Format (Version 1) as of 11/12/02. FSGDF is a way to describe a group
of subjects and their accompanying data. This can include class
membership and other continuous varibles (eg, age). The FSGDF is used
by mris_glm and tksurfer (and will be used by mri_glm, when it exists,
and tkmedit). Group desgin matrices can be computed directly from
the FSDGDF. The FSGDF format uses tags to identify information.
Example of a legal file:
------------------------- cut here ------------------
GroupDescriptorFile 1
Title MyTitle
Class OSA plus blue
CLASS Control circle green
SomeTag
Variables Age Sex Weight
Input 7000 OSA 45 0 120
Input 7001 Control 51 1 200
#Input 7002 OSA 65 1 200
DefaultVariable Age
------------------------- cut here ------------------
Notes:
1. The first line must be "GroupDescriptorFile 1".
2. Title is not necessary. This will be used for display.
3. Class only needs the class name, the next two items
will be used in the display.
4. The third input is ignored.
5. DefaultVariable is the default variable for display.
6. SomeTag is not a valid tag, so it will be ignored.
General Rules:
1. Tags are NOT case sensitive.
2. Labels are case sensitive.
3. When multiple items appear on a line, they can be
separated by any white space (ie, blank or tab).
4. Any line where # appears as the first non-white space
character is ignored (ie, a comment).
5. The Variables line should appear before the first Input line.
6. All Class lines should appear before the first Input line.
7. Variable label replications are not allowed.
8. Class label replications are not allowed.
9. Subject Id replications are not allowed.
10. If a class label is not used, a warning is printed out.
11. The DefaultVariable must be a member of the Variable list.
12. No error is generated if a tag does not match.
13. Empty lines are OK.
14. A class label can optionally be followed by a class marker.
15. A class marker can optionally be followed by a class color.
- Save in a linux location (e.g., /usr/local/freesurfer/qdec/thisdesign/fsgd.)