FreeSurfer Processing Steps

Owned by Paul Macey (admin)
Last updated: Oct 26, 2017
3 min read
  • 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/design.fsgd)
  • Run the preproce command on left then right hemispheres (note the two places left/right are indicated - the "--hemi" argument, and the "--out" argument):

[[..]]$ mris_preproc --hemi lh --fsgd  /usr/local/freesurfer/qdec/thisdesign/design.fsgd  --target fsaverage --meas thickness --out /usr/local/freesurfer/qdec/thisdesign/preproc_lh.thickness.mgh

[[..]]$ mris_preproc --hemi lr --fsgd  /usr/local/freesurfer/qdec/thisdesign/design.fsgd  --target fsaverage --meas thickness --out /usr/local/freesurfer/qdec/thisdesign/preproc_rh.thickness.mgh

  • Create a qdec table file (e.g., /usr/local/freesurfer/qdec/thisdesign/qdec.table.dat)

Example:

fsid Group Age BDI BDInormal BDIhigh BeckAnxiety BeckAnxietyNormal BeckAnxietyHigh GMvol WMvol CSFvol TIVvol Brainvol GMWMratio BrainCSFratio BrainTIVratio Epworth EpworthNormal EpworthHigh EpworthORPSQInormal EpworthORPSQIhigh Handed PSQI PSQInormal PSQIhigh Sex SexFemale SexMale
CON279 CONFEMALE 52.4545 3 1 0 3 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0.70432 0.3844 0.28584 1.3746 1.0887 male 3.8088 0.79205
CON285 CONFEMALE 62.7461 1 1 0 1 1 0 0 0 0 7 1 0 7 1 0 0 0 0 0.70588 0.47258 0.31367 1.4921 1.1785 male 3.757 0.78978
CON307 CONFEMALE 54.6776 13 0 1 13 0 1 0 0 0 25 0 1 25 0 1 0 0 0 0.62146 0.38496 0.25891 1.2653 1.0064 male 3.8872 0.79538
OSA154 OSAFEMALE 59.4962 22 0 1 0 0 0 22 0 1 17 1 0 0 0 0 17 1 0 0.67188 0.43682 0.343 1.4517 1.1087 male 3.2324 0.76373
OSA205 OSAFEMALE 56.1971 6 1 0 0 0 0 6 1 0 10 1 0 0 0 0 10 1 0 0.59438 0.4081 0.26482 1.2673 1.0025 male 3.7856 0.79104
OSA269 OSAFEMALE 37.3936 4 1 0 0 0 0 4 1 0 2 1 0 0 0 0 2 1 0 0.62829 0.36069 0.1999 1.1889 0.98898 male 4.9472 0.83185
  • Run qdec in terminial
  • Open qdec.table.dat file