- recon-all for each subject
- check Check brainmask, if changed re-run recon-all from that step
- check Check gray matter/white matter boundaries, if changed re-run recon-all from that step
- create Create a FreeSurfer Group Descriptor File (FSGDF)
...
- 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