Dear Freesurfer Experts,

I would like the mean thickness measures of each clusters i found in qdec from both control and patient group.

I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group.

I found 30 different significant clusters after FDR. I would like to extract the mean cortical thickness of each significant cluster in the patient group and in the healthy control group.

I went though previous post and run the following command:

mri_glmfit-sim --glmdir lh-Diff-Control-HF-Intercept-thickness --cache 1.3 abs --cwpvalthresh .99

and found following output:

cmdline mri_glmfit --y /home/virtualuser/freesurfer/subjects/qdec/glmdir/y.mgh --fsgd /home/virtualuser/freesurfer/subjects/qdec/glmdir/qdec.fsgd doss --glmdir /home/virtualuser/freesurfer/subjects/qdec/glmdir --surf fsaverage lh --label /home/virtualuser/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /home/virtualuser/freesurfer/subjects/qdec/glmdir/contrasts/lh-Avg-Intercept-thickness.mat --C /home/virtualuser/freesurfer/subjects/qdec/glmdir/contrasts/lh-Diff-Control-HF-Intercept-thickness.mat

WARNING: unrecognized mri_glmfit cmd option doss

SURFACE: fsaverage lh set: No match. FreeSurfer:~/freesurfer/subjects/qdec/glmdir>

Any help would be great.

With regards,

Santosh