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

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