HI, I am trying to see difference in groupmap between 2 time-point within 1 group with glmfit.

I followed the instruction"PairedAnalysis". mris_preproc .... --paired-diff

mri_glmfit --surf fsaverage "$hemi" --y "$hemi"_cope1_"$grp".sm"$fwhmsrc".mgh --yffxvar "$hemi"_varcope1_"$grp".sm"$fwhmsrc".mgh --glmdir $fsdir/group_surf//"$hemi"_cope"$num"_"$grp".sm"$fwhmsrc"_ffx --ffxdof 1872 --osgm

When I checked the output of the mri_glmfit, the mask file does not cover the entire brain as the cope/varcope does. it is much smaller and missing parietal brain.

the log file says "Reshaping mriglm->mask..." Is this the issue?

YUMI