Doug, thank you very much. One subject result from mris_preproc only have partial brain data. this caused error. But I dont know why this subject data failed in mris_preproc.

my command is the following,

mris_preproc --target fsaverage --hemi $hemi --out sub1.mgh --paired-diff --iv subj1.run1_cope1.nii subj1.run1_reg.dat --iv subj1.run2_cope1.nii subj1.run2_reg.dat

YUMI

Reshaping is not the issue. How many subjects are there? If any subject is missing data in a vertex, that entire vertex is excluded, so if you have one subject that is missing that area, it will not be processed. doug

On 05/30/2012 02:53 PM, YUMI MAEDA wrote:

...

HI, I figured out, one of the cope file had problem... YUMI

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

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