Hi,

I am not entirely sure I am doing it right, therefore would like to have a confirmation if possible.

I am runing a paired ttest between two conditions by specifying file names. Here is an example of 2 subjects

mris_preproc \
--target fsaverage \
--hemi lh \
--out /ResultsDir/lh.outfilename.mgh \
--fsgd pairs.fsgd \
--is /subject1/condition1.mgh \
--is /subject1/condition2.mgh \
--is /subject2/condition1.mgh \
--is /subject2/condition2.mgh \

--srcfmt curv \
--paired-diff

mri_surf2surf --s fsaverage \
--hemi lh \
--fwhm 5\
--sval /ResultsDir/lh.outfilename.mgh \
--tval /ResultsDir/lh.outfilename.sm05.mgh

mri_glmfit \
--glmdir /ResultsDir \
--y /ResultsDir/lh.outfilename.sm05.mgh \
--fsgd paired-diff.fsgd \
--C mean.mtx \
--surf fsaverage lh \
--cortex

%% my pairs.fsgd file

GroupDescriptorFile 1
Title StudyTitle
Class Main

Input subject1 Main
Input subject1 Main
Input subject2 Main
Input subject2 Main

%% my paired-diff.fsgd

GroupDescriptorFile 1
Title StudyTitle
Class Main

Input subject1 Main
Input subject2 Main

%% my mean.mtx file

1

Thanks,

Dace