[Freesurfer] paired ttest by specifying file names

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