I'm trying to make a statistics of resting state fMRI data in fsfast. I have one group of patients and two timepionts. 

I read how to perform the paired analysis in structural studies in freesurfer. In structural images the difference between the timepoints should be prepared in mri_preproc command. Should I add the same command --paired-diff to isxconncat?

If not, how to perform the paired test?

Best regards, 

Agnieszka