Dear Dr Greve,

I am new to FSFAST so I highly appreciate your response.

I have resting state fMRI data and I am following the steps as reported in wiki. I want to study the difference in functional connectivity between two groups

My questions are regarding motion evaluation and the contrasts.

1. The attached figure is an output of "plot-twf-sess". Given the plotted data can we say that including run 003 is more reliable that all the other runs?

2. In the attached figure the command "plot-twf-sess" provides the maximum and minimum motion for every run on Y axes. I am wondering if there is any way to create a cutoff value of motion parameters for all the runs in the study were data can be included/excluded depending on lower/upper than this cutoff? 

3. I used the following commands to study the differnc ein functional connectivity between two groups (each group has one run):

## preprocessing

preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh -mni305-2mm -fsd bold -per-run -init-spm

### First-Level (Group) Analysis

mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 -notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run 

mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 -notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run 

mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run 

#####Analyze First Level

selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok

selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok

selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok

Now for the next step I need to concatenate the sessions using isxconcat but this command needs a contrast which I didn't create it in the previous step. Given that I am looking for a differnce in the functional connectivity between two groups how can I create the contrast for this anlaysis.

Thank you for any help and feedback!!

John