Hi-I am trying to work out a work flow of integrating fsl and freesurfer. the basic goal is to do surface-based group analysis.<br><br>what I have now is the run1.feat, run2.feat and mean.gfeat for each subject done by FSL Feat and the processing anatomy using recon-all in freesurfer. so the question now is how to combine them.
<br><br>It seems to me that one way is to (1) use reg-feat2anat to register the feat to freesurfer anatomy; (2) using mris_preproc to resample it into common surface space, and (3) using mri_glmfit to computer the mean for each subject; and repeat (2) and (3) for group analysis.&nbsp; 
<br><br>but if I want to use feat to do the whole statistics, I am not sure how should I proceed. I will still use (1) to do the registration, and use (4) feat2surf to resample each feat into common surface space.&nbsp; but then I am not&nbsp; sure how to do statistics using Feat (both fixed effect to combine two runs and random effect to combine across subjects).
<br><br>any help will be greatly appreciated.<br>Gui<br>