Gui, Have you had a look at the tutorial page that describes the FSL/Freesurfer integration?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial see slide #4, and session 2b. I can't offer any other help than this, as I do not have experience performing this integration, but your approach is similar to the tutorial. Nick On Tue, 2007-12-18 at 16:26 -0800, Gui Xue wrote: > 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. > > 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. > > 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. > > 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. > but then I am not sure how to do statistics using Feat (both fixed > effect to combine two runs and random effect to combine across > subjects). > > any help will be greatly appreciated. > Gui > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer