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