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
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