Dear all,
I'm having a slight problem with reg-feat2anat to transform functional data (FSL) to anatomical (Freesurfer) in that the resulting transformation seems completely wrong. What I've done so far is the following:
1) run FEAT including the normal FEAT registration (which I know fails due to a lack of FOV in the functional data) 2) re-run the Flirt for a proper registration (i.e. by using the -usesqform option to obtain better registration) 3) overwrite the example_func2highres.mat, highres2standard.mat and example_func2standard.mat file with the newly obtained registration files. (The resulting files are now properly registered when viewing in e.g. fslview) 4) Run updatefeatreg <featdir.feat> 5) Start FEAT and change the mode to run Post-stats only. Select the FEAT output directory as input. Go into the registration tab and turn off all registration. Press GO. (steps 3-5 following the FSL FAQ on custom registration into a FEAT analysis)
6) run a complete freesurfer segmentation and all the rest using recon-all etc 7) reg-feat2anat --feat featdir.feat --subject subjectid
When I now check the registration, it seems completely wrong... My guess would be that it has to do with the re-registration in steps 2-5 but as far as I can tell the files are registered properly to the anatomy scan (and to the template (or standard), the MNI152_T1_1mm_brain file)
Any ideas? (Not sure whether it is appreciated if I send a screenshot as attachment, so I'll leave it for now)
Cheers, Cris