Which version of freesurfer are you running? At one point, reg-feat2anat was dependent on the feat registration, but "now" it is not. I don't know whether you fall into the "now" category. If you have a partial FOV, then it will probably fail. You can test this by running bbregister outside of the reg-feat2anat. You can look in the reg-feat2anat for a command line, but it should be something like:

bbregister --s subject --mov example_func.nii.gz --bold --init-fsl --reg register.dat

If this fails, you have a couple of options. If the functional and anatomical were acquired in the same session, then you can use --init-header instead of --init-fsl. If they are not but you have a full-brain of anything acquired during the same session as the functional, you can pass that as an intermediate volume to bbregister (--int).

doug

Cris Lanting wrote:

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

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