Dear all,
I am using the command reg-feat2anat to transform functional data pre-processed in FSL to the anatomical image in Freesurfer.

As suggested, I check the registration with reg-feat2anat --feat run2.feat —manual.

I have 3 runs of functional data for each subject. Surprisingly, some runs are registered well but others not (even of the same subject, so using the same reference anatomical images: see the attached image. Upper row: bad registration of one run and lower row: good registration of another run).

I have no problem to manually correct the registrations, it works well, but as I have many subjects, I wonder if there may be a way to change some options of reg-feat2anat to make it work better? Can you see from the attached image what is the problem with my images? (I viewed the functional and anatomical data of a few subjects, some woth good and some with bad registration and see no difference or flip)

Thanks a lot for your help!
Aga