T1w anatomical normalization issue about ciftify HOT 2 CLOSED

Thanks for posting this. The good news is that the T1w normalization shouldn't be to detrimental to the surface based fMRI. The same (bad) warp is used for both the functional and surfaces - so even though they look weird - they should still be aligned to each other. In this way, the quality of the T1w to functional registration is more important.

While I say that - the deformity after in the MNI warp in your participant does look particularly bad. This type of deformity is known to happen with FSL's FNIRT (which is what ciftify is using). I beleive it has something to do with the brain masking? Might be worth checking FSL supports on neurostars to see if there are any fixes?

from ciftify.

Thanks for posting this. The good news is that the T1w normalization shouldn't be to detrimental to the surface based fMRI. The same (bad) warp is used for both the functional and surfaces - so even though they look weird - they should still be aligned to each other. In this way, the quality of the T1w to functional registration is more important.

While I say that - the deformity after in the MNI warp in your participant does look particularly bad. This type of deformity is known to happen with FSL's FNIRT (which is what ciftify is using). I beleive it has something to do with the brain masking? Might be worth checking FSL supports on neurostars to see if there are any fixes?

Thank you for your reply. I will look into what I can do regarding FNIRT based normalization.

from ciftify.