Thanks, yes the registrations are way off
I’d be wary of calling it a “registration”; the issue arises from inconsistent interpretation of image axes, there’s no “registration” step per se.
Can I check regarding the inputs for
labelsgmfix?
So the input parcellation and T1 images don’t strictly have to be defined on the same voxel grid: FIRST provides its segmentations as surface meshes, which are converted from FIRST’s axis convention to scanner-space coordinates, and them mapped to the parcellation image voxel grid via the mesh2pve command. This process does however require that those two images be intrinsically aligned with one another in scanner space. I’m reasonably confident that the conversion from FIRST to scanner space coordinates is correct, so my suspicion is that FreeSurfer has done some form of axis conversion / permutation at the subject import step. But you’ll need to look very closely at your images at the input & output of all steps to figure out where the discrepancy is coming from. Make sure you use the “Overlay” tool in mrview to assess whether or not two images are aligned with one another; flicking between two images with the “snap to axes” option on snaps the camera position to each image as you switch, so may not give a faithful representation.
Normally my suggested quick solution would be to provide as the T1 image the orig.mgz file imported & saved by FreeSurfer, but:
I then tried the freesurfer T1 but fsl first failed.
:-/
I am assuming the registrations to diffusion are performed after the
labelsgmfix?
Your main issue here is independent of inter-modal registration. Nevertheless, registration between T1 and DWI can happen before or after T1 processing. The trick is that if you perform any transformation of the T1 after processing, any images derived from that T1 need to undergo the same transformation; otherwise you will have aligned the T1 with your DWIs, but e.g. the parcellation image remains misaligned.
Rob