I found an optical rat spinal cord atlas (RatAtlas.nii.gz) that contains one spinal cord segment per slice.
This I would like to register to MR scans (e.g. here T2.nii.gz). (The mentioned example files are all in this zip file )
What I tried so far:
Some preprocessing is needed just to get any registration without error. RatAtlas_refit.nii.gz is a version shifted in space to have the same geometry as T2.nii.gz (using AFNI 3drefit), so that they at least roughly overlap (otherwise ants produces an error).
T2_straight.nii.gz is the straightened cord after using sct_straighten_spinalcord, to hopefully simplify the registration a bit.
For both the atlas and target scan there are also the spinal cord segmentations (*_seg.nii.gz) available (binary mask of the sc).
With sct_register_multimodal I got a registration, but when looking more closely, the individual segments don’t really correspond. Since the atlas goes from C1 all the way to L4, but the MR scan only from ~C5 to ~T6, the result should’t contain all atlas slices in the first place.
I don’t know if registration of partially overlapping images is even possible with sct_register_multimodal.