I’m trying to register mFFE 3D volume consisting of 14 slices to the template space. I’ve registered several scans already, but for some of them the registration is rotated, misaligned, not registered, or only has one slice that is registered. I’ve attached a ppt showing the issues. I’m particularly concerned about the scans that are not registering or have compressed registration. These scans have mFFE crops that work and remain in the same space, are segmented appropriately, and have correct labels, but don’t register to the template space. When analyzing the deformation fields in mipav, the field is completely dark and the transformation is not apparent. The deformation fields for the empty registered scans are all very large (~3.48*10^33). I’m using the following command for registration: sct_register_to_template -i mFFE_crop.nii -s mFFE_crop_seg.nii -l labels_vert.nii.gz -c t2 -param step=1,type=seg,algo=centermassrot,metric=MeanSquares:step=2,type=seg,algo=columnwise,metric=MeanSquares -ref subject. Vertebral straightening by removing “-ref subject” does not change the issue. Please let me know if you have any suggestions.
Faulty Registrations copy.pptx (607.4 KB)