Dear SCT community,
I have a question to which some of you might have an answer:
I did some B1+ shimming experiments (homogenization of the radiofrequency field to obtain more uniform images). As I want to homogenize the signal in the spinal cord only, I performed SC segmentation on anatomical images using sct_deepseg_sc. I now want to compare the signal homogeneity in the SC before and after shimming, but the patient moved between the unshimmed/shimmed acquisitions and the segmentation is no longer matching the actual position of the SC on the shimmed images. I would thus like to do a registration to make sure that I compare the signal in the same anatomical region. I never played around with registration tools so I was wondering if anybody would be able to help me with that, by guiding me towards good tools and tutorials or giving me some advice.
I also don’t know if the best way to go would be to transform the anatomical images (I imagine this to be a standard procedure) or to transform the segmentation.
This link will redirect you to the NIfTI files I want to register:
- INV2.nii.gz - anatomical GRE image used for segmentation
- INV2_shim.nii.gz - anatomical GRE image after shimming in which I would like the segmentation to be registered
- INV2_seg.nii.gz - SC segmentation to register
In the end, I would end up with other images to register, this is why I would like to learn how to do it 
Thank you very much !