I have spinal cord scans from MS patients and healthy controls, done on 3T Siemens Tim Trio according to SCT SOP protocol. I am wondering, apart from standard SCT analysis, if it possible to compute something like voxel-wise morphometry in FSL to asses regional atrophy in WM and GM in the cord segment corresponding to MEDIC sequence location. As an alternative idea I have though about using the PAM50 atlas WM and GM segmentations to calculate volume for each of them and then compare them between the groups.
I would appreciate any kind of information that could point me in the right direction.
All the best,
Thank you for reaching out. Yes, it is definitely possible to run a classical VBM analysis in the spinal cord, assuming your scans are properly registered. So, for example, you could do you the preprocessing with SCT, and then launch a VBM pipeline, as done in Moccia et al. 2019.
Alternatively, as you rightfully suggested, you could compute spinal cord, WM and GM volumes, and then compare across groups. I prefer this approach as it is less sensitive to mis-registration. This approach was applied in a few publications. I suggest you look at the list of articles using SCT, and search for the keyword “atrophy”.
Hope that helps,