VMB like analysis in SCT


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,

Hi Pawel,

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,

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