HI Julien & the SCT team,
I was hoping you can shed some light on how sct_label_vertebrae and sct_register_to_template deal with vertebral alignment.
Test case - if I notice that vertebral labelling has failed with sct_label_vertebrae I’ve switched to using -discfile where I can explicitly input the locations of discs 3->9 and avoid having the program try to detect them. This seems to solve most of our problematic registrations. Is this in any way comparable to using the -ldisc option in sct_register_to_template? I.e. can you “force” vertebral alignment using this option?
From the London course material (p61):
However, if your volume spans a large superior-inferior length (e.g., C2 —> L1), the linear scaling between your subject and the template might produce inaccurate vertebral level matching between C2 and L1. In that case, you might prefer to rely on all inter-vertebral discs for a more accurate registration: sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_labels_disc.nii.gz -c t2
The reason I ask is that in some cases (particularly EPI to template registration) we have some issues with vertebral alignment. From looking at the London course material (p47) it seems that under normal circumstances vertebral alignment is dealt with by an affine transform - would this step be ignored if forcing alignment (as per above)?
I was wondering whether affine registration can fail in the case of age-related spinal degeneration as you might find e.g. that the C5 vertebra is smaller than the others, so a linear transform would not be able to cope with this? Although in general there must be quite a bit of variation in the disc to disc spacing in the general population, so I guess this problem must be broader than just age-related change.
Sorry for the rambling brain burp.