hi
When extracting metrics between c1 ad c3 for all my subjects, I can find out that corresponding slices’ numers are very different between subects. As it can be seen in the following two .csv files: slices 10:13 for subject 1 and 3:7 for subject 2:
the slices are based on the vertebral labeling you did, so if you are skeptical about this, i suggest you check your vertebral labeling.
I used sct_labels_utils on 3dT1 image as suggested as sct_label_vertebrae gave an error.
Do you confirm slice number 0 is the first starting from the top of spinal cord?
Thanks
Rosella
Do you confirm slice number 0 is the first starting from the top of spinal cord?
it depends on your data orientation. Open a viewer, e.g. FSLeyes to verify.
OK. THANK YOU. As regards vertebral labeling instead, I find no alternative apart from doing it manually:
`
sct_label_utils -i …/…/3dt1/3dT1.nii.gz -create-viewer 1,4 -msg “Create label at the posterior tip of the top of C1 vertebra and at C3-C4 disc” -o labels_disc1-4.nii.gz
`
so I hope it gives reliable results. How could I check my labelling is correct?
you must of course make sure that the T1 is somewhat aligned (at least in the S-I direction) with your diffusion scan. E.g., if there was repositioning between the T1 and the diffusion scan, that method would not be valid anymore and you would need to do the labeling on the diffusion scan (or, better, on the localizer).
If slices are numbered in the I->S direction of the image, as it is output by sct_extract_metric selected slices appear more consistent across subjects.
We had already verified 3dT1 and DKI scan were alligned in the S->I direction, hopefully.
I attached some example subjects with selected slices corresponding to c1:c3 according to my labelling
