I am currently processing my t2s scan file and would like to obtain the CSA of the gray matter and white matter for each vertebra. Is it possible to use the sct_label_utils function to display the t2s on top of the t2 image so that I can create a labeling file for the t2s?
I would then take the new file (vert_labels.nii.gz) and apply this to the sct_process_segmentation function in the -vertfile add on.
If you have any other suggestions let me know.
there are various ways you can do this. The easiest (it seems), would be to create the vertebral labels on the T2 image, then resample this label files in the space of the T2* image, and then run
sct_process_segmentation. Code would look like this (update with your custom names and specs):
sct_label_vertebrae -i t2.nii -s t2_seg.nii -c t2
sct_register_multimodal -i t2_seg_labeled.nii -d t2star.nii -identity 1 -x nn
sct_process_segmentation -i t2star_gmseg.nii -vertfile t2_seg_labeled_reg.nii -vert 3:5 -perlevel 1
That makes sense. Perfect it works.