Vertebral labeling

SCT
1

Dear SCT team:
Hi!
I have used ‘sct_label_vertebrae’ to label the spinal cord vertebral levels.But the result don’t include C3-6 levels. I hope to know how to fix that.

spinal
spinal1092×410 121 KB

The exact syntax I used is as follows:

sct_deepseg -i t2.nii.gz -task seg_sc_contrast_agnostic -o t2_seg.nii.gz
sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc ~/qc_singleSubj

Thank you very much!

2

t2 and t2_seg look like this:

t2
t2776×649 101 KB

t2_seg
t2_seg782×652 26.5 KB

3

Hi @janessa,

Vertebral labeling is not 100% robust. Two options:

  • If you notice that in your data labeling often fails (>20%) and your dataset is relatively small (<100 subjects), then you’d better do manual disc labeling and then re-run the pipeline. See eg this project.
  • If vertebral labeling only happens in a few subjects, then my suggestion would be to run your pipeline on all the subjects, then perform QC, flag the subjects that fail, retrospectively perform manual correction on the failing labels, save the manual labels in your derivative folder, and re-run the automatic analysis while taking into account manual labels if they exist.

Cheers,
Julien