Options for manual disc labeling

Hello!

I am following the instructions here for vertebral labeling:

Question 1

After both automated vertebral labeling and labeling vertebrae with manual C2-C3 initialization (p.57) had failed, I am manually labeling the disc (p.59) as follows:

sct_label_utils -i t2.nii.gz -create-viewer 3,4,5 -o labels_disc.nii.gz -msg “Place labels at the posterior tip of each inter-vertebral disc. E.g. Label 3: C2/C3, Label 4: C3/C4, Label 5: C4/C5”

This outputs only labels_disc.nii.gz

What is the step after this? According to your instructions, it seems like the following is the next step but t2_labels_vert has not been output.

sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_labels_vert.nii.gz -c t2

Question 2

Also, is it okay to do the following to manually label C3 and C5 vertebrae (screenshot attached) instead of manually labeling the disc? If not, why?

sct_label_utils -i t2.nii.gz -create-viewer 3,5 -o t2_labels_vert.nii.gz -msg “Click at the spine C3 and C5 level, NOT the posterior tip of the disc”;

Then, proceed with

sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_labels_vert.nii.gz -c t2

Thank you for your help!

Sincerely,
Lisa

Hi @lisaeylee !

About Question 1:

  • If you label discs, then sct_register_to_template should be run with flag -ldisc instead of -l.
  • Also, you should then input the label file you created in sct_register_to_template, i.e.: labels_disc.nii.gz instead of t2_labels_vert.nii.gz.
  • Finally, if you wish to account for more levels, then I suggest you only label two discs (instead of three, because when using more than 2 labels, a non-linear scaling is performed, so you loose information above the top and bottom label, see more details here).

So, if you are interested in quantifying things between C2 and C5 you would do something like this:

# Label discs
sct_label_utils -i t2.nii.gz -create-viewer 3,5 -o t2_labels_disc.nii.gz -msg “Place labels at the posterior tip of each inter-vertebral disc: Label 3: C2/C3, Label 5: C4/C5”
# Register to template
sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_labels_disc.nii.gz -c t2

About Question 2: You are absolutely right. You can instead label vertebral bodies. In this case, to be consistent and clear about the syntax and file names, I would do this:

# Label vertebral bodies
sct_label_utils -i t2.nii.gz -create-viewer 3,5 -o t2_labels_vert.nii.gz -msg “Place labels in front of vertebral bodies, centered in the spinal cord: Label 3: C3, Label 5: C5”
# Register to template
sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_labels_vert.nii.gz -c t2

Note: I recommend you use our online tutorial instead of the course PDF. The tutorial is not used for SCT courses and is always up-to-date.

Excellent. Thank you, Julien!

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