Possible new output in label_vertebrae

Dear all,

We are wondering whether sct_label_vertebrae could automatically produce the file needed for sct_register_to_template.

Nowadays we are using the seg_labeled_discs file with the -ldisc option, but this is not entirely correct, and maybe you disapprove it?

If this is not possible, how do you suggest the creation of the -lspinal file? Would it be “as easy as” calculating the middle point between two marks in the labeled_discs file? Or should this middle point be projected into the centerline file?

Would this last option be done with the sct_get_centerline function?

Looking forward to hearing from you!
Peace,

Aran

Hi Aran,

Thank you for sharing your thoughts, these are quite relevant for improving the workflow of SCT.

Nowadays we are using the seg_labeled_discs file with the -ldisc option, but this is not entirely correct, and maybe you disapprove it?

I do not disapprove it. For more context/discussion, please see Best practices for manually defining vertebral levels

If this is not possible, how do you suggest the creation of the -lspinal file? Would it be “as easy as” calculating the middle point between two marks in the labeled_discs file? Or should this middle point be projected into the centerline file?

The -lspinal flag is something different: it refers to the spinal (not vertebral) levels. So, this flag should only be used if you know the spinal levels. These could be identified manually if the image shows the nerve rootlets, or if it concerns a post mortem scan where the surgeon identified the nerve rootlets.

Hope that helps,
Julien

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Hello Julien,

My concerns come from the documentation of sct_register_to_template. Particularly, the -ldisc flag.
There it says Labels located at the posterior edge of the intervertebral discs.. Furthermore, the flag -l says One or two labels (preferred) located at the center of the spinal cord, on the mid-vertebral slice. And the file seg_labeled_discs is marked in the intervertebral disks BUT at the center of the spinal cord.

So, we have two different flags to register our images to the template and a labeled file which does not fully accomplish any of the definitions.

I am picturing a way to obtain only two labels from the seg_labeled_discs in order to use it with the -l flag but I don’t know if this is appropriate.

Overall, my question would be, is this code “good enough”?

sct_register_to_template -i T1.nii -s T1_seg.nii -ldisc T1_seg_labeled_discs.nii -c t1

Thank you!

Aran

My concerns come from the documentation of sct_register_to_template. Particularly, the -ldisc flag.
There it says Labels located at the posterior edge of the intervertebral discs.. Furthermore, the flag -l says One or two labels (preferred) located at the center of the spinal cord, on the mid-vertebral slice. And the file seg_labeled_discs is marked in the intervertebral disks BUT at the center of the spinal cord.
So, we have two different flags to register our images to the template and a labeled file which does not fully accomplish any of the definitions.

I agree this is confusing. I’ve opened an issue, feel free to chip in. Thank you for pointing that out.

Overall, my question would be, is this code “good enough”?
sct_register_to_template -i T1.nii -s T1_seg.nii -ldisc T1_seg_labeled_discs.nii -c t1

Yes, this is absolutely good enough.