CSA at disc level

SCT
1

Hello,

Is there any way that csa could be computed at the disc level?
I have been checking the commend sct_process_segmentation to see if there is an option for computing csa at disc level instead of vertebral level, but I did not reach any answer. I would really appreciate it if you can guide me on how to find the csa at different disc levels of the spinal cord.

Thanks very much,
Maryam

2

Hi Maryam,

What you could do is input your labeled discs file as if it was a vertebral labeling file. What sct_process_segmentation does is simply get the center of mass of each label value (e.g. “3”) and find the associated slice(s). So, if there is only a single label (in the case of a disc label), then it will also work.

For example:

sct_process_segmentation -i t2_seg.nii.gz -vertfile t2_seg_labeled_discs.nii.gz -vert 2:7 -perlevel 1 -o csa_discs.csv

Gives me this:

Filename Slice (I->S) VertLevel DistancePMJ MEAN(area)
/Users/julien/sct_example_data/t2/t2_seg.nii.gz 103 7 58.322241540660000
/Users/julien/sct_example_data/t2/t2_seg.nii.gz 123 6 62.43443205364000
/Users/julien/sct_example_data/t2/t2_seg.nii.gz 142 5 68.77400737215910
/Users/julien/sct_example_data/t2/t2_seg.nii.gz 165 4 74.10800540239120
/Users/julien/sct_example_data/t2/t2_seg.nii.gz 187 3 72.56737195942480
/Users/julien/sct_example_data/t2/t2_seg.nii.gz 206 2 72.74423857359600

Cheers,
Julien

3

Thank you, Julien. So, for any image that I want to find the csa at disc level, I should make the labeled disc file manually, and then use the above command…

4

You can either do the labeling manually, or use sct_label_vertebrae, which automatically outputs labeled discs (this is all explained in the tutorials).

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