Verification of correct labelling

Hello team,

I want to verify the correctness of labelling. As I checked the “sct_process_segmentation” command, it needs the segmented image and the pam50 levels. Just to do an initial investigation, I opened these two images in fsleyes and it seems that they are not correctly mapped on each other. Since I had some incorrect labellings and so per-level CSA computations, I wanted to make sure that the labelling is true. If it is true, I can say that the resultant CSA exactly belongs to the reported level. Please guide me on how to verify this. Any suggestion is appreciated.



Hi @Maryam ,

the vertebral labeling is incorrect. You can use the “-qc” feature in sct_label_vertebrae to more easily spot mis-labeling.

you can fix that by either providing manual initialization (see flag “-discfile”).

hope that helps!

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Thank you @jcohenadad for your response.

I explain my question in another way: I want to compute the per level CSA as accurate as possible. As I checked the command line for CSA computation, it only needs the segmented image and the pam-50 levels. It does not seem that vertebral labelling of image be considered in the calculation of CSA. I will add the command line as follows:

sct_process_segmentation -i ${file_t2_seg}.nii.gz -vert 2:5 -perlevel 1 -vertfile label_T2/template/PAM50_levels.nii.gz -o ${PATH_RESULTS}/csa-SC_T2.csv -append 1

The question is how to verify that the above command line maps pam-50 levels on the segmented image accurately and so results in a correct CSA?

P.S. I did not find any helpful flag in “sct_process_segmentation”. to help with this problem.


Not necessarily. The only things needed are:

  • a segmented image (ie: spinal cord segmentation)
  • a vertebral level image, which could either be the PAM50 level as you mentioned (under label_T2/template/PAM50_levels.nii.gz), but it could also be the labeled segmentation (eg: ${file_t2_seg}_labeled.nii.gz).

So, you don’t necessarily need to register your image with the PAM50 template if your goal is to compute CSA across various levels.

I hope that helps

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