How does the '-vert' flag work?

Dear all,

After using sct_process_segmentation, we noticed that the output is not what we expected.

Here is the comand

sct_process_segmentation -i SC_Segmentation.nii.gz -o OutputSC_csa_2.csv -perslice 0 -append 1 -vert 2:3 -vertfile seg_labeled_discs.nii

After visually checking the output with our image, the slices only cover the C2 section but initially we wanted to include also the C3 section. If we understood it correctly, the code is right, but not the results?

Should we write -vert 2:4? Or -vert 2,3? Or perhaps something else :slight_smile:


hi Aran,
thank you for posting-- please make sure to use the vertebral labeled segmentation (ie: all voxels of the segmentation are labeled, based on the vertebral level), not the disc labels (only one voxel per disc).

try again with the proper -vertfile input and let us know how it goes


I see… Now everything makes sense.

Thanks Julien!

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