Upper and lower slices of disc

SCT
1

Hello team,
Is there is any way to obtain features from upper and lower slices of a disc level in spinal cord? I have a few t1, t2 images and maybe some dwi images. It will be so appreciated if you give me some hints in this regard. Thanks.

2

Hi @Roberto_r,

The first thing to do is identify the slice corresponding to the disc level you are interested in. This is explained in the following post: CSA at disc level - #2 by jcohenadad

Once you’ve identified the disc of interest, you can add the desired amount of slices above and below. Reusing the example from the post I referred to, computing metrics up to 3 slices above and below disc C3-C4, it would look like this:

# 3 slices above
sct_process_segmentation -i t2_seg.nii.gz -z 165:168 -o csa_disc4_above.csv
# 3 slices below
sct_process_segmentation -i t2_seg.nii.gz -z 162:165 -o csa_disc4_below.csv

Of course you can easily fetch the slice number automatically from the CSV file using any scripting language (SHELL, Python, etc.).

3

Thank you so much @jcohenadad. I understand it better now.

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