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