Dorsal column cross-sectional area


So I want to measure the cross sectional area of the dorsal column. I read that it can be done with the sct_process_segmentation but how can I get the binary or probabilistic mask of my image with the dorsal column. I already have the labels of the atlas from the tutorial of the atlas-based analysis but I don’t know if I need them for the process segmentation.

Kind regards


See this post: Measuring dorsal column cross-sectional area

Yeah i have seen this post but I dont get how to make the file I need for the process segmentation of the dorsal colomn. Is this somewhere explained and I haven’t seen it?

from the path where the label/ folder is created, run:

cd label/atlas/
sct_maths -i PAM50_atlas_00.nii.gz -add PAM50_atlas_01.nii.gz PAM50_atlas_02.nii.gz PAM50_atlas_03.nii.gz -o PAM50_atlas_dorsalcolumn.nii.gz
cd ../../
sct_process_segmentation -i label/atlas/PAM50_atlas_dorsalcolumn.nii.gz