Using binary masks to compute CSA for gray and white matter#

First, we will use the gray and white matter segmentations to compute the cross sectional area of GM and WM. This is achieved using sct_process_segmentation.

sct_process_segmentation -i t2s_wmseg.nii.gz -o csa_wm.csv -perslice 1 -angle-corr 0
sct_process_segmentation -i t2s_gmseg.nii.gz -o csa_gm.csv -perslice 1 -angle-corr 0
Input arguments:
  • -i : The input segmentation file.

  • -o : The output CSV file.

  • -perslice : Set this option to 1 to turn on per-slice computation.

  • -angle-corr 0: Normally, angle correction will be applied during sct_process_segmentation to account for scans where the spinal cord is positioned at an angle with respect to the superior-inferior axis. While this works well when the input is a full spinal cord segmentation, in this case we are instead providing GM/WM segmentations only. The shape of these segmentations can have a negative effect on so the estimation of the cord centerline, which in turn may cause the estimated angle to be incorrect. So, here we specify 0 to turn off angle correction.

  • Note: Turning off angle correction is only safe to do if you know that your axial slices were acquired roughly orthogonal to the cord.

Output files/folders:
  • csa_wm.csv and csa_gm.csv: Two CSV files containing shape metrics for both the white and gray matter segmentations.

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/gm-wm-metric-computation/io-sct_process_segmentation.png