Hands-on: Using sct_propseg on T1 data

Next, we will switch to the T1 directory so that we can try out sct_propseg on a different contrast.

cd ../t1
sct_propseg -i t1.nii.gz -c t1 -qc ~/qc_singleSubj
Input arguments
  • -i : Input image

  • -c : Contrast of the input image

  • -qc : Directory for Quality Control reporting. QC reports allow us to evaluate the segmentation slice-by-slice

Output files/folders
  • t1_seg.nii.gz : 3D binary mask of the segmented spinal cord

Once the command has finished, at the bottom of your terminal there will be instructions for inspecting the results using Quality Control (QC) reports. You may also simply refresh the QC Report webpage generated in the previous section to see the new results.

This time, however, there is an issue. The spinal cord segmentation has leaked outside of the expected area. This is caused by a bright outer region that is too close to the spinal cord. sct_propseg relies on contrast between the CSF and the spinal cord; without sufficient contrast, the segmentation may fail (as it has here).

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/spinalcord-segmentation/t1_propseg_before_after.png

Segmentation leakage with sct_propseg