Hands-on: Using sct_propseg on T2 dataΒΆ

Run the following command to process the image:

sct_propseg -i t2.nii.gz -c t2 -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
  • t2_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. Optionally, If you have FSLeyes installed, a fsleyes command will printed as well.