Hands-on: Using sct_deepseg_sc on T1 data

Since we aim to improve the T1 segmentation, ensure that you are still in the T1 directory ({PATH_TO_DOWNLOADED_DATA}/single_subject/data/t1). Once there, run this command:

sct_deepseg_sc -i t1.nii.gz -c t1 -ofolder deepseg -qc ~/qc_singleSubj
Input arguments

  • -i : Input image

  • -c : Contrast of the input image

  • -ofolder : The folder to output files to. We specify this here so that we don’t overwrite the t2_seg.nii.gz file that was produced by sct_propseg.

  • -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. You may also simply refresh the webpage that was generated in the previous sections to see the new results.

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/spinalcord-segmentation/t1_deepseg_before_after.png

No leakage with sct_deepseg_sc

Looking at the relevant slices, we can see that sct_deepseg_sc has managed fix the leakage from sct_propseg.