Applying the gray matter segmentation algorithm#

sct_deepseg_gm can be applied to T2* data using the following command:

sct_deepseg_gm -i t2s.nii.gz -qc ~/qc_singleSubj
Input arguments:
  • -i : Destination image the template will be warped to.

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

Output:
  • t2s_gmseg.nii.gz : The image file containing the gray matter segmentation.

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/gm-wm-segmentation/io-sct_deepseg_gm.png