Spinal nerve rootlets segmentation

SCT provides a deep learning model for the segmentation of spinal nerve rootlets from T2*-weighted images. The model is available in SCT v6.2 and higher via sct_deepseg -task seg_spinal_rootlets_t2w.

This model was trained on 3D T2-weighted images and provides level-specific semantic segmentation (i.e., 2: C2 rootlet, 3: C3 rootlet, etc.) of the dorsal spinal nerve rootlets.

Run the following command to segment the spinal nerve rootlets from the input image:

sct_deepseg -i t2.nii.gz -task seg_spinal_rootlets_t2w -qc ~/qc_singleSubj
Input arguments:

  • -i : Input T2w image

  • -task : Task to perform. In our case, we use the seg_spinal_rootlets_t2w task.

  • -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 level-specific segmentation (i.e., 2: C2 rootlet, 3: C3 rootlet, etc.) of the dorsal spinal nerve rootlets

  • t2_seg.json : JSON file containing details about the segmentation model

Details: