Before starting this tutorialΒΆ

This tutorial is intended to be run following the previous Segmentation tutorial, as vertebral labeling relies on having a spinal cord segmentation mask.

You can either run that tutorial first, or download the necessary files below:

  1. Make sure that you have the following files in your working directory:

    • single_subject/data/t2/t2.nii.gz : An anatomical spinal cord scan in the T2 contrast.

    • single_subject/data/t2/t2_seg.nii.gz : A 3D binary mask for the spinal cord.

    You can get these files by downloading

  2. Open a terminal and navigate to the single_subject/data/t2/ directory:

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/t2/