Before starting this tutorialΒΆ

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

    • single_subject/data/t2/t2_seg.nii.gz: A 3D binary mask for the spinal cord of a T2 anatomical image.

    • single_subject/data/t2/label/template/PAM50_levels.nii.gz: A PAM50 template object containing vertebral levels, that has been transformed to the space of the T2 anatomical image.

    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/