Before starting this tutorialΒΆ

This tutorial is intended to be run following the previous Segmentation and Vertebral labeling tutorials, as shape analysis relies on having a spinal cord segmentation mask as well as a vertebral level file.

You can either run those tutorials 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_seg.nii.gz: A 3D binary mask for the spinal cord of a T2 anatomical image.

    • single_subject/data/t2/t2_seg_labeled.nii.gz: A image file containing a vertebral level labels.

    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/