Before starting this tutorial

This tutorial is intended to be run following the previous Segmentation and Vertebral labeling tutorials, as registration to the PAM50 template relies on having a spinal cord segmentation mask as well as a point-label file representing vertebral level landmarks.

You can either run those tutorials first, or download the necessary files below:

  1. Read through the following pages to familiarize yourself with key SCT concepts:

    • PAM50 Template: An overview of the PAM50 template’s features, as well as context for why the template is used.

    • Warping fields: Background information on the image transformation format used by the registration process.

  2. 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.

    • single_subject/data/t2/t2_labels_vert.nii.gz : Image containing the 2 single-voxel vertebral labels

    You can get these files by downloading

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

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/t2/