Before starting this tutorial¶
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.
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 data_template-registration.zip.
Open a terminal and navigate to the