Before starting this tutorialΒΆ

This rootlets-based registration tutorial is separate from the previous registration tutorials, meaning it can be run standalone.

  1. Make sure that you are working with SCT 7.0 or higher, and have an up-to-date copy of the PAM50 template:

    sct_download_data -d PAM50

    For older versions of SCT, you can download the latest release of the PAM50 template manually, then copy the files into the $SCT_DIR/data/PAM50 folder. (We recommend making a backup of the PAM50 folder if you are performing ongoing work with a stable release of SCT, that way you can go back to the older copy when resuming your work.)

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

    • single_subject/data/t2/t2.nii.gz : T2w anatomical scan of the spinal cord.

    • single_subject/data/t2/t2_seg.nii.gz : Segmentation of the spinal cord in the T2w image.

    You can get this file by downloading data_rootlets-registration.zip.

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

    cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/t2/