Before starting this tutorialΒΆ

  1. Make sure that you are working with a copy of SCT 6.1 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_lumbar/t2_lumbar.nii.gz : T2w anatomical scan of the lumbar spinal cord.

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

  3. Open a terminal and navigate to the single_subject/data/t2_lumbar/ directory:

    cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/t2_lumbar/