Before starting this tutorial#

This tutorial is intended to be run following the previous Registering labeled anatomical images to the PAM50 template tutorial, as we will be re-using the previously generated warping field to register an additional contrast.

You will also need to download the image file for the additional contrast. Both files are provided below for convenience:

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

    • single_subject/data/mt/mt1.nii.gz : The magnetization transfer image with the off-resonance RF pulse applied.

    • single_subject/data/t2/warp_template2anat.nii.gz : The warping field that defines the transformation from the PAM50 template to the T2 anatomical space.

    You can get these files by downloading data_coregistration.zip.

  2. Open a terminal and navigate to the single_subject/data/mt/ directory:

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/mt/