Before starting this tutorialΒΆ

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

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

    • single_subject/data/mt/mtr.nii.gz: An image containing the voxel-wise magnetization transfer ratio.

    • single_subject/data/mt/warp_template2mt.nii.gz : The 4D warping field that defines the transform from the template image to the MT image.

    You can get these files by downloading


If you would like to learn how to compute the magnetization transfer ratio (mtr.nii.gz), please visit the following tutorial:

Additionally, if you would like to learn how to register MT data with the PAM50 template (which is how the warp_template2mt.nii.gz file was generated), please visit either of the following tutorials:

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

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/mt/