Before starting this tutorial#

For this tutorial, because the dMRI data is axially acquired with thick slices, it helps to re-use the registration results from another contrast to initialize template registration for the dMRI data.

That is why, alongside the dMRI data, we provide T2s-based warping fields below:

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

    • single_subject/data/dmri/dmri.nii.gz : A 4D dMRI image comprised of 35 3D volumes.

    • single_subject/data/dmri/bvals.txt : A text file containing a b-value for each volume in the dMRI image, indicating the diffusion weightings for each of the volumes in the dMRI image.

    • single_subject/data/dmri/bvecs.txt : A text file with three lines, each containing a value for each volume in the dMRI image. Together, the the three sets of values represent the (x, y, z) coordinates of the b-vectors, which indicate the direction of the diffusion encoding for each volume of the dMRI image.

    • single_subject/data/t2s/warp_template2t2s.nii.gz : A “template->data” warping field from a previous registration. We will use this to initialize the dMRI registration.

    • single_subject/data/t2s/warp_t2s2template.nii.gz : A “data->template” warping field from a previous registration. We will use this to initialize the dMRI registration.

    You can get these files by downloading data_processing-dmri-data.zip.

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

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/dmri/