ENIGMA Diffusion Weighted Imaging Data Preprocessing Tutorial

Before You Begin - Required Software

FSL - https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation
MRtrix3 - https://www.mrtrix.org/download/

First Steps - Understanding Your Data

Diffusion-Weighted Imaging (DWI) Volume Files and Corresponding Gradient Tables

There are 4 files that are required for us to reach our end goal in diffusion-weighted image processing of fitting a specific model to our data. In this case, we are focused on fitting the diffusion tensor model or 'DTI'. These required files are detailed below with explanations as to how they integrate with the main DWI volume.
This tutorial uses the data included in this repository that can be found here which assumes a directory structure like the one pictured below.

1 . The DWI Volume

Here we can see a screen capture of the header of our DWI volume in our terminal. We used the command 'mrinfo' to generate an output containing the image header information. In this case, we can see that our image is of 128 x 128 x 75 x 65 dimensions. This means that we have a 3-dimensional image of matrix size 128x128x75 with 64 diffusion volumes plus 1 b0 volume. In the movie, we can see our diffusion volumes from volume 0 to 64 (the bright image at the end being our b0 volume).

The entire diffusion volume as a movie.

2. The DWI JSON File

The DWI bvec and bval files

3. bvecs

4. bvals

Preprocessing Pipeline

Step_1 Script - PCA-Based Denoising

Command: dwidenoise

Pre and Post-denoising

Step_2 Script - Removal of Gibbs Ringing Artifacts

Gibbs ringing artifacts are often seen in magnetic resonance imaging (MRI) where we are transforming MR signals into a series of 2D images. This occurs when we reduce our sample of frequencies when constructing a Fourier series. Gibbs artifacts can be seen in the image to the right.

Source: mriquestions/gibbs-artifact

Command: mrdegibbs

Step_3 Script - Creating a Brain Mask With Brain Extraction Tool (BET)

In this step, we create a mask containing solely the brain tissue, removing the skull and all non-brain tissue from the DWI volume. This new brain-only volume will be used as our input to the next step where we will correct for Eddy-induced currents and motion-related artifacts.

Command: BET

Step_4 Script - Eddy Current and Motion Correction

Command: dwifslpreproc

Step_5 Script - Creating a Post-Eddy Brain Mask With Brain Extraction Tool (BET)