A brief introduction to diffusion weighted MRI (DWMRI) processing

This article serves as a brief introduction to DWMRI processing.

Tools and files used in this article:

dwmri.dcm is a 32 direction, 1000 b-value DWMRI dicom file, dcm2niix is a commonly used DICOM to NIFTI converter, nifti_utils is a library to work with NIFTIs in MATLAB, dwmri_visualizer is a visualization tool for diffusion images in MATLAB, and FSL is a powerful and commonly used medical image processing library.

A very common pipeline for dwmri processing is:

1.\ ACQUISITION
\downarrow
2.\ DICOM
\downarrow
3.\ NIFTI,\ BVEC,\ BVAL
\downarrow
4.\ PREPROCESSING
\downarrow
5.\ PROCESSING

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Working with NIFTI(-1) files in MATLAB

This article will discuss the NIFTI-1 format and how to work with these files in MATLAB. The purpose of this article is to give a high-level introduction to “get you going”.

Tools and files used in this article:

What is a NIFTI file?

It’s essentially: a file containing a 3D array with an associated orientation. Technically, it’s a file containing a 348 byte header followed by image data. There’s more information here, here, and here about the specifics of what’s contained in the header. In this article, I’ll simply discuss how the orientation is stored in the header and how to use it, as well as a couple other fields which are important to properly using and manipulating the data. There are some other fields specific to certain modalities (i.e. fMRI), but they are not discussed here.
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