Working with NIFTI(-1) files in MATLAB

This post 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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