Introduction to MRtrix 3

I’ve been trying out MRtrix 3 recently. It’s impressive software. I’ll post a guide about installing it and using it later but there is enough information to get started on the Google+ site, the GitHub repository (and associated sparse but growing wiki), and the old mrtrix2 site. The developers are quick to respond to questions and are very helpful. I’m a novice at the software at this point but am enjoying learning to use it. As an example of what it can do, I created a video scrolling through a brain in the three common planes – axial, sagittal, and coronal. In this video, I display a track density image (TDI) created from a Constrained Spherical Deconvolution (CSD) whole brain fiber tracking with 25,000,000 fibers calculated.

MRtrix is one of the most promising fiber tracking packages I’ve encountered.

Image below is a 3D rendering of the TDI created for the video.

tdi_3D_mrtrix3

About Jared Tanner

I have a PhD in Clinical and Health Psychology with an emphasis in neuropsychology at the University of Florida. I previously studied at Brigham Young University. I am currently a Research Assistant Professor at the University of Florida. I spend the bulk of my research time dealing with structural magnetic resonance images of the brain. My specialty is with traditional structural MR images, such as T1-weighted and T2-weighted images, as well as diffusion weighted images. I also look at the cognitive and behavioral functioning of individuals with PD and older adults undergoing orthopedic surgery. Funding for the images came from NINDS K23NS060660 (awarded to Catherine Price, University of Florida). Brain images may not be used without my written permission (grant and software requirements).