MRTrix

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Preprocessing

Nifti DWI gradients in .bvec and .bval can be converted to MRTrix format with the mrtrix_grad.py script.

MRTrix CSD estimation volume can be automated with the mrtrix_compcsd.sh script, the default harmonics is set at 8.

NOTE that it's important to check the CSD estimate to see if the gradients are correct, if not they will need to be inverted along x,y or z dimensions. The reason is that MRTrix is written for Siemens scanners, but our scanner is GE. By default the script will attempt this correction, but it's important to verify this.

Setup

MRTrix has been updated to version 3, it is the recommended version to use. Primary changes include:

  • Updated CSD code for mathematical compatibility with other packages (presumably Dipy)
  • Added feature for anatomically based fiber tracking

Downloads

https://github.com/jdtournier/mrtrix3

Wiki

https://github.com/jdtournier/mrtrix3/wiki


Instructions

Build MRTrix

$ git clone https://github.com/jdtournier/mrtrix3.git
$ cd mrtrix3/
$ ./configure 
$ ./build

Add environment paths in ~/.bashrc

$ export PATH=/<edit as appropriate>/mrtrix-0.3/bin:$PATH

Test:

mrview


Old links to verison 2

Download
Docs