MRtrix 2016

Introduction

MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. It is designed with consistency, performance, and stability in mind, and is freely available under an open-source license. ¹

Installed version(s)

The following versions are installed and currently available...

... on environment hpc-env/8.3:

• MRtrix/3.0.2-intel-2019b-Python-3.7.4
• MRtrix/3.0.3-intel-2019b-Python-3.7.4

Loading MRtrix

To load the desired version of the module, use the module load command, e.g.

$ module load hpc-env/8.3
$ module load MRtrix

Always remember: these commands are case-sensitive!

Using MRtrix

MRtrix comes with a lot of binaries which you can make use of. To getyou a quick overview about the binary content, you can take a look at the softwares bin folder aftert loading the module:

$ ml MRtrix
$ ls -la $EBROOTMRTRIX/bin

Most of the displayed executables do come with a help function if you just call the corresponding binary without any arguments entailed. For example:

$ mrtransform 

MRtrix 3.0.3                       mrtransform                       Oct 24 2022

     mrtransform: part of the MRtrix3 package

SYNOPSIS

     Apply spatial transformations to an image

USAGE

     mrtransform [ options ] input output

        input        input image to be transformed.

        output       the output image.


DESCRIPTION

     If a linear transform is applied without a template image the command will
     modify the image header transform matrix

     FOD reorientation (with apodised point spread functions) can be performed
     if the number of volumes in the 4th dimension equals the number of
     coefficients in an antipodally symmetric spherical harmonic series (e.g.
     6, 15, 28 etc). For such data, the -reorient_fod yes/no option must be
     used to specify if reorientation is required.

     The output image intensity can be modulated using the (local or global)
     volume change if a linear or nonlinear transformation is applied. 'FOD'
     modulation preserves the apparent fibre density across the fibre bundle
MRtrix 3.0.3                       mrtransform                       Oct 24 2022

     mrtransform: part of the MRtrix3 package

SYNOPSIS

     Apply spatial transformations to an image

USAGE

     mrtransform [ options ] input output

        input        input image to be transformed.

        output       the output image.


DESCRIPTION

     If a linear transform is applied without a template image the command will
     modify the image header transform matrix

     FOD reorientation (with apodised point spread functions) can be performed
     if the number of volumes in the 4th dimension equals the number of
     coefficients in an antipodally symmetric spherical harmonic series (e.g.
     6, 15, 28 etc). For such data, the -reorient_fod yes/no option must be
     used to specify if reorientation is required.

     The output image intensity can be modulated using the (local or global)
     volume change if a linear or nonlinear transformation is applied. 'FOD'
     modulation preserves the apparent fibre density across the fibre bundle
     width and can only be applied if FOD reorientation is used. Alternatively,
     non-directional scaling by the Jacobian determinant can be applied to any
     image type. 

     If a DW scheme is contained in the header (or specified separately), and
     the number of directions matches the number of volumes in the images, any
     transformation applied using the -linear option will also be applied to
     the directions.

     When the -template option is used to specify the target image grid, the
     image provided via this option will not influence the axis data strides of
     the output image; these are determined based on the input image, or the
     input to the -strides option.

Affine transformation options

  -linear transform
     specify a linear transform to apply, in the form of a 3x4 or 4x4 ascii
     file. Note the standard 'reverse' convention is used, where the transform
     maps points in the template image to the moving image. Note that the
     reverse convention is still assumed even if no -template image is supplied

  -flip axes
     flip the specified axes, provided as a comma-separated list of indices
     (0:x, 1:y, 2:z).

  -inverse
     apply the inverse transformation

Documentation

The full documentation can be found here.