We are proud to announce that MRtrix now includes commands for image registration and fixel-based analysis!
mrregister command can be used to perform robust rigid, linear and non-linear registration. In a similar vein to Avants et al. (2008) images are symmetrically aligned to a 'midway' space. See
mrregister --help for complete details.
mrregister can align any two 3D or 4D images, it has been specifically designed for registration of Fibre Orientation Distributions (FOD). If the input images contain a spherical harmonic series, then FOD registration will be automatically performed and include the required FOD reorientation.
The current version of
mrregister is limited to using a mean squared intensity metric, and therefore it requires input images to be in the same intensity range. However we intend to include a normalised cross-correlation metric for both linear and non-linear registration in the near future.
We have also made significant changes to the
mrtransform command, so that it can now apply both the forward and reverse linear and non-linear transformations generated from
mrregister (including transformation to the midway space). Like
mrtransform command will automatically detect if the input is a spherical harmonic series and perform FOD reorientation. In addition, modulation of FODs can be optionally applied to preserve the total fibre density across a fibre bundle's width.
Population template script
The recent update also includes a python script called
population_template for building an unbiased study-specific template using an iterative averaging approach. The script can be used on either scalar 3D or FOD images. Using the
-rigid option will ensure the initial linear alignment is rigid, which is suited for intra-subject registration of longitudinal data. While not a requirement, we recommend users use the
-mask_dir option to supply brain masks for the input subject images, as this will reduce computation time substantially.
This update also includes a number of commands to perform a fixel-based analysis. What's a fixel? It's just a fancy word for a specific fibre population in a voxel (a.k.a a fibre bundle element) - see here for a more detailed description. Group strudies using traditional voxel-based analysis permit white matter changes to be localised to a voxel. However, in a fixel-based analysis individual fixels are compared across individuals, which enables significant differences to be localised to a specific fibre pathway, even in regions containing crossing fibres.
For more information on fixel-based analysis and group statistics on fixel images see our paper on connectivity-based fixel enhancement and our upcoming paper on fixel-based morphometry (under review).
Step by step instructions for DWI preprocessing and fixel-based analysis can be found in the MRtrix documentation.
List of new commands
mrregister: performs rigid, linear and non-linear registration of images
fixelreorient: Reorient fixel directions based on the Jacobian (local affine transform) in a non-linear warp
fixelcorrespondence: After spatial normalisation, assign/match fixels from one image (typically a subject) to another image (typically the template).
fixellog: A simple command to take the natural log of fixel values. Will likely be incorporated into
fixelcalc in the future
mraverageheader: Estimates the orientation of the average image grid. Used to obtain an unbiased image grid for alignment of subjects to a template.
mrcheckerboardmask: Used to inspect image alignment after registration.
mrmetric: Compute the similarity between two images
warp2metric: Output a map of Jacobian matrices, Jacobian determinats or fibre cross-section for the analysis of white matter morphology.
warpconvert: Convert between different warp formats
scripts/population_template: Generate an unbiased population template
scripts/dwiintensitynorm: Perform a global intensity normalisation of multiple DWI images using the median white matter b=0 value.