# Image registration and fixel-based analysis now available in MRtrix!
**URL:** https://community.mrtrix.org/t/image-registration-and-fixel-based-analysis-now-available-in-mrtrix/207
**Category:** Announcements
**Created:** [May 6, 2016, 8:06am UTC](https://community.mrtrix.org/t/image-registration-and-fixel-based-analysis-now-available-in-mrtrix/207 "2016-05-06T08:06:40Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Dave](https://community.mrtrix.org/u/Dave)
#### Post date: [May 6, 2016, 8:06am UTC](https://community.mrtrix.org/t/image-registration-and-fixel-based-analysis-now-available-in-mrtrix/207/1 "2016-05-06T08:06:41Z")
#### We are proud to announce that MRtrix now includes commands for image registration and fixel-based analysis!
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# Image registration
The new [`mrregister`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mrregister) command can be used to perform robust rigid, linear and non-linear registration. In a similar vein to [Avants et al. (2008)](http://www.ncbi.nlm.nih.gov/pubmed/17659998) images are symmetrically aligned to a ‘midway’ space. See [`mrregister --help`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mrregister) for complete details.
While [`mrregister`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mrregister) can align any two 3D or 4D images, it has been specifically designed for [registration of Fibre Orientation Distributions (FOD)](http://www.ncbi.nlm.nih.gov/pubmed/21316463). If the input images contain a spherical harmonic series, then FOD registration will be automatically performed and include the required [FOD reorientation](http://www.ncbi.nlm.nih.gov/pubmed/22183751).
The current version of [`mrregister`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#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.
### mrtransform
We have also made significant changes to the [`mrtransform`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mrtransform) command, so that it can now apply both the forward and reverse linear and non-linear transformations generated from [`mrregister`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mrregister) (including transformation to the midway space). Like [`mrregister`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mrregister), the [`mrtransform`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mrtransform) command will automatically detect if the input is a spherical harmonic series and perform FOD reorientation. In addition, [modulation of FODs](http://www.ncbi.nlm.nih.gov/pubmed/22036682) 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`](http://userdocs.mrtrix.org/en/latest/getting_started/scripts_list.html#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.
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# Fixel-based analysis.
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](http://userdocs.mrtrix.org/en/latest/concepts/dixels_fixels.html). 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](http://www.ncbi.nlm.nih.gov/pubmed/26004503) and our upcoming paper on fixel-based morphometry (under review).
Step by step instructions for [DWI preprocessing](http://mrtrix.readthedocs.io/en/0.3.16/workflows/DWI_preprocessing_for_quantitative_analysis.html) and [fixel-based analysis](http://mrtrix.readthedocs.io/en/0.3.16/workflows/fixel_based_analysis.html) can be found in the MRtrix documentation.
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# List of new commands
- [`mrregister`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mrregister): performs rigid, linear and non-linear registration of images
- [`fixelreorient`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#fixelreorient): Reorient fixel directions based on the Jacobian (local affine transform) in a non-linear warp
- [`fixelcorrespondence`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#fixelcorrespondence): After spatial normalisation, assign/match fixels from one image (typically a subject) to another image (typically the template).
- [`fixellog`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#fixellog): A simple command to take the natural log of fixel values. Will likely be incorporated into `fixelcalc` in the future
- [`mraverageheader`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mraverageheader): Estimates the orientation of the average image grid. Used to obtain an unbiased image grid for alignment of subjects to a template.
- [`mrcheckerboardmask`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mrcheckerboardmask): Used to inspect image alignment after registration.
- [`mrmetric`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#mrmetric): Compute the similarity between two images
- [`warp2metric`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#warp2metric): Output a map of Jacobian matrices, Jacobian determinats or fibre cross-section for the analysis of white matter morphology.
- [`warpconvert`](http://userdocs.mrtrix.org/en/latest/getting_started/commands_list.html#warpconvert): Convert between different warp formats
- [`scripts/population_template`](http://userdocs.mrtrix.org/en/latest/getting_started/scripts_list.html#population-template): Generate an unbiased population template
- [`scripts/dwiintensitynorm`](http://userdocs.mrtrix.org/en/latest/getting_started/scripts_list.html#dwiintensitynorm): Perform a global intensity normalisation of multiple DWI images using the median white matter b=0 value.
Cheers,
Dave
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### Author:  [@rtabbara](https://community.mrtrix.org/u/rtabbara)
#### Post date: [May 16, 2016, 1:36am UTC](https://community.mrtrix.org/t/image-registration-and-fixel-based-analysis-now-available-in-mrtrix/207/2 "2016-05-16T01:36:20Z")
Great work @Dave !