registration_anattodwi

Registration computing transformations moving images from anatomical space into diffusion space. The moving_image represents the anatomical space, moving to diffusion space, onto its fixed_image and its metric representations.

Configuration, direction and order of the registration follows the tractoflow publication.

Keywords : nifti, registration, anatomical, dwi

---

Inputs

Input 1

Format : tuple val(meta), path(fixed_image), path(moving_image), path(metric), path(fixed_mask), path(moving_mask)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
fixed_image	file	Nifti image file - fixed DWI image (usually b0)	True	*.{nii,nii.gz}
moving_image	file	Nifti image file - moving image to register (usually T1w)	True	*.{nii,nii.gz}
metric	file	Nifti image file - additional fixed metric (usually FA)	True	*.{nii,nii.gz}
fixed_mask	file	Fixed image mask	False	*.{nii,nii.gz}
moving_mask	file	Moving image mask	False	*.{nii,nii.gz}

---

Outputs

image_warped

Format : tuple val(meta), path(*_warped.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_warped.nii.gz	file	Anatomical image warped to DWI space	True	*_warped.nii.gz

fixed_warped

Format : tuple val(meta), path(*_warped_reference.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_warped_reference.nii.gz	file	Fixed image warped to moving space.	True	*_warped_reference.nii.gz

forward_affine

Format : tuple val(meta), path(*_forward1_affine.mat)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_forward1_affine.mat	file	Affine transformation matrix to fixed space.	True	*_forward1_affine.mat

forward_warp

Format : tuple val(meta), path(*_forward0_warp.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_forward0_warp.nii.gz	file	Deformation field to fixed space.	True	*_forward0_warp.nii.gz

backward_warp

Format : tuple val(meta), path(*_backward1_warp.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_backward1_warp.nii.gz	file	Deformation field to moving space.	True	*_backward1_warp.nii.gz

backward_affine

Format : tuple val(meta), path(*_backward0_affine.mat)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_backward0_affine.mat	file	Affine transformation matrix to moving space.	True	*_backward0_affine.mat

forward_image_transform

Format : tuple val(meta), val(*_forward*.{nii.gz,mat})

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
_forward.{nii.gz,mat}	list	Tuple, Transformation files to warp images in fixed space, in the correct order for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ forward_warp, forward_affine ] ].	True	*_forward*.{nii.gz,mat}

backward_image_transform

Format : tuple val(meta), val(*_backward*.{nii.gz,mat})

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
_backward.{nii.gz,mat}	list	Tuple, transformation files to warp images in moving space, in the correct order for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ backward_affine, backward_warp ] ].	True	*_backward*.{nii.gz,mat}

forward_tractogram_transform

Format : tuple val(meta), val(*_backward*.{nii.gz,mat})

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
_backward.{nii.gz,mat}	list	Tuple, transformation files to warp tractograms into fixed space, in the correct order for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ backward_affine, backward_warp ] ].	True	*_backward*.{nii.gz,mat}

backward_tractogram_transform

Format : tuple val(meta), val(*_forward*.{nii.gz,mat})

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
_forward.{nii.gz,mat}	list	Tuple, transformation files to warp tractograms into moving space, in the correct order for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ forward_affine, forward_warp ] ].	True	*_forward*.{nii.gz,mat}

mqc

Format : tuple val(meta), path(*_registration_anattodwi_mqc.gif)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*_registration_anattodwi_mqc.gif	file	.gif file containing quality control image for the registration process. For use in MultiQC report.	False	*_registration_anattodwi_mqc.gif

versions

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions	True	versions.yml

---

Arguments (see process.ext)

	Type	Description	Default	Choices
suffix	string	Custom suffix to add to the output file name. In any case, the suffix “_warped” will be appended to the supplied suffix or directly used to prevent overwriting input files. e.g. : the suffix to_T1w will result in the name image_to_T1w_warped.nii.gz.	warped
run_qc	boolean	Run quality control for the registration process	False
suffix_qc	string	Suffix for the QC image file.	“
single_thread	boolean	If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task.	False
ants_rng_seed	integer	Random seed for ANTs registration. Setting a fixed seed can help with reproducibility of results.	1234

---

Tools

	Description	DOI
ANTs	Advanced Normalization Tools.	10.1038/s41598-021-87564-6
ImageMagick	ImageMagick is a software suite to create, edit, compose, or convert bitmap images.
MRtrix3	MRtrix3 is a software package for processing diffusion MRI data.	10.1016/j.neuroimage.2019.116137
Scilpy	Scilpy is a Python library for processing diffusion MRI data.

---

Authors

• @medde
• @AlexVCaron

---

Last updated : 2026-09-24