registration_anattodwi

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

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

Keywords : nifti, registration, anatomical, dwi

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Inputs

Input 1

Format : tuple val(meta), path(fixed_reference), path(moving_anat), path(metric)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
fixed_reference	file	Nifti image file - fixed DWI reference (usually b0)	True	*.{nii,nii.gz}
moving_anat	file	Nifti image file - moving anat to register (usually T1w)	True	*.{nii,nii.gz}
metric	file	Nifti image file - additional fixed metric (usually FA)	True	*.{nii,nii.gz}

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Outputs

anat_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

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

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Arguments (see process.ext)

	Type	Description	Default	Choices
run_qc	boolean	Run quality control for the registration process	False

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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.

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Authors

• @medde
• @AlexVCaron

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Last updated : 2025-12-22