registration_easyreg

Image registration and SynthSeg v2 segmentation with easyreg from freesurfer

Keywords : nifti, registration, segmentation, neural network, Artificial intelligence, machine learning

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Inputs

Input 1

Format : tuple val(meta), path(fixed_image), path(moving_image), path(fixed_segmentation), path(moving_segmentation)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
fixed_image	file	Reference image in .nii(.gz) or .mgz format (note that, since the method is symmetric, the choice of reference vs floating is arbitrary).	True	*.{nii,nii.gz,mgz}
moving_image	file	Image to register in .nii(.gz) or .mgz format.	True	*.{nii,nii.gz,mgz}
fixed_segmentation	file	File with the SynthSeg v2 (non-robust) segmentation + parcellation of the reference image. If it does not exist, EasyReg will create it.	False	*.{nii,nii.gz}
moving_segmentation	file	File with the SynthSeg v2 (non-robust) segmentation + parcellation of the floating image. If it does not exist, EasyReg will create it.	False	*.{nii,nii.gz}

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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:'sample1', single_end:false ]	True
*_warped.nii.gz	file	Image warped onto the reference.	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:'sample1', single_end:false ]	True
*_warped_reference.nii.gz	file	Reference warped.	True	*_warped_reference.nii.gz

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:'sample1', single_end:false ]	True
*_forward0_warp.nii.gz	file	Forward deformation field, composed of all registration stages (affine+deformation).	False	*_forward0_warp.nii.gz

backward_warp

Format : tuple val(meta), path(*_backward0_warp.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*_backward0_warp.nii.gz	file	Backward deformation field, composed of all registration stages (inv-deformation+inv-affine).	False	*_backward0_warp.nii.gz

segmentation_warped

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*_warped_segmentation.nii.gz	file	SynthSeg v2 (non-robust) segmentation + parcellation on the warped image. Will produce image only if not passed as input.	False	*_warped_segmentation.nii.gz

fixed_segmentation_warped

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*_warped_reference_segmentation.nii.gz	file	SynthSeg v2 (non-robust) segmentation + parcellation on the reference image. Will produce image only if not passed as input.	False	*_warped_reference_segmentation.nii.gz

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
affine_only	boolean	Only perform affine registration	False
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

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Tools

	Description	DOI
Freesurfer	Open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.	10.1016/j.neuroimage.2012.01.021

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Authors

• @ThoumyreStanislas
• @AlexVCaron

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Last updated : 2026-05-12