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(reference), path(floating), path(ref_segmentation), path(flo_segmentation)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
reference	file	the 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}
floating	file	the floating image in .nii(.gz) or .mgz format.	True	*.{nii,nii.gz,mgz}
ref_segmentation	file	file with the SynthSeg v2 (non-robust) segmentation + parcellation of the reference image. If it does not exist, EasyReg will create it. If it already exists (e.g., from a previous EasyReg run), then EasyReg will read it from disk (which is faster than segmenting).	True	*.{nii,nii.gz}
flo_segmentation	file	file with the SynthSeg v2 (non-robust) segmentation + parcellation of the floating image. If it does not exist, EasyReg will create it. If it already exists (e.g., from a previous EasyReg run), then EasyReg will read it from disk (which is faster than segmenting).	True	*.{nii,nii.gz}

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Outputs

ref_reg

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*_reference_registered.nii.gz	file	this is the file where the deformed (registered) reference image is written.	True	*_reference_registered.nii.gz

flo_reg

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*_floating_registered.nii.gz	file	this is the file where the deformed (registered) floating image is written.	True	*_floating_registered.nii.gz

ref_seg

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

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

flo_seg

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

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

fwd_field

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*_forward_field.nii.gz	file	this is the file where the forward deformation field is written. The deformation includes both the affine and nonlinear components. Must be a nifti (.nii/.nii.gz) or .mgz file; it is encoded as the real world (RAS) coordinates of the target location for each voxel.	True	*_forward_field.nii.gz

bak_field

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]	True
*_backward_field.nii.gz	file	this is the file where the backward deformation field is written. It must also be a nifty or mgz file.	True	*_backward_field.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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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

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Last updated : 2025-10-30