preproc_eddy

Apply Eddy (and Topup if already run)

Keywords : distorsion correction, preproc, eddy

Inputs

`Input 1`

Format : tuple val(meta), path(dwi), path(bval), path(bvec), path(rev_dwi), path(rev_bval), path(rev_bvec), path(corrected_b0s), path(topup_fieldcoef), path(topup_movpart)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
dwi	file	DWI Nifti image	True	`*.{nii,nii.gz}`
bval	file	B-values in FSL format [DWI].	True	`*.bval`
bvec	file	B-values in FSL format [DWI].	True	`*.bvec`
rev_dwi	file	DWI Nifti image [rev-DWI].	True	`*.{nii,nii.gz}`
rev_bval	file	B-values in FSL format [rev-DWI].	True	`*.bval`
rev_bvec	file	B-vectors in FSL format [rev-DWI].	True	`*.bvec`
corrected_b0s	file	Nifti volume b0 corrected	True	`*__corrected_b0s.nii.gz`
topup_fieldcoef	file	Nifti volume - topup field to correct for distorsion	True	`*_fieldcoef.nii.gz`
topup_movpart	file	Text file - topup movpart	True	`*__movpar.txt`

Outputs

`dwi_corrected`

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*__dwi_corrected.nii.gz	file	Nifti volume - DWI corrected.	True	`*__dwi_corrected.nii.gz`

`bval_corrected`

Format : tuple val(meta), path(*__dwi_eddy_corrected.bval)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*__dwi_eddy_corrected.bval	file	B-values corrected in FSL format	True	`*__dwi_eddy_corrected.bval`

`bvec_corrected`

Format : tuple val(meta), path(*__dwi_eddy_corrected.bvec)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*__dwi_eddy_corrected.bvec	file	B-vectors corrected in FSL format	True	`*__dwi_eddy_corrected.bvec`

`b0_mask`

Format : tuple val(meta), path(*__b0_bet_mask.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*__b0_bet_mask.nii.gz	file	Nifti volume - Mask for b0 corrected	True	`*__b0_bet_mask.nii.gz`

`dwi_eddy_mqc`

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

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

`rev_dwi_eddy_mqc`

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*__rev_dwi_eddy_mqc.gif	file	.gif file containing quality control image for the eddy process for the rev_dwi. Made for use in MultiQC report.	True	`*_rev_dwi_eddy_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
slice_drop_flag	boolean	If set, will activate eddy’s outlier correction, which includes slice drop correction.	False
bet_topup_before_eddy_f	float	Fractional intensity threshold for BET before running topup	0.16
prefix_topup	string	Prefix for the topup output.	topup_results
b0_thr_extract_b0	integer	Threshold under which b-values are considered to be b0s.	10
encoding	string	Encoding direction of the forward DWI.	y	- x - y or z
readout	float	Total readout time from the DICOM metadata.	0.062
dilate_b0_mask_prelim_brain_extraction	integer	Number of times to repeatedly apply the filter.	5
eddy_cmd	string	Command to run Eddy.	eddy_cpu
bet_prelim_f	float	Fractional intensity threshold for BET if TOPUP has not been run.	0.16
extra_args	string	Extra arguments for Eddy.
run_qc	boolean	Run QC for Eddy.	False

Tools

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.
MRtrix3	MRtrix3 is a software package for various types of diffusion imaging data, including diffusion-weighted, diffusion-tensor, and q-ball imaging.	10.1016/j.neuroimage.2019.116137
FSL	FSL Toolbox	10.1016/j.neuroimage.2011.09.015

Authors

@arnaudbore

Last updated : 2025-10-30