topup_eddy

Subworkflow performing distorsions correction/eddy correction/motion correction. If a reverse B0 or a reverse DWI is provided it will run topup and then eddy, otherwise only eddy will run. --------- Steps -------------------- PREPROC_TOPUP (topup, FSL) Prepare data and apply FSL topup PREPROC_EDDY (eddy, FSL) Apply Eddy (and Topup if already run) UTILS_EXTRACTb0 (scilpy, scilus) Extract a b0 volume from a DWI image.

Keywords : preprocessing, dwi, topup, eddy, distorsion, extract_b0

Components : preproc/topup, preproc/eddy, utils/extractb0, betcrop/fslbetcrop

Inputs

	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-vectors in FSL format [DWI].	True	`*.bvec`
b0	file	b0 [DWI]. Optional	True	`*.{nii,nii.gz}`
rev_dwi	file	DWI Nifti image [rev-DWI]. Optional	True	`*.{nii,nii.gz}`
rev_bval	file	B-values in FSL format [rev-DWI]. Optional	True	`*.bval`
rev_bvec	file	B-vectors in FSL format [rev-DWI]. Optional	True	`*.bvec`
rev_b0	file	Reversed b0 [rev-DWI]. Optional	True	`*.{nii,nii.gz}`
config_topup	file	topup config file. Optional. See https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide#Configuration_files	True	`*cnf`

Outputs

	Type	Description	Optional	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	False
dwi_corrected	file	Nifti volume - DWI corrected	False	`*__dwi_corrected.nii.gz`
bval_corrected	file	B-values corrected in FSL format	False	`*__bval_eddy`
bvec_corrected	file	B-vectors corrected in FSL format	False	`*__dwi_eddy_corrected.bvec`
b0	file	Nifti volume - b0 corrected	False	`*__b0_mask.nii.gz`
b0_mask	file	Nifti volume - Mask for b0 corrected	False	`*__b0_bet_mask.nii.gz`
mqc	file	Channel containing the quality control images for MultiQC. Structure: `[ val(meta), path(mqc) ]`	False	`*_mqc.{gif,png}`
versions	file	File containing software versions	False	`versions.yml`

Authors

@arnaudbore

Last updated : 2025-10-30