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 --------------------

1. PREPROC_TOPUP (topup, FSL)
Prepare data and apply FSL topup
2. PREPROC_EDDY (eddy, FSL)
Apply Eddy (and Topup if already run)
3. 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, utils_options

Inputs

	Type	Description	Mandatory	Pattern
ch_dwi	file	The input channel containing the DWI file, B-values and B-vectors in FSL format files. Structure : `tuple val(meta), path(dwi), path(bval), path(bvec)` meta [map] Metadata map. dwi [file] DWI image file. bval [file] B-values in FSL format. bvec [file] B-vectors in FSL format.	True	`*\{.nii,.nii.gz,.bval,.bvec\}`
ch_b0	file	The input channel containing the b0 reference for the DWI. Structure : `tuple val(meta), path(b0)` meta [map] Metadata map. b0 [file] B0 image file.	False	`*\{.nii,.nii.gz\}`
ch_rev_dwi	file	The input channel containing the reverse DWI file, B-values and B-vectors in FSL format files. Structure : `tuple val(meta), path(rev_dwi), path(bval), path(bvec)` meta [map] Metadata map. rev_dwi [file] Reverse phase-encoded DWI image file. bval [file] B-values in FSL format. bvec [file] B-vectors in FSL format.	False	`*\{.nii,.nii.gz,.bval,.bvec\}`
ch_rev_b0	file	The input channel containing the reverse b0 file. Structure : `tuple val(meta), path(rev_b0)` meta [map] Metadata map. rev_b0 [file] Reverse phase-encoded B0 image file.	False	`*\{.nii,.nii.gz\}`
config_topup	file	Topup config file. Optional. See https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide#Configuration_files Structure : `tuple path(config_topup)` config_topup [file] Topup configuration file.	False	`*cnf`
options	map	Map of options for the topup_eddy subworkflow. topup_eddy_run_topup (boolean) [Default: True] Run FSL Topup for distorsion correction. topup_eddy_run_eddy (boolean) [Default: True] Run FSL Eddy for motion and eddy current correction.	False

Outputs

	Type	Description	Mandatory	Pattern
dwi	file	Nifti volume - DWI corrected Structure : `tuple val(meta), path(dwi)` meta [map] Metadata map. dwi [file] Corrected DWI image file.	True	`*__dwi_corrected.nii.gz`
bval	file	B-values corrected in FSL format Structure : `tuple val(meta), path(bval)` meta [map] Metadata map. bval [file] Corrected B-values file.	True	`*__bval_eddy`
bvec	file	B-vectors corrected in FSL format Structure : `tuple val(meta), path(bvec)` meta [map] Metadata map. bvec [file] Corrected B-vectors file.	True	`*__dwi_eddy_corrected.bvec`
b0	file	Nifti volume - b0 corrected Structure : `tuple val(meta), path(b0)` meta [map] Metadata map. b0 [file] Corrected B0 image file.	True	`*__b0_mask.nii.gz`
b0_mask	file	Nifti volume - Mask for b0 corrected Structure : `tuple val(meta), path(b0_mask)` meta [map] Metadata map. b0_mask [file] B0 mask file.	True	`*__b0_bet_mask.nii.gz`
mqc	file	Channel containing the quality control images for MultiQC. Structure : `tuple path(mqc)` mqc [file] Quality control images.	False	`*_mqc.\{gif,png\}`
versions	file	File containing software versions	True	`versions.yml`

Authors

@arnaudbore

Last updated : 2026-03-17