Module: 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.

Inputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
dwi	file	DWI Nifti image	*.{nii,nii.gz}
bval	file	B-values in FSL format [DWI].	*.bval
bvec	file	B-vectors in FSL format [DWI].	*.bvec
b0	file	b0 [DWI]. Optional	*.{nii,nii.gz}
rev_dwi	file	DWI Nifti image [rev-DWI]. Optional	*.{nii,nii.gz}
rev_bval	file	B-values in FSL format [rev-DWI]. Optional	*.bval
rev_bvec	file	B-vectors in FSL format [rev-DWI]. Optional	*.bvec
rev_b0	file	Reversed b0 [rev-DWI]. Optional	*.{nii,nii.gz}
config_topup	file	topup config file. Optional. See https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide#Configuration_files	*cnf

Outputs

	Type	Description	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
dwi_corrected	file	Nifti volume - DWI corrected	*__dwi_corrected.nii.gz
bval_corrected	file	B-values corrected in FSL format	*__bval_eddy
bvec_corrected	file	B-vectors corrected in FSL format	*__dwi_eddy_corrected.bvec
b0	file	Nifti volume - b0 corrected	*__b0_mask.nii.gz
b0_mask	file	Nifti volume - Mask for b0 corrected	*__b0_bet_mask.nii.gz
versions	file	File containing software versions	versions.yml

Components

preproc/topup
preproc/eddy
utils/extractb0
betcrop/fslbetcrop

Keywords

preprocessing
dwi
topup
eddy
distorsion
extract_b0

Authors

@arnaudbore