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, betcrop/fslbetcrop
Inputs
Section titled “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: [ val(meta), path(dwi), path(bval), path(bvec) ] | True | *\{.nii,.nii.gz,.bval,.bvec\} |
| ch_b0 | file | The input channel containing the b0 reference for the DWI. Structure: [ val(meta), path(b0) ] | 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: [ val(meta), path(rev_dwi), path(bval), path(bvec) ] | False | *\{.nii,.nii.gz,.bval,.bvec\} |
| ch_rev_b0 | file | The input channel containing the reverse b0 file. Structure: [ val(meta), path(rev_b0) ] | 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: [ path(config_topup) ] | False | *cnf |
| options | map | Map of options for the subworkflow. - topup_eddy_run_topup (bool): If ‘true’, the subworkflow will run FSL Topup for distorsion correction. - topup_eddy_run_eddy (bool): If ‘true’, the subworkflow will run FSL Eddy for motion and eddy current correction. | True |
Outputs
Section titled “Outputs”| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| dwi | file | Nifti volume - DWI corrected Structure: [ val(meta), path(dwi) ] | True | *__dwi_corrected.nii.gz |
| bval | file | B-values corrected in FSL format Structure: [ val(meta), path(bval) ] | True | *__bval_eddy |
| bvec | file | B-vectors corrected in FSL format Structure: [ val(meta), path(bvec) ] | True | *__dwi_eddy_corrected.bvec |
| b0 | file | Nifti volume - b0 corrected Structure: [ val(meta), path(b0) ] | True | *__b0_mask.nii.gz |
| b0_mask | file | Nifti volume - Mask for b0 corrected Structure: [ val(meta), path(b0_mask) ] | True | *__b0_bet_mask.nii.gz |
| mqc | file | Channel containing the quality control images for MultiQC. Structure: [ path(mqc), ... ] | False | *_mqc.\{gif,png\} |
| versions | file | File containing software versions | True | versions.yml |
Authors
Section titled “Authors”Last updated : 2026-02-12