topup
Module: preproc/topup
Run magnetic susceptibility distortions correction using FSL Topup. The module can take either b0 or DWI volumes. The latter activates b0 extraction prior to running Topup. Extraction can be configured to take one (default) or many b0 volumes in each forward and reverse acquired DWI and perform averaging if needed. Note that running Topup with more than one volume per encoding direction greatly increases computation time.
Keywords : DWI, distorsion, topup
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 | *.{nii,nii.gz} | |
| bval | file | B-values in FSL format [DWI]. | *.bval | |
| bvec | file | B-values in FSL format [DWI]. | *.bvec | |
| b0 | file | b0 [DWI]. | *.bvec | |
| rev_dwi | file | DWI Nifti image [rev-DWI]. | *.{nii,nii.gz} | |
| rev_bval | file | B-values in FSL format [rev-DWI]. | *.bval | |
| rev_bvec | file | B-vectors in FSL format [rev-DWI]. | *.bvec | |
| rev_b0 | file | Reversed b0 [rev-DWI]. | *.{nii,nii.gz} | |
| config_topup | file | topup config file. 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 ] | |
| topup_corrected_b0s | file | Nifti volume - b0 corrected | *__corrected_b0s.nii.gz |
| topup_fieldcoef | file | Nifti volume - topup field to correct for distorsion | *_fieldcoef.nii.gz |
| topup_movpart | file | Text file - topup movpart | *__movpar.txt |
| rev_b0_warped | file | Nifti volume - rev b0 warped on b0 | *__rev_b0_warped.nii.gz |
| rev_b0_mean | file | Nifti volume - rev b0 mean | *__rev_b0_mean.nii.gz |
| b0_mean | file | Nifti volume - b0 mean | *__b0_mean.nii.gz |
| mqc | file | .gif file containing quality control image for the topup process (Comparison with dwi and rev_dwi). Made for use in MultiQC report. | *_b0_topup_mqc.gif |
| versions | file | File containing software versions. | versions.yml |
Tools
| Description | DOI | |
|---|---|---|
| ANTs | Advanced Normalization Tools (ANTs) for image processing. | |
| FSL | FSL Toolbox and Scilpy Toolbox | |
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Last updated : 2025-07-15