Subworkflow: 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.
| 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-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 |
| mqc | file | Channel containing the quality control images for MultiQC. Structure: [ val(meta), path(mqc) ] | *_mqc.{gif,png} |
| versions | file | File containing software versions | versions.yml |
Components
|
|---|
| preproc/topup |
| preproc/eddy |
| utils/extractb0 |
| betcrop/fslbetcrop |
Authors
@arnaudbore
