Module: preproc/topup
Prepare data and apply FSL topup
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-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 |
Arguments
| Type | Description | Choices | Default | |
|---|---|---|---|---|
| encoding | string | Encoding direction of the forward DWI. | x, y or z | y |
| readout | float | Total readout time from the DICOM metadata. | 0.062 | |
| b0_thr_extract_b0 | int | Threshold under which b-values are considered to be b0s. | 10 | |
| run_qc | boolean | Run quality control. | True |
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 | Homepage | DOI | |
|---|---|---|---|
| ANTs | Advanced Normalization Tools (ANTs) for image processing. | http://stnava.github.io/ANTs/ | |
| FSL | FSL Toolbox and Scilpy Toolbox | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki | |
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | https://github.com/scilus/scilpy.git |
Keywords
| DWI |
| distorsion |
| topup |
Authors
@arnaudbore