Module: preproc/eddy
Apply Eddy (and Topup if already run)
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 |
| 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 |
| 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 |
Arguments
| Type | Description | Choices | Default | |
|---|---|---|---|---|
| slice_drop_flag | boolean | If set, will activate eddy’s outlier correction, which includes slice drop correction. | False | |
| bet_topup_before_eddy_f | float | Fractional intensity threshold for BET before running topup | 0.16 | |
| prefix_topup | string | Prefix for the topup output. | topup_results | |
| b0_thr_extract_b0 | int | Threshold under which b-values are considered to be b0s. | 10 | |
| encoding | string | Encoding direction of the forward DWI. | x, y or z | y |
| readout | float | Total readout time from the DICOM metadata. | 0.062 | |
| dilate_b0_mask_prelim_brain_extraction | int | Number of times to repeatedly apply the filter. | 5 | |
| eddy_cmd | string | Command to run Eddy. | eddy_cpu | |
| bet_prelim_f | float | Fractional intensity threshold for BET if TOPUP has not been run. | 0.16 | |
| extra_args | string | Extra arguments for Eddy. | ||
| run_qc | boolean | Run QC for Eddy. | False |
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_mask | file | Nifti volume - Mask for b0 corrected | *__b0_bet_mask.nii.gz |
| dwi_eddy_mqc | file | .gif file containing quality control image for the eddy process. Made for use in MultiQC report. | *_dwi_eddy_mqc.gif |
| rev_dwi_eddy_mqc | file | .gif file containing quality control image for the eddy process for the rev_dwi. Made for use in MultiQC report. | *_rev_dwi_eddy_mqc.gif |
| versions | file | File containing software versions | versions.yml |
Tools
| Description | Homepage | DOI | |
|---|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | https://github.com/scilus/scilpy.git | |
| MRtrix3 | Toolbox for image processing, analysis and visualisation of dMRI. | https://mrtrix.readthedocs.io/en/latest/ | |
| FSL | FSL Toolbox and Scilpy Toolbox | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki |
Keywords
| distorsion correction |
| preproc |
| eddy |
Authors
@arnaudbore