betcrop_dwi2mask
Obtain a brain mask from a diffusion weighted image using MRtrix3’s dwi2mask
Keywords : nifti, betcrop, dwi2mask
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(dwi), path(bval), path(bvec)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| dwi | file | Nifti dwi file to mask | True | *.{nii,nii.gz} |
| bval | file | B-values in FSL format. | True | *.bval |
| bvec | file | B-vectors in FSL format. | True | *.bvec |
Outputs
Section titled “Outputs”Format : tuple val(meta), path(*_dwi_mask.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_dwi_mask.nii.gz | file | DWI mask. | True | *_dwi_mask.{nii,nii.gz} |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
| Description | DOI | |
|---|---|---|
| MRtrix3 | MRtrix3 is a software package for various types of diffusion imaging data, including diffusion-weighted, diffusion-tensor, and q-ball imaging. | 10.1016/j.neuroimage.2019.116137 |
Authors
Section titled “Authors”Last updated : 2025-12-22