utils_extractb0
Extract a b0 volume from a DWI image.
Keywords : dwi, extract, b0
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 volume to perform BET + crop. | 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(*_b0.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_b0.nii.gz | file | b0 image(s) extracted from the DWI | True | *_b0*.{nii,nii.gz} |
Format : tuple val(meta), path(*_copy_dwi.bval)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_copy_dwi.bval | file | B-values corrected in FSL format | True | *_copy_dwi.bval |
Format : tuple val(meta), path(*_copy_dwi.bvec)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_copy_dwi.bvec | file | B-vectors corrected in FSL format | True | *_copy_dwi.bvec |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
Arguments (see process.ext)
Section titled “Arguments (see process.ext)”| Type | Description | Default | Choices | |
|---|---|---|---|---|
| extraction_strategy | string | Extract either: all b0 (all), mean b0 (mean), mean of each continuous cluster of b0s (cluster-mean), first b0 of each continuous cluster of b0s (cluster-first). | mean | - all - mean - cluster-mean - cluster-first |
| b0_threshold | integer | Threshold under which b-values are considered to be b0s. | 20 | |
| output_series | boolean | If output b0 volume has multiple time points, only outputs a single image instead of a numbered series of images.scil_dwi_extract_b0 | False | |
| extract_bval_bvec | boolean | If true, the command will also output bval and bvec files. | False | |
| single_thread | boolean | If true, the command will be run in single-threaded mode. By default, the command will use multiple threads based on the number of CPUs allocated to the task. | False |
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2026-06-26