utils_dwishell
Extracts the DWI volumes that are on specific b-value shells in the same order as in the original file.
Keywords : dwi, extract, shell
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. | 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_sh_shells.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__dwi_sh_shells.nii.gz | file | DWI volume with shells fitted. | True | *__dwi_sh_shells.nii.gz |
Format : tuple val(meta), path(*__bval_sh_shells)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__bval_sh_shells | file | B-values of the fitted shells in FSL format. | True | *__bval_sh_shells |
Format : tuple val(meta), path(*__bvec_sh_shells)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__bvec_sh_shells | file | B-vectors of the fitted shells in FSL format. | True | *__bvec_sh_shells |
out_indices
Section titled “out_indices”Format : tuple val(meta), path(*__out_indices)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__out_indices | file | Text file containing indices of the fitted shells. | True | *__out_indices |
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 | |
|---|---|---|---|---|
| b0_thr_extract_b0 | integer | Volumes with b-values up to this threshold are considered b0 (unweighted). | 10 | |
| max_shell_bvalue | integer | Maximum b-value to consider when extracting shells. | 1500 | |
| shell_to_fit | integer | Only use volumes with this b-value. Required if input is multi-shell. | None | |
| out_indices | boolean | Whether to output the valid indices of the input dwi volume. | False | |
| block_size | integer | Useful when the data is too large to be loaded in memory. A block size of X means that X DWI volumes are loaded at a time for processing. | None | |
| tolerance | integer | The tolerated gap between the b-values to extract and the actual b-values. | 20 |
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2025-10-30