image_cropvolume
Crop empty planes around the data in a volume
Keywords : nifti, crop, scilpy
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(image), path(bounding_box)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| image | file | Nifti image file to crop | True | *.{nii,nii.gz} |
| bounding_box | file | Input bounding box to use to crop the image | True | *.{pkl} |
Outputs
Section titled “Outputs”Format : tuple val(meta), path(*_cropped.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *_cropped.nii.gz | file | Cropped Nifti image file | True | *_cropped.{nii,nii.gz} |
bounding_box
Section titled “bounding_box”Format : tuple val(meta), path(*.pkl)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *.pkl | file | Bouding box defining the limits of the crop | True | *.pkl |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
| Description | DOI | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2025-10-30