Module: stats/metricsinroi
Module to compute statistics (mean, std) of scalar maps (metrics), which can represent diffusion metrics, in ROIs or labels.
Keywords : nifti, volume, scilpy, stats, rois
| Type | Description | Mandatory | Pattern |
|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | true | |
| metrics | file | Metrics volume(s) in Nifti | | *.{nii,nii.gz} |
| rois | file | ROI or Label volume(s) in Nifti | | *.{nii,nii.gz} |
| rois_lut | file | LUT file corresponding to labels, used to name the regions of interest | | *.{nii,nii.gz} |
Outputs
| Type | Description | Pattern |
|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| mqc | file | JSON file containing mean/std per pair of roi/metrics or label/metrics | *__stats.json |
| versions | file | File containing software versions | versions.yml |
| Type | Description | Default | Choices |
|---|
| suffix | string | It will add an extra string before “_stats.json” | | |
| bin | boolean | If set, will consider every value of the mask higherthan 0 to be part of the mask (equivalent weighting for every voxel). It will be used if use_label is false. | False | |
| normalize_weights | boolean | If set, the weights will be normalized to the [0,1] range. It will be used if use_label is false. | False | |
| use_label | boolean | If set, rois image will be considered as a label image with multiple indices. | False | |
| Description | DOI |
|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | |
Authors
arnaudbore
Last updated : 2025-07-15
