reconst_shmetrics
Compute FODF metrics from given FODF or SH map.
Keywords : FODF, SH, Metrics
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(sh), path(mask), path(fa), path(md)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| sh | file | SH or FODF map. | True | *.{nii,nii.gz} |
| mask | file | B0 mask. | True | *.{nii,nii.gz} |
| fa | file | FA map. | True | *.{nii,nii.gz} |
| md | file | MD map. | True | *.{nii,nii.gz} |
Outputs
Section titled “Outputs”Format : tuple val(meta), path(*peaks.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *peaks.nii.gz | file | Peaks file. | True | *peaks.nii.gz |
peak_indices
Section titled “peak_indices”Format : tuple val(meta), path(*peak_indices.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *peak_indices.nii.gz | file | Peak indices file. | True | *peak_indices.nii.gz |
peak_values
Section titled “peak_values”Format : tuple val(meta), path(*peak_values.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *peak_values.nii.gz | file | Peaks values file. | True | *peak_values.nii.gz |
afd_max
Section titled “afd_max”Format : tuple val(meta), path(*afd_max.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *afd_max.nii.gz | file | Maximum Apparent Fiber Density (AFDmax) map. | True | *afd_max.nii.gz |
afd_total
Section titled “afd_total”Format : tuple val(meta), path(*afd_total.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *afd_total.nii.gz | file | Total Apparent Fiber Density (AFDtotal) map. | True | *afd_total.nii.gz |
afd_sum
Section titled “afd_sum”Format : tuple val(meta), path(*afd_sum.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *afd_sum.nii.gz | file | Sum of all Apparent Fiber Density (Afdsum) map. | True | *afd_sum.nii.gz |
Format : tuple val(meta), path(*nufo.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *nufo.nii.gz | file | Number of Fiber Orientation (NuFO) map. | True | *nufo.nii.gz |
vent_mask
Section titled “vent_mask”Format : tuple val(meta), path(*ventricles_mask.nii.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *ventricles_mask.nii.gz | file | Ventricles mask. | True | *ventricles_mask.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 | |
|---|---|---|
| scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. |
Authors
Section titled “Authors”Last updated : 2025-10-30