connectivity_afdfixel
Compute the mean Apparent Fiber Density (AFD) and mean Radial fODF (radfODF) maps for every connections within a hdf5 (.h5) file.
Keywords : connectivity, AFD_Fixel, Metrics
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(hdf5), path(fodf)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | True | |
| hdf5 | file | HDF5 file containing decomposed connections. | True | *.h5 |
| fodf | file | FODF file. | True | *.nii.gz |
Outputs
Section titled “Outputs”Format : tuple val(meta), path(*__afd_fixel.h5)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | True | |
| *__afd_fixel.h5 | file | HDF5 file containing the computed AFD fixel and radial fODF metrics. | True | *__afd_fixel.h5 |
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 | |
|---|---|---|---|---|
| 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 : 2026-05-12