reconst_diffusivitypriors
Compute the axial (para_diff) and mean (iso_diff) diffusivity priors.
Keywords : diffusivity, axial, isotropic
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(fa), path(ad), path(rd), path(md), path(priors)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| fa | file | Nifti DTI FA volume. | True | *.{nii,nii.gz} |
| ad | file | Nifti DTI AD volume. | True | *.{nii,nii.gz} |
| rd | file | Nifti DTI RD volume. | True | *.{nii,nii.gz} |
| md | file | Nifti DTI MD volume. | True | *.{nii,nii.gz} |
| priors | directory | Folder containg text files for isotropic and parallel diffusivity values. | True | priors |
Outputs
Section titled “Outputs”para_diff
Section titled “para_diff”Format : tuple val(meta), path(*__para_diff.txt)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__para_diff.txt | file | Text files for parallel diffusivity values. | True | *__para_diff.txt |
perp_diff
Section titled “perp_diff”Format : tuple val(meta), path(*__perp_diff.txt)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__perp_diff.txt | file | Text files for perpendicular diffusivity values. | True | *__perp_diff.txt |
iso_diff
Section titled “iso_diff”Format : tuple val(meta), path(*__iso_diff.txt)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | True | |
| *__iso_diff.txt | file | Text files for isotropic diffusivity values. | True | *__iso_diff.txt |
priors
Section titled “priors”Format : path(priors)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| priors | directory | Folder containing text files for isotropic, parallel and perpendicular diffusivity values. | True | priors |
mean_para_diff
Section titled “mean_para_diff”Format : path(mean_para_diff.txt)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| mean_para_diff.txt | file | Text file for average parallel diffusivity value. | True | mean_para_diff.txt |
mean_perp_diff
Section titled “mean_perp_diff”Format : path(mean_perp_diff.txt)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| mean_perp_diff.txt | file | Text file for average perpendicular diffusivity value. | True | mean_perp_diff.txt |
mean_iso_diff
Section titled “mean_iso_diff”Format : path(mean_iso_diff.txt)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| mean_iso_diff.txt | file | Text file for average isotropic diffusivity value. | True | mean_iso_diff.txt |
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