reconst_fw_noddi
Sub-workflow that runs both RECONST/NODDI and RECONST/FREEWATER modules by handling the conditional execution of the diffusivity priors. Single-value diffusivity priors can be specified as input to this subworkflow. If not specified, the subworkflow will compute the priors automatically. They can then be averaged using the average_diff_priors argument of this workflow.
Keywords : multi-shell, freewater, noddi, diffusion
Components : reconst/noddi, reconst/freewater, reconst/diffusivitypriors, reconst/meandiffusivitypriors, reconst/dtimetrics, utils_options
Inputs
Section titled “Inputs”| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| dwi_bval_bvec | file | The input channel containing the DWI, BVAL, and BVEC files. Structure : tuple val(meta), path(dwi), path(bval), path(bvec)
| True | *.\{dwi,bval,bvec\} |
| brain_mask | file | The input channel containing the brain mask file (e.g. b0_mask). Structure : tuple val(meta), path(brain_mask)
| True | *.nii.gz |
| fa_ad_rd_md | file | The input channel containing DTI metrics (FA, AD, RD, MD). Not used when supplying custom diffusivity priors. Structure : tuple val(meta), path(fa), path(ad), path(rd), path(md)
| False | *.nii.gz |
| diffusivities | Map | The input channel containing custom diffusivity priors to use for NODDI and FreeWater models. If not provided, the diffusivity priors will be computed automatically. Can be subject-bound (i.e. different values per subject), a single-value for all subjects, or empty to compute them automatically. IMPORTANT: all priors must be provided the same way, meaning that if one prior is subject-bound, all others must be subject-bound as well (same for single-value or empty). para_diff: channel.empty(), // Example of empty to compute automatically iso_diff: channel.value(0.003), // Example of single-value for all subjects perp_diff_min: channel.of( // Example of subject-bound values tuple([ id:‘subj1’ ], 0.0001), tuple([ id:‘subj2’ ], 0.00015) ), perp_diff_max: channel.of( tuple([ id:‘subj1’ ], 0.0007), tuple([ id:‘subj2’ ], 0.00065) ) ] Structure: `[ | False | |
| options | Map | Map of options for the subworkflow.
| False |
Outputs
Section titled “Outputs”| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| noddi_dir | file | Nifti file main direction. Structure : tuple val(meta), path(dir)
| False | *__fit_dir.nii.gz |
| noddi_isovf | file | Nifti file for isotropic volume fraction. Structure : tuple val(meta), path(isovf)
| False | *__isovf.nii.gz |
| noddi_icvf | file | Nifti file for intracellular volume fraction. Structure : tuple val(meta), path(icvf)
| False | *__icvf.nii.gz |
| noddi_ecvf | file | Nifti file for Extra-Cellular Volume Fraction. Structure : tuple val(meta), path(ecvf)
| False | *__ecvf.nii.gz |
| noddi_odi | file | Nifti file for Orientation Dispersion Index. Structure : tuple val(meta), path(odi)
| False | *__odi.nii.gz |
| fw_dwi | file | Free Water corrected DWI Nifti file. Structure : tuple val(meta), path(fw_dwi)
| False | *__dwi_fw_corrected.nii.gz |
| fw_dir | file | Free Water corrected main direction Nifti file. Structure : tuple val(meta), path(fw_dir)
| False | *__dir.nii.gz |
| fw_fibervolume | file | Free Water corrected fiber volume Nifti file. Structure : tuple val(meta), path(fw_fibvolume)
| False | *__fibervolume.nii.gz |
| fw_fwf | file | Free Water corrected Free Water Fraction Nifti file. Structure : tuple val(meta), path(fw_fwf)
| False | *__fwf.nii.gz |
| fw_nrmse | file | Free Water correction NRMSE Nifti file. Structure : tuple val(meta), path(fw_nrmse)
| False | *__nrmse.nii.gz |
| fw_dti_tensor | file | Free Water corrected DTI tensor Nifti file. Structure : tuple val(meta), path(fw_dti_tensor)
| False | *__tensor.nii.gz |
| fw_dti_md | file | Free Water corrected DTI Mean Diffusivity Nifti file. Structure : tuple val(meta), path(fw_dti_md)
| False | *__md.nii.gz |
| fw_dti_rd | file | Free Water corrected DTI Radial Diffusivity Nifti file. Structure : tuple val(meta), path(fw_dti_rd)
| False | *__rd.nii.gz |
| fw_dti_ad | file | Free Water corrected DTI Axial Diffusivity Nifti file. Structure : tuple val(meta), path(fw_dti_ad)
| False | *__ad.nii.gz |
| fw_dti_fa | file | Free Water corrected DTI Fractional Anisotropy Nifti file. Structure : tuple val(meta), path(fw_dti_fa)
| False | *__fa.nii.gz |
| fw_dti_rgb | file | Free Water corrected DTI RGB Nifti file. Structure : tuple val(meta), path(fw_dti_rgb)
| False | *__rgb.nii.gz |
| fw_dti_peaks | file | Free Water corrected DTI Peaks Nifti file. Structure : tuple val(meta), path(fw_dti_peaks)
| False | *__evec_v1.nii.gz |
| fw_dti_evecs | file | Free Water corrected DTI Eigenvectors Nifti file. Structure : tuple val(meta), path(fw_dti_evecs)
| False | *__evecs.nii.gz |
| fw_dti_evals | file | Free Water corrected DTI Eigenvalues Nifti file. Structure : tuple val(meta), path(fw_dti_evals)
| False | *__evals.nii.gz |
| fw_dti_residual | file | Free Water corrected DTI Residuals Nifti file. Structure : tuple val(meta), path(fw_dti_residual)
| False | *__residual.nii.gz |
| fw_dti_ga | file | Free Water corrected DTI Geodesic Anisotropy Nifti file. Structure : tuple val(meta), path(fw_dti_ga)
| False | *__ga.nii.gz |
| fw_dti_mode | file | Free Water corrected DTI Mode Nifti file. Structure : tuple val(meta), path(fw_dti_mode)
| False | *__mode.nii.gz |
| fw_dti_norm | file | Free Water corrected DTI Norm Nifti file. Structure : tuple val(meta), path(fw_dti_norm)
| False | *__norm.nii.gz |
| versions | file | File containing software versions Structure : tuple path(versions)
| True | versions.yml |
Authors
Section titled “Authors”Maintainers
Section titled “Maintainers”Last updated : 2026-03-17