reconst_noddi

Run NODDI modelling pipeline using AMICO from DWI data.

Keywords : Diffusion MRI, NODDI, Microstructure modeling

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Inputs

Input 1

Format : tuple val(meta), path(dwi), path(bval), path(bvec), path(mask), path(kernels), val(para_diff), val(iso_diff)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
dwi	file	Nifti DWI file acquired with a NODDI compatible protocol (multi-shell).	True	*.{nii,nii.gz}
bval	file	B-values in FSL format.	True	*.bval
bvec	file	B-vectors in FSL format.	True	*.bvec
mask	file	Nifti brain mask.	True	*mask.{nii,nii.gz}
kernels	directory	Folder containg kernels.	True	kernels
para_diff	float	Parallel diffusivity value (diff prior) (mm2/s).	False
iso_diff	float	Isotropic diffusivity value (diff prior) (mm2/s).	False

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Outputs

dir

Format : tuple val(meta), path(*__dir.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__dir.nii.gz	file	Nifti file main direction.	True	*__dir.{nii,nii.gz}

isovf

Format : tuple val(meta), path(*__isovf.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__isovf.nii.gz	file	Nifti file for isotropic volume fraction (e.g. Free Water Fraction (FWF)).	True	*__isovf.{nii,nii.gz}

icvf

Format : tuple val(meta), path(*__icvf.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__icvf.nii.gz	file	Nifti file for Intra-Cellular Volume Fraction (e.g. Neurite Density Index (NDI)).	True	*__icvf.{nii,nii.gz}

ecvf

Format : tuple val(meta), path(*__ecvf.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__ecvf.nii.gz	file	Nifti file for Extra-Compartment Volume Fraction.	True	*__ecvf.{nii,nii.gz}

odi

Format : tuple val(meta), path(*__odi.nii.gz)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__odi.nii.gz	file	Nifti file for Orientation Dispersion Index.	True	*__odi.{nii,nii.gz}

kernels

Format : path(kernels)

	Type	Description	Mandatory	Pattern
kernels	directory	Folder containing kernels.	True	kernels

versions

Format : path(versions.yml)

	Type	Description	Mandatory	Pattern
versions.yml	file	File containing software versions.	True	versions.yml

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Arguments (see process.ext)

	Type	Description	Default	Choices
para_diff	float	Axial diffusivity (AD) in the CC (mm2/s). It overwrites the input para_diff if provided.	“
iso_diff	float	Mean diffusivity (MD) in ventricles (mm2/s). It overwrites the input iso_diff if provided.	“
noddi_lambda1	float	First regularization parameter for NODDI fitting.	“
noddi_lambda2	float	Second regularization parameter for NODDI fitting.	“
b_thr	float	Limit value to consider that a b-value is on an existing shell. Above this limit, the b-value is placed on a new shell. This includes b0s values.	“
compute_only	boolean	Compute kernels only.	“
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

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Tools

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.
NODDI	Method to compute neurite orientation dispersion and density imaging.	10.1016/j.neuroimage.2012.03.072
AMICO	Accelerated Microstructure Imaging via Convex Optimization.	10.1016/j.neuroimage.2014.10.026

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Authors

• @Manonedde

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Last updated : 2026-05-12