reconst_freewater

Run freewater modelling pipeline using AMICO from DWI data.

Keywords : Diffusion MRI, Freewater, Microstructure modeling

---

Inputs

Input 1

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

	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 freewater compatible protocol (single-shell or 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).	False
iso_diff	float	Isotropic diffusivity value (diff prior).	False
perp_diff_min	float	Minimum perpendicular diffusivity value (diff prior).	False
perp_diff_max	float	Maximum perpendicular diffusivity value (diff prior).	False

---

Outputs

dwi_fw_corrected

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

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

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}

fibervolume

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

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

fwf

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

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

nrmse

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

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

---

Arguments (see process.ext)

	Type	Description	Default	Choices
para_diff	float	Axial diffusivity (AD) in the CC. 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.	“
perp_diff_min	float	Radial diffusivity (RD) minimum (mm2/s). It overwrites the input perp_diff_min if provided.	“
perp_diff_max	float	Radial diffusivity (RD) maximum (mm2/s). It overwrites the input perp_diff_max if provided.	“
fw_lambda1	float	First regularization parameter for freewater fitting.	“
fw_lambda2	float	Second regularization parameter for freewater 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

---

Tools

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.
Freewater	Free water elimination and mapping from diffusion MRI.	10.1002/mrm.22055
AMICO	Accelerated Microstructure Imaging via Convex Optimization.	10.1016/j.neuroimage.2014.10.026

---

Authors

• @karanphil

---

Last updated : 2026-04-15