reconst_qball

Compute the Constant Solid Angle (CSA) or Analytical Q-ball model, the generalized fractional anisotropy (GFA) and the peaks of the model.

Keywords : Qball, reconst, scilpy

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Inputs

Input 1

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
dwi	file	Nifti DWI volume to reconstruct FODF from.	True	*.{nii,nii.gz}
bval	file	B-values in FSL format.	True	*.bval
bvec	file	B-vectors in FSL format.	True	*.bvec
mask	file	Mask.	False	*.{nii,nii.gz}

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Outputs

qball

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__qball.nii.gz	file	Qball spherical harmonics coefficients.	True	*__qball.{nii,nii.gz}

gfa

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__gfa.nii.gz	file	Generalized fractional anisotropy.	True	*__gfa.{nii,nii.gz}

peaks

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

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

peak_indices

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__peak_indices.nii.gz	file	Generated peaks indices on the sphere.	True	*__peak_indices.{nii,nii.gz}

nufo

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

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

a_power

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

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

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
b0_threshold	integer	Threshold for the b0 mask.	20
use_qball	boolean	If set, qball will be used as the odf reconstruction model instead of CSA.	False
gfa	boolean	Compute the generalized fractional anisotropy.	False
peaks	boolean	Compute the peaks.	False
peaks_indices	boolean	Compute the peaks indices on the sphere.	False
qball	boolean	Compute the qball spherical harmonics.	False
nufo	boolean	Compute the NUFO.	False
a_power	boolean	Compute the anisotropy power.	False
sh_order	integer	Spherical harmonics order. Must be a positive even number.	4

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Tools

	Description	DOI
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.

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Authors

• @EliseCos
• @arnaudbore

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Last updated : 2025-12-22