reconst_shmetrics

Compute FODF metrics from given FODF or SH map.

Keywords : FODF, SH, Metrics

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Inputs

Input 1

Format : tuple val(meta), path(sh), path(mask), path(fa), path(md)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
sh	file	SH or FODF map.	True	*.{nii,nii.gz}
mask	file	B0 mask.	True	*.{nii,nii.gz}
fa	file	FA map.	True	*.{nii,nii.gz}
md	file	MD map.	True	*.{nii,nii.gz}

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Outputs

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	Peaks file.	True	*peaks.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	Peak indices file.	True	*peak_indices.nii.gz

peak_values

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

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

afd_max

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*afd_max.nii.gz	file	Maximum Apparent Fiber Density (AFDmax) map.	True	*afd_max.nii.gz

afd_total

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*afd_total.nii.gz	file	Total Apparent Fiber Density (AFDtotal) map.	True	*afd_total.nii.gz

afd_sum

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*afd_sum.nii.gz	file	Sum of all Apparent Fiber Density (Afdsum) map.	True	*afd_sum.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	Number of Fiber Orientation (NuFO) map.	True	*nufo.nii.gz

vent_mask

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*ventricles_mask.nii.gz	file	Ventricles mask.	True	*ventricles_mask.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
sh_basis	string	SH basis of the input SH/FODF map.	tournier07	- tournier07 - descoteaux07 - csa - fibernav
relative_threshold	float	Relative threshold to apply to the FODF peaks when computing the metrics. This is a value between 0 and 1 that represents the percentage of the maximum FODF value to use as a threshold for peak detection. For example, if the maximum FODF value in a voxel is 1 and the relative threshold is 0.5, then only peaks with a value greater than 0.5 will be considered for metric computation.	0.1
fodf_metrics_a_factor	float	A-factor for the AFD metrics. This is a parameter that controls the sensitivity of the AFD metrics to the FODF values. A higher A-factor will make the AFD metrics more sensitive to higher FODF values, while a lower A-factor will make them more sensitive to lower FODF values. The default value is 8, which is a commonly used value in the literature.	8.0
fa_threshold	float	FA threshold to apply to the FA map when computing the metrics. This is a value between 0 and 1 that represents the minimum FA value for a voxel to be included in the metric computation. For example, if the FA threshold is set to 0.2, then only voxels with an FA value greater than 0.2 will be included in the metric computation.	0.2
md_threshold	float	MD threshold to apply to the MD map when computing the metrics. This is a value in mm^2/s that represents the maximum MD value for a voxel to be included in the metric computation. For example, if the MD threshold is set to 0.001, then only voxels with an MD value less than 0.001 mm^2/s will be included in the metric computation.	0.001
absolute_peaks	boolean	If true, the absolute values of the FODF peaks will be used to compute the metrics instead of the relative values. This means that the metrics will be computed based on the actual FODF values at the peaks rather than their values relative to the maximum FODF value in the voxel. This can be useful in cases where the FODF values are not normalized or when comparing across subjects with different FODF scaling.	False
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.

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Authors

• @karanphil

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Last updated : 2026-05-12