reconst_fodf

Perform FODF reconstruction and compute FODF metrics from a dwi volume for a selected number of shells. Note that multiple choices of FODF reconstruction method are available through the method argument. The single-shell single-tissue (ssst) method is performed by selecting only one shell (task.ext.fodf_shells) and choosing the ssst method (task.ext.method). The multi-shell single-tissue (msst) method (default) is performed by selecting multiple shells (task.ext.fodf_shells) and choosing the ssst method (task.ext.method). Both ssst and msst are expected to output only WM FODF. The multi-shell multi-tissue (msmt) method is performed by selecting multiple shells (task.ext.fodf_shells) and choosing the msmt method (task.ext.method). The msmt method is expected to output WM FODF, GM FODF and CSF FODF, along with volume fraction (vf) maps. In every case, chosen FODF metrics are outputed.

Keywords : FODF, Local Model, Reconst

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Inputs

Input 1

Format : tuple val(meta), path(dwi), path(bval), path(bvec), path(mask), path(fa), path(md), path(wm_frf), path(gm_frf), path(csf_frf)

	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	B0 mask.	True	*.{nii,nii.gz}
fa	file	FA map.	True	*.{nii,nii.gz}
md	file	MD map.	True	*.{nii,nii.gz}
wm_frf	file	Fiber Response Function (FRF) for the white matter (WM). In the case of single-shell method, this should be the only input FRF. In the case of multi-shell method, gm_frf and csf_frf are also mandatory.	True	*.txt
gm_frf	file	Fiber Response Function (FRF) for the grey matter (GM). Only use with multi-shell method, along with wm_frf and csf_frf.	True	*.txt
csf_frf	file	Fiber Response Function (FRF) for the CSF. Only use with multi-shell method, along with wm_frf and gm_frf.	True	*.txt

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Outputs

fodf

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

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

wm_fodf

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

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

gm_fodf

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

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

csf_fodf

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

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

vf

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

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

vf_rgb

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	True
*__vf_rgb.nii.gz	file	Volume fraction map in rgb.	True	*__vf_rgb.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	Peaks file.	True	*__peaks.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	Peak values file.	True	*__peak_values.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

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	Ventricule mask estimated from an MD and FA threshold.	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
dwi_shell_tolerance	integer	Tolerance in s/mm2 for grouping b-values into shells. E.g. with a tolerance of 20, b-values between 0 and 20 will be considered as b=0.	None
min_fodf_shell_value	integer	Minimum b-value to use for FODF fitting. All shells above this value will be used.	100
b0_thr_extract_b0	integer	Threshold under which b-values are considered to be b0s.	10
fodf_shells	string	Space separated list of b-values to use for FODF fitting. If None, all shells above min_fodf_shell_value will be used.	None
sh_order	integer	Spherical harmonics order to use for FODF fitting.	None
sh_basis	string	Spherical harmonics basis to use for FODF fitting.	None	- tournier07 - descoteaux07 - descoteaux07_legacy - tournier07_legacy
method	string	FODF reconstruction method to use.	ssst	- ssst - msmt
relative_threshold	float	Relative threshold to apply on FODF peaks.	None
fodf_metrics_a_factor	float	Absolute threshold to apply on FODF peaks.	2.0
fa_threshold	float	Threshold to apply on the FA map to extract voxels in ventricles.	None
md_threshold	float	Threshold to apply on the MD map to extract voxels in ventricles.	None
absolute_peaks	boolean	If set, the peak values are not max-normalized for each voxel, but kept as the actual fODF amplitude.	False
wm_fodf	boolean	If set, will output the white matter (WM) FODF map when using the msmt method.	True
gm_fodf	boolean	If set, will output the grey matter (GM) FODF map when using the msmt method.	False
csf_fodf	boolean	If set, will output the CSF FODF map when using the msmt method.	False
vf	boolean	If set, will output the volume fraction (vf) maps when using the msmt method.	False
vf_rgb	boolean	If set, will output the volume fraction (vf) maps in rgb when using the msmt method.	False
peaks	boolean	If set, will output the peaks file.	False
peak_values	boolean	If set, will output the peak values file.	False
peak_indices	boolean	If set, will output the peak indices file.	False
afd_max	boolean	If set, will output the maximum Apparent Fiber Density (AFDmax) map.	False
afd_total	boolean	If set, will output the total Apparent Fiber Density (AFDtotal) map.	False
afd_sum	boolean	If set, will output the sum of all Apparent Fiber Density (Afdsum) map.	False
nufo	boolean	If set, will output the Number of Fiber Orientation (NuFO) map.	False
ventricles_mask	boolean	If set, will output the ventricle mask estimated from an MD and FA threshold.	False

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Tools

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

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Authors

• @gagnonanthony
• @karanphil

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Last updated : 2025-10-30