reconst_frf

Compute a Fiber Response Function (FRF) from a DWI. Note that multiple types of FRF are available through the method argument. The single-shell single-tissue (ssst) FRF is performed by choosing the ssst method (task.ext.method). This is expected to output a single WM FRF. The multi-shell multi-tissue (msmt) FRF is performed by choosing the msmt method (task.ext.method). This is expected to output a WM FRF, a GM FRF and a CSF FRF, each containing values for every shells.

Keywords : Fiber Orientation Distribution Function, Diffusion MRI, Fiber Response Function

Inputs

`Input 1`

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
dwi	file	Nifti image of DWI.	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 b0 binary mask.	True	`*.{nii,nii.gz}`
wm_mask	file	Nifti binary WM mask.	True	`*.{nii,nii.gz}`
gm_mask	file	Nifti binary GM mask.	True	`*.{nii,nii.gz}`
csf_mask	file	Nifti binary CSF mask.	True	`*.{nii,nii.gz}`

Outputs

`frf`

Format : tuple val(meta), path(*__frf.txt)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*__frf.txt	file	Fiber Response Function (FRF), in the case of ssst_frf.	True	`*__frf.txt`

`wm_frf`

Format : tuple val(meta), path(*__wm_frf.txt)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*__wm_frf.txt	file	WM Fiber Response Function (FRF), in the case of msmt_frf.	True	`*__wm_frf.txt`

`gm_frf`

Format : tuple val(meta), path(*__gm_frf.txt)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*__gm_frf.txt	file	GM Fiber Response Function (FRF), in the case of msmt_frf.	True	`*__gm_frf.txt`

`csf_frf`

Format : tuple val(meta), path(*__csf_frf.txt)

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
*__csf_frf.txt	file	CSF Fiber Response Function (FRF), in the case of msmt_frf.	True	`*__csf_frf.txt`

`versions`

Format : path(versions.yml)

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

Tools

	Description	DOI
DIPY	DIPY is the paragon 3D/4D+ imaging library in Python.
scilpy	The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox.

Authors

Last updated : 2025-10-30