reconst_shsignal

shsignal

Compute the SH coefficient directly on the raw DWI signal

Keywords : sh, dwi, signal

Inputs

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`	True
dwi	file	Nifti DWI volume used to extract DTI metrics.	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 volume file used to mask the input image.	True	`*.{nii,nii.gz}`
ue	integer	Dummy entry for lint to run succesfully. Refer to nf-core/tools#3483	True	`remove-me`

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

	Type	Description	Mandatory	Pattern
meta	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	True
*__dwi_sh.nii.gz	file	Output filename for the SH coefficients.	True	`*__dwi_sh.{nii,nii.gz}`

Format : path(versions.yml)

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

	Type	Description	Default	Choices
dwi_shell_tolerance	integer	Volumes with b-values that differ by this tolerance are considered of same weighting.	`20`
b0_thr_extract_b0	integer	Volumes with b-values up to this threshold are considered b0 (unweighted).	`10`
shell_to_fit	integer	Only use volumes with this b-value. Required if input is multi-shell.	`None`
sh_order	integer	Truncate spherical harmonics coefficients to this order.	`4`
sh_basis	string	Spherical harmonics basis to use.	`descoteaux07_legacy`	- descoteaux07 - tournier07 - descoteaux07_legacy - tournier07_legacy
smoothing	float	Regularization coefficient used for the spherical harmonics fit.	`0.006`
attenuation_only	boolean	If enabled, divide the weighted volumes by the b0 before fitting.	`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`

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

Last updated : 2026-04-23