Module: reconst/shsignal
Compute the SH coefficient directly on the raw DWI signal
Keywords : sh, dwi, signal
| 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. | | *.{nii,nii.gz} |
| bval | file | B-values in FSL format. | | *.bval |
| bvec | file | B-vectors in FSL format. | | *.bvec |
| mask | file | Nifti volume file used to mask the input image. | | *.{nii,nii.gz} |
Outputs
| Type | Description | Pattern |
|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | |
| sh_signal | file | Output filename for the SH coefficients. | *__dwi_sh.{nii,nii.gz} |
| versions | file | File containing software versions | versions.yml |
| Type | Description | Default | Choices |
|---|
| dwi_shell_tolerance | int | Volumes with b-values that differ by this tolerance are considered of same weighting. | 20 | |
| b0_thr_extract_b0 | int | Volumes with b-values up to this threshold are considered b0 (unweighted). | 10 | |
| shell_to_fit | int | Only use volumes with this b-value. Required if input is multi-shell. | None | |
| sh_order | int | Truncate spherical harmonics coefficients to this order. | 4 | |
| sh_basis | string | Spherical harmonics basis to use. Options : - descoteaux07 - tournier07 - descoteaux07_legacy - tournier07_legacy | descoteaux07_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 | |
| Description | DOI |
|---|
| Scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | |
Authors
AlexVCaron
Maintainers
AlexVCaron
Last updated : 2025-07-15
