Module: reconst/freewater
Run freewater modelling pipeline using AMICO from DWI data.
Inputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| dwi | file | Nifti DWI file acquired with a freewater compatible protocol (single-shell or multi-shell). | *.{nii,nii.gz} |
| bval | file | B-values in FSL format. | *.bval |
| bvec | file | B-vectors in FSL format. | *.bvec |
| mask | file | Nifti brain mask. | *mask.{nii,nii.gz} |
| kernels | directory | Folder containg kernels. | kernels |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| dwi_fw_corrected | file | Nifti file freewater corrected DWI. | *__dwi_fw_corrected.{nii,nii.gz} |
| dir | file | Nifti file main direction. | *__FIT_dir.{nii,nii.gz} |
| fibervolume | file | Nifti file for fiber volume. | *__FIT_fibervolume.{nii,nii.gz} |
| fw | file | Nifti file for freewater (isotropic volume). | *__FIT_FW.{nii,nii.gz} |
| nrmse | file | Nifti file for nrmse. | *__FIT_nrmse.{nii,nii.gz} |
| kernels | directory | Folder containing kernels. | kernels |
| versions | file | File containing software versions. | versions.yml |
Tools
| Description | Homepage | DOI | |
|---|---|---|---|
| Scilpy | The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox. | https://github.com/scilus/scilpy.git | |
| Freewater | Free water elimination and mapping from diffusion MRI. | 10.1002/mrm.22055 | |
| AMICO | Accelerated Microstructure Imaging via Convex Optimization. | https://github.com/daducci/AMICO | 10.1016/j.neuroimage.2014.10.026 |
Keywords
| Diffusion MRI |
| Freewater |
| Microstructure modeling |
Authors
@karanphil