Module: 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.
| 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. | | *.{nii,nii.gz} |
| bval | file | B-values in FSL format. | | *.bval |
| bvec | file | B-vectors in FSL format. | | *.bvec |
| mask | file | B0 mask. | | *.{nii,nii.gz} |
| fa | file | FA map. | | *.{nii,nii.gz} |
| md | file | MD map. | | *.{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. | | *.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. | | *.txt |
| csf_frf | file | Fiber Response Function (FRF) for the CSF. Only use with multi-shell method, along with wm_frf and gm_frf. | | *.txt |
Outputs
| Type | Description | Pattern |
|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | |
| fodf | file | FODF map. | *fodf.nii.gz |
| wm_fodf | file | WM FODF map. | *wm_fodf.nii.gz |
| gm_fodf | file | GM FODF map. | *gm_fodf.nii.gz |
| csf_fodf | file | CSF FODF map. | *csf_fodf.nii.gz |
| vf | file | Volume fraction map. | *vf.nii.gz |
| vf_rgb | file | Volume fraction map in rgb. | *vf_rgb.nii.gz |
| peaks | file | Peaks file. | *peaks.nii.gz |
| peak_values | file | Peak values file. | *peak_values.nii.gz |
| peak_indices | file | Peak indices file. | *peak_indices.nii.gz |
| afd_max | file | Maximum Apparent Fiber Density (AFDmax) map. | *afd_max.nii.gz |
| afd_total | file | Total Apparent Fiber Density (AFDtotal) map. | *afd_total.nii.gz |
| afd_sum | file | Sum of all Apparent Fiber Density (Afdsum) map. | *afd_sum.nii.gz |
| nufo | file | Number of Fiber Orientation (NuFO) map. | *nufo.nii.gz |
| vent_mask | file | Ventricule mask estimated from an MD and FA threshold. | *ventricles_mask.nii.gz |
| versions | file | File containing software versions | versions.yml |
Authors
@gagnonanthony, @karanphil
