MRtrix3 Fiber Orientation Distribution Estimation¶
Library: MRtrix3 | Docker Image: mrtrix3/mrtrix3
Function¶
Estimates fiber orientation distributions (FODs) using constrained spherical deconvolution to resolve crossing fibers.
Modality: 4D diffusion-weighted NIfTI with multi-shell or single-shell data, plus tissue response functions.
Typical Use: Estimating fiber orientations for subsequent tractography.
Key Parameters¶
Key Points¶
Use msmt_csd for multi-shell data (recommended), csd for single-shell. Response functions from dwi2response.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
algorithm |
string |
Yes | FOD algorithm (csd/msmt_csd) | |
input |
File |
Yes | Input DWI image | |
wm_response |
File |
Yes | White matter response function | |
wm_fod |
string |
Yes | Output WM FOD image filename | |
gm_response |
File |
No | Grey matter response (required before CSF) | |
gm_fod |
string |
No | Output GM FOD filename (required before CSF) | |
csf_response |
File |
No | CSF response (requires GM inputs) | |
csf_fod |
string |
No | Output CSF FOD filename (requires GM inputs) | |
mask |
File |
No | Processing mask | -mask |
Accepted Input Extensions¶
- input:
.mif,.nii,.nii.gz,.mgh,.mgz - wm_response:
.txt - gm_response:
.txt - csf_response:
.txt - mask:
.mif,.nii,.nii.gz,.mgh,.mgz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
wm_fod_image |
File |
$(inputs.wm_fod) |
gm_fod_image |
File |
`${ |
| if (inputs.gm_fod) | ||
| else | ||
| } | ||
| ` | ||
csf_fod_image |
File |
`${ |
| if (inputs.csf_fod) | ||
| else | ||
| } | ||
| ` | ||
log |
File |
dwi2fod.log |
Output Extensions¶
- wm_fod_image:
.mif,.nii,.nii.gz - gm_fod_image:
.mif,.nii,.nii.gz - csf_fod_image:
.mif,.nii,.nii.gz
Docker Tags¶
Available versions: latest, 3.0.8, 3.0.7, 3.0.5, 3.0.4, 3.0.3
Categories¶
- Diffusion MRI > MRtrix3 > Tensor/FOD