AMICO NODDI Fitting¶
Library: AMICO | Docker Image: cookpa/amico-noddi
Function¶
Fits the NODDI (Neurite Orientation Dispersion and Density Imaging) model to multi-shell diffusion MRI data using convex optimization for fast and robust estimation.
Modality: Multi-shell diffusion MRI (4D NIfTI) with b-values and b-vectors, plus brain mask.
Typical Use: Microstructural imaging for neurite density and orientation dispersion in white matter.
Key Parameters¶
Python: amico.core.setup(), amico.core.load_data(), amico.core.set_model("NODDI"), amico.core.fit()
Key Points¶
Requires multi-shell acquisition (recommended: b=0,1000,2000 s/mm2). Outputs NDI (neurite density), ODI (orientation dispersion), and fISO (isotropic fraction). Much faster than original NODDI MATLAB toolbox.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
dwi |
File |
Yes | Multi-shell diffusion MRI 4D image | |
bvals |
File |
Yes | b-values file | |
bvecs |
File |
Yes | b-vectors file | |
mask |
File |
Yes | Brain mask image | |
num_threads |
int |
No | Maximum number of CPU threads (default 1) | --num-threads |
b0_threshold |
int |
No | Threshold for considering measurements b=0 (default 10) | --b0-threshold |
csf_diffusivity |
double |
No | CSF diffusivity in mm^2/s (default 0.003) | --csf-diffusivity |
parallel_diffusivity |
double |
No | Intracellular diffusivity parallel to neurites in mm^2/s (default 0.0017) | --parallel-diffusivity |
ex_vivo |
boolean |
No | Use ex-vivo AMICO model | --ex-vivo |
Accepted Input Extensions¶
- dwi:
.nii,.nii.gz - bvals:
.bval - bvecs:
.bvec - mask:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
ndi_map |
File |
output/NODDI*ICVF.nii.gz |
odi_map |
File |
output/NODDI*OD.nii.gz |
fiso_map |
File |
output/NODDI*ISOVF.nii.gz |
log |
File |
amico_noddi.log |
err_log |
File |
amico_noddi.err.log |
Output Extensions¶
- ndi_map:
.nii.gz - odi_map:
.nii.gz - fiso_map:
.nii.gz
Docker Tags¶
Available versions: latest, 0.1.2, 0.1.1, 0.0.4
Categories¶
- Diffusion MRI > AMICO > Microstructure Modeling