Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.

brainprep.interfaces.amico.noddi_fit

brainprep.interfaces.amico.noddi_fit(dwi_file, mask_file, workspace_dir, output_dir, entities, dryrun=False)[source]

NODDI model fitting.

This function compute diffusion NODDI microstructural maps using AMICO for a single subject.

NODDI fitting is performed with default parameters and estimates neurite density and orientation dispersion using a multi-compartment model, producing maps such as Neurite Density Index (NDI), Free Water Fraction (FWF), and Orientation Dispersion Index (ODI).

Parameters:
dwi_fileFile

Path to the preprocessed diffusion weighted image file of one subject.

mask_fileFile

Path to the associated brain image file.

workspace_dir: Directory

Working directory with the workspace of the current processing.

output_dirDirectory

Directory where the reoriented image will be saved.

entitiesdict

A dictionary of parsed BIDS entities including modality.

dryrunbool

If True, skip actual computation and file writing. Default False.

Returns:
outputstuple[File]

  • config_file : File - AMICO internal configuration.

  • ndi_file : File - Neurite Density Index map.

  • fwf_file : File - Free Water Fraction map.

  • odi_file : File - Orientation Dispersion Index map.

Raises:
RuntimeError

If AMICO is not installed.