kwneuro.noddi¶

Classes¶

A Noddi result

class kwneuro.noddi.Noddi¶

A Noddi result

volume: kwneuro.resource.VolumeResource¶: The NODDI image volume. It is a 4D volume, with the first three dimensions being spatial and the final dimension indexing the noddi outputs.

directions: kwneuro.resource.VolumeResource¶: The NODDI image volume. It is a 4D volume, with the first three dimensions being spatial and the final dimension indexing the directions.

load() → Noddi¶: Load any on-disk resources into memory and return a DTI with all loadable resources loaded.

Save all resources to disk and return a Noddi with all resources being on-disk.

Returns: A Noddi with its internal resources being on-disk.

static estimate_from_dwi(dwi: kwneuro.dwi.Dwi, mask: kwneuro.resource.VolumeResource | None = None, dpar: float = 0.0017, n_kernel_dirs: int = 500) → Noddi¶

Estimate Noddi from a DWI.

Parameters:

dwi – The source DWI
mask – Optionally, a boolean 3D volume that has indicates where the fit should take place, such as a brain mask.
dpar – The parallel diffusivity to be used in the model fitting. If not provided, the default value of 1.7e-3 mm^2/s is used, which is suitable for white matter. For gray matter, a value of 1.3e-3 mm^2/s is recommended.
n_kernel_dirs – The number of directions to use when generating the AMICO NODDI kernels. This value represents the total count of possible orientations for the response functions across the half-sphere. Default: 500.

Returns: A Noddi resource containing the estimated parameters.

property ndi: kwneuro.resource.VolumeResource¶: Neurite Density Index (NDI) map as a 3D volume.

property odi: kwneuro.resource.VolumeResource¶: Orientation Dispersion Index (ODI) map as a 3D volume.

property fwf: kwneuro.resource.VolumeResource¶: Free Water Fraction (FWF) map as a 3D volume.

Compute the modulated maps, NDI*TF and ODI*TF, where TF = 1 - FWF.

Returns:: Returns 3D volumes for modulated NDI and ODI maps, as VolumeResources.