qsirecon.workflows.recon.amico module

AMICO Reconstruction workflows

qsirecon.workflows.recon.amico.init_amico_noddi_fit_wf(inputs_dict, name='amico_noddi_recon', qsirecon_suffix='', params={})[source]

Reconstruct NODDI scalars using AMICO.

Parameters:

params (dict) – Parameters for the NODDI model. See qsirecon.interfaces.amico.NODDI for more details.

Additionally, the following parameters are supported:

saveModulatedMaps: boolean. Whether to save modulated maps for ICVF and ODI.
rmse: boolean. Whether to compute the root mean square error between predicted and measured signal.
nrmse: boolean. Whether to compute the normalized root mean square error between the predicted and measured signal (normalized by the mean of the measured signal).
plot_reports: boolean. Whether to plot reports for the NODDI model.

Inputs:

*qsirecon outputs*

Outputs:

directions – Image of directions
icvf – Voxelwise ICVF.
od – Voxelwise Orientation Dispersion
isovf – Voxelwise ISOVF
modulated_icvf – Voxelwise modulated ICVF (ICVF * (1 - ISOVF))
modulated_od – Voxelwise modulated Orientation Dispersion (OD * (1 - ISOVF))
rmse – Voxelwise root mean square error between predicted and measured signal
nrmse – Voxelwise normalized root mean square error between predicted and measured signal
config – Pickle file with model configurations in it
fibgz