qsirecon.interfaces.amico module

Workflows for AMICO

class qsirecon.interfaces.amico.AmicoReconInterface(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

• bval_file (a pathlike object or string representing an existing file)

• bvec_file (a pathlike object or string representing an existing file)

• dwi_file (a pathlike object or string representing an existing file)

Optional Inputs:

• b0_threshold (a float) – (Nipype default value: 50)

• big_delta (a float or None) – (Nipype default value: None)

• little_delta (a float or None) – (Nipype default value: None)

• mask_file (a pathlike object or string representing an existing file)

• write_fibgz (a boolean)

• write_mif (a boolean)

Outputs:

• extrapolated_b (a pathlike object or string representing a file)

• extrapolated_bvals (a pathlike object or string representing a file)

• extrapolated_bvecs (a pathlike object or string representing a file)

• extrapolated_dwi (a pathlike object or string representing a file)

• fibgz (a pathlike object or string representing a file)

• fod_sh_mif (a pathlike object or string representing a file)

• odf_amplitudes (a pathlike object or string representing a file)

• odf_directions (a pathlike object or string representing a file)

class qsirecon.interfaces.amico.NODDI(from_file=None, resource_monitor=None, **inputs)

Bases: AmicoReconInterface

Recon Spec Options

b0_threshold (a float)

Threshold below which a b-value is considered a b0.

Default50.0

dIso (a float)

Isotropic diffusivity constant in mm^2/s. Passed to AMICO as dIso. Defined in the recon spec as dIso. Stored in the metadata as IsotropicDiffusivity.

dPar (a float)

Parallel diffusivity constant in mm^/2. Passed to AMICO as dPar. Defined in the recon spec as dPar. Stored in the metadata as ParallelDiffusivity.

doNormalize (a boolean)

Flag indicating whether to normalize the data during fitting. Default: True.

DefaultTrue

fitMethod ('OLS' or 'WLS')

Fitting method to use. Options are 'OLS' (Ordinary Least Squares) or 'WLS' (Weighted Least Squares). Default: 'OLS'.

DefaultOLS

isExvivo (a boolean)

Flag indicating whether acquired data is ex vivo or fixed tissue. Fixed tissue requires an additional dot compartment estimation.

DefaultFalse

nrmse (a boolean)

Flag indicating whether to compute the normalized root mean square error (NRMSE) between the measured and fitted signals. Default: True.

DefaultTrue

rmse (a boolean)

Flag indicating whether to compute the root mean square error (RMSE) between the measured and fitted signals. Default: True.

DefaultTrue

saveModulatedMaps (a boolean)

Flag indicating whether to save modulated maps for ICVF and ODI. Default: True.

DefaultTrue

Developer Information

Mandatory Inputs:

• bval_file (a pathlike object or string representing an existing file)

• bvec_file (a pathlike object or string representing an existing file)

• dIso (a float) – Isotropic diffusivity constant in mm^2/s. Passed to AMICO as dIso. Defined in the recon spec as dIso. Stored in the metadata as IsotropicDiffusivity.

• dPar (a float) – Parallel diffusivity constant in mm^/2. Passed to AMICO as dPar. Defined in the recon spec as dPar. Stored in the metadata as ParallelDiffusivity.

• dwi_file (a pathlike object or string representing an existing file)

Optional Inputs:

• b0_threshold (a float) – Threshold below which a b-value is considered a b0. (Nipype default value: 50.0)

• big_delta (a float or None) – (Nipype default value: None)

• doNormalize (a boolean) – Flag indicating whether to normalize the data during fitting. Default: True. (Nipype default value: True)

• fitMethod (‘OLS’ or ‘WLS’) – Fitting method to use. Options are ‘OLS’ (Ordinary Least Squares) or ‘WLS’ (Weighted Least Squares). Default: ‘OLS’. (Nipype default value: OLS)

• isExvivo (a boolean) – Flag indicating whether acquired data is ex vivo or fixed tissue. Fixed tissue requires an additional dot compartment estimation. (Nipype default value: False)

• little_delta (a float or None) – (Nipype default value: None)

• mask_file (a pathlike object or string representing an existing file)

• nrmse (a boolean) – Flag indicating whether to compute the normalized root mean square error (NRMSE) between the measured and fitted signals. Default: True. (Nipype default value: True)

• num_threads (an integer) – (Nipype default value: 1)

• rmse (a boolean) – Flag indicating whether to compute the root mean square error (RMSE) between the measured and fitted signals. Default: True. (Nipype default value: True)

• saveModulatedMaps (a boolean) – Flag indicating whether to save modulated maps for ICVF and ODI. Default: True. (Nipype default value: True)

• write_fibgz (a boolean)

• write_mif (a boolean)

Outputs:

• config_file (a pathlike object or string representing a file)

• directions (a pathlike object or string representing a file)

• directions_metadata (a dictionary with keys which are any value and with values which are any value)

• extrapolated_b (a pathlike object or string representing a file)

• extrapolated_bvals (a pathlike object or string representing a file)

• extrapolated_bvecs (a pathlike object or string representing a file)

• extrapolated_dwi (a pathlike object or string representing a file)

• fibgz (a pathlike object or string representing a file)

• fod_sh_mif (a pathlike object or string representing a file)

• icvf (a pathlike object or string representing a file)

• icvf_metadata (a dictionary with keys which are any value and with values which are any value)

• isovf (a pathlike object or string representing a file)

• isovf_metadata (a dictionary with keys which are any value and with values which are any value)

• modulated_icvf (a pathlike object or string representing a file)

• modulated_icvf_metadata (a dictionary with keys which are any value and with values which are any value)

• modulated_od (a pathlike object or string representing a file)

• modulated_od_metadata (a dictionary with keys which are any value and with values which are any value)

• nrmse (a pathlike object or string representing a file)

• nrmse_metadata (a dictionary with keys which are any value and with values which are any value)

• od (a pathlike object or string representing a file)

• od_metadata (a dictionary with keys which are any value and with values which are any value)

• odf_amplitudes (a pathlike object or string representing a file)

• odf_directions (a pathlike object or string representing a file)

• rmse (a pathlike object or string representing a file)

• rmse_metadata (a dictionary with keys which are any value and with values which are any value)

class qsirecon.interfaces.amico.NODDITissueFraction(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

• isovf (a pathlike object or string representing an existing file)

• mask_image (a pathlike object or string representing an existing file)

Outputs:

tf (a pathlike object or string representing a file)