qsirecon.interfaces.amico module

Workflows for AMICO

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

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)[source]

Bases: AmicoReconInterface

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)[source]

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)