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)

  • dPar (a float)

  • 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)

  • isExvivo (a boolean) – (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)

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

  • write_fibgz (a boolean)

  • write_mif (a boolean)

Outputs:

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

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

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

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

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

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

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

  • od_image (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)

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

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

Bases: SimpleInterface

Mandatory Inputs:

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

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

Outputs:

tf_image (a pathlike object or string representing a file)