qsirecon.interfaces.dipy module

Image tools interfaces

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

Bases: DipyReconInterface

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)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’)

  • l1_alpha (a float) – (Nipype default value: 1.0)

  • l1_cv (an integer or None) – (Nipype default value: None)

  • l1_maxiter (an integer) – (Nipype default value: 1000)

  • l1_positive_constraint (a boolean) – (Nipype default value: False)

  • l1_verbose (a boolean) – (Nipype default value: False)

  • lambdaL (a float) – (Nipype default value: 1e-08)

  • lambdaN (a float) – (Nipype default value: 1e-08)

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

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

  • pos_grid (an integer) – (Nipype default value: 11)

  • pos_radius (a float) – (Nipype default value: 0.02)

  • radial_order (an integer) – (Nipype default value: 6)

  • regularization (‘L2’ or ‘L1’) – (Nipype default value: L2)

  • regularization_weighting (a string) – (Nipype default value: CV)

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

  • tau (a float) – (Nipype default value: 0.025330295910584444)

  • write_fibgz (a boolean)

  • write_mif (a boolean)

  • zeta (a float) – (Nipype default value: 700)

Outputs:

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

  • cnr_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)

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

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

  • r2_image (a pathlike object or string representing a file)

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

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

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

class qsirecon.interfaces.dipy.DipyReconInterface(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)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’)

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

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

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

  • 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.dipy.KurtosisReconstruction(from_file=None, resource_monitor=None, **inputs)[source]

Bases: DipyReconInterface

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)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’)

  • kurtosis_clip_max (a float) – (Nipype default value: 10.0)

  • kurtosis_clip_min (a float) – (Nipype default value: -0.42857142857142855)

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

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

  • plot_reports (a boolean) – (Nipype default value: True)

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

  • write_fibgz (a boolean)

  • write_mif (a boolean)

Outputs:

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

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

  • colorFA (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)

  • fa (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)

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

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

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

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

  • mkt (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)

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

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

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

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

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

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

Bases: DipyReconInterface

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)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’)

  • kurtosis_clip_max (a float) – (Nipype default value: 10.0)

  • kurtosis_clip_min (a float) – (Nipype default value: -0.42857142857142855)

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

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

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

  • write_fibgz (a boolean)

  • write_mif (a boolean)

Outputs:

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

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

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

  • axonald (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)

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

  • md (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)

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

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

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

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

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

Bases: DipyReconInterface

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:

  • anisotropic_scaling (a boolean) – (Nipype default value: True)

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

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

  • bval_threshold (a float)

  • cvxpy_solver (a string)

  • dti_scale_estimation (a boolean) – (Nipype default value: True)

  • eigenvalue_threshold (a float) – (Nipype default value: 0.0001)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’)

  • laplacian_regularization (a boolean) – (Nipype default value: True)

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

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

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

  • pos_grid (an integer) – (Nipype default value: 15)

  • pos_radius (a string or an integer) – (Nipype default value: adaptive)

  • positivity_constraint (a boolean) – (Nipype default value: False)

  • radial_order (an integer) – (Nipype default value: 6)

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

  • static_diffusivity (a float) – (Nipype default value: 0.0007)

  • 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)

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

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

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

  • ng (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)

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

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

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

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

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

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

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

Bases: DipyReconInterface

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)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’)

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

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

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

  • write_fibgz (a boolean)

  • write_mif (a boolean)

Outputs:

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

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

  • color_fa_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)

  • fa_image (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)

  • md_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)

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