qsirecon.interfaces.dipy module

Image tools interfaces

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

Bases: DipyReconInterface

Recon Spec Options

b0_threshold (a float)
B-value threshold. Any b-values below this threshold are considered b0s. Documented as 'B0Threshold' in the BIDS metadata.
Default50
big_delta (a float or None)
Large delta in seconds. Documented as 'LargeDelta' in the BIDS metadata.
DefaultNone
extrapolate_scheme ('HCP' or 'ABCD' or 'DSIQ5')
Sampling scheme to extrapolate the DWI data to. Documented as 'ExtrapolateScheme' in the BIDS metadata.
small_delta (a float or None)
Small delta in seconds. Documented as 'SmallDelta' in the BIDS metadata.
DefaultNone
write_fibgz (a boolean)
write_mif (a boolean)

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)

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

Optional Inputs:

  • b0_threshold (a float) – B-value threshold. Any b-values below this threshold are considered b0s. Documented as ‘B0Threshold’ in the BIDS metadata. (Nipype default value: 50)

  • big_delta (a float or None) – Large delta in seconds. Documented as ‘LargeDelta’ in the BIDS metadata. (Nipype default value: None)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’) – Sampling scheme to extrapolate the DWI data to. Documented as ‘ExtrapolateScheme’ in the BIDS metadata.

  • 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) – Small delta in seconds. Documented as ‘SmallDelta’ in the BIDS metadata. (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

Recon Spec Options

b0_threshold (a float)
B-value threshold. Any b-values below this threshold are considered b0s. Documented as 'B0Threshold' in the BIDS metadata.
Default50
big_delta (a float or None)
Large delta in seconds. Documented as 'LargeDelta' in the BIDS metadata.
DefaultNone
extrapolate_scheme ('HCP' or 'ABCD' or 'DSIQ5')
Sampling scheme to extrapolate the DWI data to. Documented as 'ExtrapolateScheme' in the BIDS metadata.
small_delta (a float or None)
Small delta in seconds. Documented as 'SmallDelta' in the BIDS metadata.
DefaultNone
write_fibgz (a boolean)
write_mif (a boolean)

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)

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

Optional Inputs:

  • b0_threshold (a float) – B-value threshold. Any b-values below this threshold are considered b0s. Documented as ‘B0Threshold’ in the BIDS metadata. (Nipype default value: 50)

  • big_delta (a float or None) – Large delta in seconds. Documented as ‘LargeDelta’ in the BIDS metadata. (Nipype default value: None)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’) – Sampling scheme to extrapolate the DWI data to. Documented as ‘ExtrapolateScheme’ in the BIDS metadata.

  • 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) – Small delta in seconds. Documented as ‘SmallDelta’ in the BIDS metadata. (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

Recon Spec Options

b0_threshold (a float)
B-value threshold. Any b-values below this threshold are considered b0s. Documented as 'B0Threshold' in the BIDS metadata.
Default50
big_delta (a float or None)
Large delta in seconds. Documented as 'LargeDelta' in the BIDS metadata.
DefaultNone
extrapolate_scheme ('HCP' or 'ABCD' or 'DSIQ5')
Sampling scheme to extrapolate the DWI data to. Documented as 'ExtrapolateScheme' in the BIDS metadata.
small_delta (a float or None)
Small delta in seconds. Documented as 'SmallDelta' in the BIDS metadata.
DefaultNone
write_fibgz (a boolean)
write_mif (a boolean)

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)

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

Optional Inputs:

  • b0_threshold (a float) – B-value threshold. Any b-values below this threshold are considered b0s. Documented as ‘B0Threshold’ in the BIDS metadata. (Nipype default value: 50)

  • big_delta (a float or None) – Large delta in seconds. Documented as ‘LargeDelta’ in the BIDS metadata. (Nipype default value: None)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’) – Sampling scheme to extrapolate the DWI data to. Documented as ‘ExtrapolateScheme’ in the BIDS metadata.

  • 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) – Small delta in seconds. Documented as ‘SmallDelta’ in the BIDS metadata. (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.KurtosisReconstructionMSDKI(from_file=None, resource_monitor=None, **inputs)[source]

Bases: DipyReconInterface

Recon Spec Options

b0_threshold (a float)
B-value threshold. Any b-values below this threshold are considered b0s. Documented as 'B0Threshold' in the BIDS metadata.
Default50
big_delta (a float or None)
Large delta in seconds. Documented as 'LargeDelta' in the BIDS metadata.
DefaultNone
extrapolate_scheme ('HCP' or 'ABCD' or 'DSIQ5')
Sampling scheme to extrapolate the DWI data to. Documented as 'ExtrapolateScheme' in the BIDS metadata.
small_delta (a float or None)
Small delta in seconds. Documented as 'SmallDelta' in the BIDS metadata.
DefaultNone
write_fibgz (a boolean)
write_mif (a boolean)

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)

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

Optional Inputs:

  • b0_threshold (a float) – B-value threshold. Any b-values below this threshold are considered b0s. Documented as ‘B0Threshold’ in the BIDS metadata. (Nipype default value: 50)

  • big_delta (a float or None) – Large delta in seconds. Documented as ‘LargeDelta’ in the BIDS metadata. (Nipype default value: None)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’) – Sampling scheme to extrapolate the DWI data to. Documented as ‘ExtrapolateScheme’ in the BIDS metadata.

  • 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) – Small delta in seconds. Documented as ‘SmallDelta’ in the BIDS metadata. (Nipype default value: None)

  • write_fibgz (a boolean)

  • write_mif (a boolean)

Outputs:

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

  • di (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)

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

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

  • msk (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.KurtosisReconstructionMicrostructure(from_file=None, resource_monitor=None, **inputs)[source]

Bases: DipyReconInterface

Recon Spec Options

b0_threshold (a float)
B-value threshold. Any b-values below this threshold are considered b0s. Documented as 'B0Threshold' in the BIDS metadata.
Default50
big_delta (a float or None)
Large delta in seconds. Documented as 'LargeDelta' in the BIDS metadata.
DefaultNone
extrapolate_scheme ('HCP' or 'ABCD' or 'DSIQ5')
Sampling scheme to extrapolate the DWI data to. Documented as 'ExtrapolateScheme' in the BIDS metadata.
small_delta (a float or None)
Small delta in seconds. Documented as 'SmallDelta' in the BIDS metadata.
DefaultNone
write_fibgz (a boolean)
write_mif (a boolean)

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)

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

Optional Inputs:

  • b0_threshold (a float) – B-value threshold. Any b-values below this threshold are considered b0s. Documented as ‘B0Threshold’ in the BIDS metadata. (Nipype default value: 50)

  • big_delta (a float or None) – Large delta in seconds. Documented as ‘LargeDelta’ in the BIDS metadata. (Nipype default value: None)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’) – Sampling scheme to extrapolate the DWI data to. Documented as ‘ExtrapolateScheme’ in the BIDS metadata.

  • 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) – Small delta in seconds. Documented as ‘SmallDelta’ in the BIDS metadata. (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

Apply MAPMRI reconstruction to the DWI data.

See also

dipy.reconst.mapmri.MapmriModel

Recon Spec Options

anisotropic_scaling (a boolean)
If True, uses the standard anisotropic MAP-MRI basis. If False, uses the isotropic MAP-MRI basis. Documented as 'AnisotropicScaling' in the BIDS metadata.
DefaultTrue
b0_threshold (a float)
B-value threshold. Any b-values below this threshold are considered b0s. Documented as 'B0Threshold' in the BIDS metadata.
Default50
big_delta (a float or None)
Large delta in seconds. Documented as 'LargeDelta' in the BIDS metadata.
DefaultNone
bval_threshold (a float)
Sets the b-value threshold to be used in the scale factor estimation. In order for the estimated non-Gaussianity to have meaning this value should set to a lower value (b<2000 s/mm^2) such that the scale factors are estimated on signal points that reasonably represent the spins at Gaussian diffusion. Documented as 'BValThreshold' in the BIDS metadata.
cvxpy_solver (a string or None)
Cvxpy solver name. Optionally optimize the positivity constraint with a particular cvxpy solver. See https://www.cvxpy.org/ for details. Documented as 'CVXPYSolver' in the BIDS metadata.
DefaultNone
dti_scale_estimation (a boolean)
Whether or not DTI fitting is used to estimate the isotropic scale factor for isotropic MAP-MRI. When set to False the algorithm presets the isotropic tissue diffusivity to static_diffusivity. This vastly increases fitting speed but at the cost of slightly reduced fitting quality. Can still be used in combination with regularization and constraints. Documented as 'DTIScaleEstimation' in the BIDS metadata.
DefaultTrue
eigenvalue_threshold (a float)
Sets the minimum of the tensor eigenvalues in order to avoid stability problems. Documented as 'EigenvalueThreshold' in the BIDS metadata.
Default0.0001
extrapolate_scheme ('HCP' or 'ABCD' or 'DSIQ5')
Sampling scheme to extrapolate the DWI data to. Documented as 'ExtrapolateScheme' in the BIDS metadata.
global_constraints (a boolean)
If set to False, positivity is enforced on a grid determined by pos_grid and pos_radius. If set to True, positivity is enforced everywhere using the constraints of Merlet2013. Documented as 'GlobalConstraints' in the BIDS metadata.
DefaultFalse
laplacian_regularization (a boolean)
Regularize using the Laplacian of the MAP-MRI basis. Documented as 'LaplacianRegularization' in the BIDS metadata.
DefaultTrue
laplacian_weighting (a list of items which are a float or a float or 'GCV')
The string 'GCV' makes it use generalized cross-validation to find the regularization weight. A scalar sets the regularization weight to that value and an array will make it selected the optimal weight from the values in the array. Documented as 'LaplacianWeighting' in the BIDS metadata.
DefaultGCV
pos_grid (an integer)
The number of points in the grid that is used in the local positivity constraint. Documented as 'PositivityGrid' in the BIDS metadata.
Default15
pos_radius (a float or 'adaptive' or 'infinity')
If set to a float, the maximum distance the local positivity constraint constrains to posivity is that value. If set to 'adaptive', the maximum distance is dependent on the estimated tissue diffusivity. If 'infinity', semidefinite programming constraints are used. Documented as 'PositivityRadius' in the BIDS metadata.
Defaultadaptive
positivity_constraint (a boolean)
Constrain the propagator to be positive. Documented as 'PositivityConstraint' in the BIDS metadata.
DefaultFalse
radial_order (an integer)
An even integer that represents the order of the basis. Documented as 'RadialOrder' in the BIDS metadata.
Default6
small_delta (a float or None)
Small delta in seconds. Documented as 'SmallDelta' in the BIDS metadata.
DefaultNone
static_diffusivity (a float)
The tissue diffusivity that is used when dti_scale_estimation is set to False. The default is that of typical white matter D=0.7e-3. Documented as 'StaticDiffusivity' in the BIDS metadata.
Default0.0007
write_fibgz (a boolean)
write_mif (a boolean)

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)

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

Optional Inputs:

  • anisotropic_scaling (a boolean) – If True, uses the standard anisotropic MAP-MRI basis. If False, uses the isotropic MAP-MRI basis. Documented as ‘AnisotropicScaling’ in the BIDS metadata. (Nipype default value: True)

  • b0_threshold (a float) – B-value threshold. Any b-values below this threshold are considered b0s. Documented as ‘B0Threshold’ in the BIDS metadata. (Nipype default value: 50)

  • big_delta (a float or None) – Large delta in seconds. Documented as ‘LargeDelta’ in the BIDS metadata. (Nipype default value: None)

  • bval_threshold (a float) – Sets the b-value threshold to be used in the scale factor estimation. In order for the estimated non-Gaussianity to have meaning this value should set to a lower value (b<2000 s/mm^2) such that the scale factors are estimated on signal points that reasonably represent the spins at Gaussian diffusion. Documented as ‘BValThreshold’ in the BIDS metadata.

  • cvxpy_solver (a string or None) – Cvxpy solver name. Optionally optimize the positivity constraint with a particular cvxpy solver. See https://www.cvxpy.org/ for details. Documented as ‘CVXPYSolver’ in the BIDS metadata. (Nipype default value: None)

  • dti_scale_estimation (a boolean) – Whether or not DTI fitting is used to estimate the isotropic scale factor for isotropic MAP-MRI. When set to False the algorithm presets the isotropic tissue diffusivity to static_diffusivity. This vastly increases fitting speed but at the cost of slightly reduced fitting quality. Can still be used in combination with regularization and constraints. Documented as ‘DTIScaleEstimation’ in the BIDS metadata. (Nipype default value: True)

  • eigenvalue_threshold (a float) – Sets the minimum of the tensor eigenvalues in order to avoid stability problems. Documented as ‘EigenvalueThreshold’ in the BIDS metadata. (Nipype default value: 0.0001)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’) – Sampling scheme to extrapolate the DWI data to. Documented as ‘ExtrapolateScheme’ in the BIDS metadata.

  • global_constraints (a boolean) – If set to False, positivity is enforced on a grid determined by pos_grid and pos_radius. If set to True, positivity is enforced everywhere using the constraints of Merlet2013. Documented as ‘GlobalConstraints’ in the BIDS metadata. (Nipype default value: False)

  • laplacian_regularization (a boolean) – Regularize using the Laplacian of the MAP-MRI basis. Documented as ‘LaplacianRegularization’ in the BIDS metadata. (Nipype default value: True)

  • laplacian_weighting (a list of items which are a float or a float or ‘GCV’) – The string ‘GCV’ makes it use generalized cross-validation to find the regularization weight. A scalar sets the regularization weight to that value and an array will make it selected the optimal weight from the values in the array. Documented as ‘LaplacianWeighting’ in the BIDS metadata. (Nipype default value: GCV)

  • 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) – The number of points in the grid that is used in the local positivity constraint. Documented as ‘PositivityGrid’ in the BIDS metadata. (Nipype default value: 15)

  • pos_radius (a float or ‘adaptive’ or ‘infinity’) – If set to a float, the maximum distance the local positivity constraint constrains to posivity is that value. If set to ‘adaptive’, the maximum distance is dependent on the estimated tissue diffusivity. If ‘infinity’, semidefinite programming constraints are used. Documented as ‘PositivityRadius’ in the BIDS metadata. (Nipype default value: adaptive)

  • positivity_constraint (a boolean) – Constrain the propagator to be positive. Documented as ‘PositivityConstraint’ in the BIDS metadata. (Nipype default value: False)

  • radial_order (an integer) – An even integer that represents the order of the basis. Documented as ‘RadialOrder’ in the BIDS metadata. (Nipype default value: 6)

  • small_delta (a float or None) – Small delta in seconds. Documented as ‘SmallDelta’ in the BIDS metadata. (Nipype default value: None)

  • static_diffusivity (a float) – The tissue diffusivity that is used when dti_scale_estimation is set to False. The default is that of typical white matter D=0.7e-3. Documented as ‘StaticDiffusivity’ in the BIDS metadata. (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) – Voxelwise norm of the Laplacian.

  • lapnorm_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the lapnorm file.

  • mapcoeffs (a pathlike object or string representing a file) – Voxelwise MAPMRI coefficients.

  • mapcoeffs_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the mapcoeffs file.

  • msd (a pathlike object or string representing a file) – Voxelwise MSD.

  • msd_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the msd file.

  • ng (a pathlike object or string representing a file) – Voxelwise Nematic Gradient.

  • ng_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the ng file.

  • ngpar (a pathlike object or string representing a file) – Voxelwise Parallel Nematic Gradient.

  • ngpar_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the ngpar file.

  • ngperp (a pathlike object or string representing a file) – Voxelwise Perpendicular Nematic Gradient.

  • ngperp_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the ngperp file.

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

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

  • qiv (a pathlike object or string representing a file) – Voxelwise q-space inverse variance.

  • qiv_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the qiv file.

  • rtap (a pathlike object or string representing a file) – Voxelwise Return-to-axis probability.

  • rtap_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the rtap file.

  • rtop (a pathlike object or string representing a file) – Voxelwise Return-to-origin probability.

  • rtop_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the rtop file.

  • rtpp (a pathlike object or string representing a file) – Voxelwise Return-to-plane probability.

  • rtpp_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the rtpp file.

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

Bases: DipyReconInterface

Recon Spec Options

b0_threshold (a float)
B-value threshold. Any b-values below this threshold are considered b0s. Documented as 'B0Threshold' in the BIDS metadata.
Default50
big_delta (a float or None)
Large delta in seconds. Documented as 'LargeDelta' in the BIDS metadata.
DefaultNone
extrapolate_scheme ('HCP' or 'ABCD' or 'DSIQ5')
Sampling scheme to extrapolate the DWI data to. Documented as 'ExtrapolateScheme' in the BIDS metadata.
small_delta (a float or None)
Small delta in seconds. Documented as 'SmallDelta' in the BIDS metadata.
DefaultNone
write_fibgz (a boolean)
write_mif (a boolean)

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)

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

Optional Inputs:

  • b0_threshold (a float) – B-value threshold. Any b-values below this threshold are considered b0s. Documented as ‘B0Threshold’ in the BIDS metadata. (Nipype default value: 50)

  • big_delta (a float or None) – Large delta in seconds. Documented as ‘LargeDelta’ in the BIDS metadata. (Nipype default value: None)

  • extrapolate_scheme (‘HCP’ or ‘ABCD’ or ‘DSIQ5’) – Sampling scheme to extrapolate the DWI data to. Documented as ‘ExtrapolateScheme’ in the BIDS metadata.

  • 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) – Small delta in seconds. Documented as ‘SmallDelta’ in the BIDS metadata. (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)