Index

A

add_b0() (in module eddymotion.testing.simulations) advanced_clip() (in module eddymotion.data.filtering) affine (eddymotion.data.dmri.DWI attribute) (eddymotion.data.pet.PET attribute)

apply_affines() (in module eddymotion.data.utils) AverageDWModel (class in eddymotion.model) (class in eddymotion.model.dmri) AverageModel (class in eddymotion.model) (class in eddymotion.model.base)

B

BaseDWIModel (class in eddymotion.model.dmri) BaseModel (class in eddymotion.model.base) BOUNDS_A (in module eddymotion.model.gpr) BOUNDS_LAMBDA (in module eddymotion.model.gpr)

brainmask (eddymotion.data.dmri.DWI attribute) (eddymotion.data.pet.PET attribute) bvalue_iterator() (in module eddymotion.utils) bzero (eddymotion.data.dmri.DWI attribute)

C

calculate_sphere_pts() (in module eddymotion.viz.signals) centralsym_iterator() (in module eddymotion.utils) compute_angle() (in module eddymotion.math.utils) compute_dmri_convex_hull() (in module eddymotion.viz.signals) compute_pairwise_angles() (in module eddymotion.model.gpr) CONFIGURABLE_OPTIONS (in module eddymotion.model.gpr) create_diffusion_encoding_gradient_dirs() (in module eddymotion.testing.simulations)

create_random_diffusivity_eigenvalues() (in module eddymotion.testing.simulations) create_random_polar_angles() (in module eddymotion.testing.simulations) create_random_polar_coordinates() (in module eddymotion.testing.simulations) create_single_fiber_evecs() (in module eddymotion.testing.simulations) create_single_shell_gradient_table() (in module eddymotion.testing.simulations) create_three_fiber_random_volume_fractions() (in module eddymotion.testing.simulations) create_two_fiber_dominant_random_volume_fractions() (in module eddymotion.testing.simulations) create_two_fiber_nondominant_random_volume_fractions() (in module eddymotion.testing.simulations)

D

dataobj (eddymotion.data.dmri.DWI attribute) (eddymotion.data.pet.PET attribute) DEFAULT_CLIP_PERCENTILE (in module eddymotion.model.dmri) DEFAULT_DTYPE (in module eddymotion.data.filtering) DEFAULT_HIGHB_THRESHOLD (in module eddymotion.model.dmri) DEFAULT_LOWB_THRESHOLD (in module eddymotion.model.dmri) DEFAULT_MAX_BVAL (in module eddymotion.model.dmri) DEFAULT_MAX_BVALUE (in module eddymotion.model.dmri) DEFAULT_MAX_S0 (in module eddymotion.model.dmri) DEFAULT_MIN_S0 (in module eddymotion.model.dmri) DEFAULT_MULTISHELL_BIN_COUNT_THR (in module eddymotion.model.dmri)

DEFAULT_NUM_BINS (in module eddymotion.model.dmri) DEFAULT_TIMEFRAME_MIDPOINT_TOL (in module eddymotion.model.pet) diag() (eddymotion.model.gpr.ExponentialKriging method) (eddymotion.model.gpr.SphericalKriging method) displacement_framewise() (in module eddymotion.registration.utils) displacements_within_mask() (in module eddymotion.registration.utils) DKIModel (class in eddymotion.model) (class in eddymotion.model.dmri) DTIModel (class in eddymotion.model) (class in eddymotion.model.dmri) DWI (class in eddymotion.data.dmri)

E

eddymotion.cli module eddymotion.cli.parser module eddymotion.cli.run module eddymotion.data module eddymotion.data.dmri module eddymotion.data.filtering module eddymotion.data.pet module eddymotion.data.splitting module eddymotion.data.utils module eddymotion.estimator module eddymotion.exceptions module eddymotion.math module eddymotion.math.utils module eddymotion.model module eddymotion.model.base module

eddymotion.model.dmri module eddymotion.model.gpr module eddymotion.model.pet module eddymotion.registration module eddymotion.registration.ants module eddymotion.registration.utils module eddymotion.testing module eddymotion.testing.simulations module eddymotion.utils module eddymotion.viz module eddymotion.viz.signals module EddyMotionEstimator (class in eddymotion.estimator) EddyMotionGPR (class in eddymotion.model.gpr) em_affines (eddymotion.data.dmri.DWI attribute) (eddymotion.data.pet.PET attribute) estimate() (eddymotion.estimator.EddyMotionEstimator static method) exponential_covariance() (in module eddymotion.model.gpr) ExponentialKriging (class in eddymotion.model.gpr)

F

fieldmap (eddymotion.data.dmri.DWI attribute) find_shelling_scheme() (in module eddymotion.model.dmri) fit() (eddymotion.model.AverageDWModel method) (eddymotion.model.AverageModel method) (eddymotion.model.base.AverageModel method) (eddymotion.model.base.BaseModel method) (eddymotion.model.base.TrivialModel method) (eddymotion.model.dmri.AverageDWModel method) (eddymotion.model.dmri.BaseDWIModel method) (eddymotion.model.pet.PETModel method) (eddymotion.model.PETModel method) (eddymotion.model.TrivialModel method)

frame_time (eddymotion.data.pet.PET attribute) from_filename() (eddymotion.data.dmri.DWI class method) (eddymotion.data.pet.PET class method)

G

generate_command() (in module eddymotion.registration.ants) get_filename() (eddymotion.data.dmri.DWI method) get_query_vectors() (in module eddymotion.testing.simulations)

GPModel (class in eddymotion.model) (class in eddymotion.model.dmri) gradients (eddymotion.data.dmri.DWI attribute) group_values() (in module eddymotion.testing.simulations)

H

hyperparameter_a (eddymotion.model.gpr.ExponentialKriging property) (eddymotion.model.gpr.SphericalKriging property)

hyperparameter_beta_l (eddymotion.model.gpr.ExponentialKriging property) (eddymotion.model.gpr.SphericalKriging property)

I

init() (eddymotion.model.base.ModelFactory static method) (eddymotion.model.ModelFactory static method) is_fitted (eddymotion.model.AverageModel property) (eddymotion.model.base.AverageModel property) (eddymotion.model.base.BaseModel property) (eddymotion.model.base.TrivialModel property) (eddymotion.model.pet.PETModel property) (eddymotion.model.PETModel property) (eddymotion.model.TrivialModel property)

is_positive_definite() (in module eddymotion.math.utils) is_stationary() (eddymotion.model.gpr.ExponentialKriging method) (eddymotion.model.gpr.SphericalKriging method)

L

LBFGS_CONFIGURABLE_OPTIONS (in module eddymotion.model.gpr) linear_iterator() (in module eddymotion.utils)

load() (in module eddymotion.data.dmri) (in module eddymotion.data.pet) lovo_split() (in module eddymotion.data.splitting)

M

main() (in module eddymotion.cli.run) ModelFactory (class in eddymotion.model) (class in eddymotion.model.base) ModelNotFittedError module eddymotion.cli eddymotion.cli.parser eddymotion.cli.run eddymotion.data eddymotion.data.dmri eddymotion.data.filtering eddymotion.data.pet eddymotion.data.splitting eddymotion.data.utils eddymotion.estimator eddymotion.exceptions eddymotion.math eddymotion.math.utils eddymotion.model eddymotion.model.base eddymotion.model.dmri eddymotion.model.gpr eddymotion.model.pet eddymotion.registration eddymotion.registration.ants eddymotion.registration.utils eddymotion.testing eddymotion.testing.simulations eddymotion.utils eddymotion.viz eddymotion.viz.signals

N

NONGRADIENT_METHODS (in module eddymotion.model.gpr)

P

parse_args() (in module eddymotion.cli.parser) PET (class in eddymotion.data.pet) PETModel (class in eddymotion.model) (class in eddymotion.model.pet) plot_correlation() (in module eddymotion.viz.signals) plot_error() (in module eddymotion.viz.signals) plot_estimation_carpet() (in module eddymotion.viz.signals) plot_gradients() (eddymotion.data.dmri.DWI method) plot_mosaic() (eddymotion.data.dmri.DWI method) plot_prediction_surface() (in module eddymotion.viz.signals) plot_signal_data() (in module eddymotion.viz.signals)

plot_surface() (in module eddymotion.viz.signals) predict() (eddymotion.model.AverageDWModel method) (eddymotion.model.AverageModel method) (eddymotion.model.base.AverageModel method) (eddymotion.model.base.BaseModel method) (eddymotion.model.base.TrivialModel method) (eddymotion.model.dmri.AverageDWModel method) (eddymotion.model.dmri.BaseDWIModel method) (eddymotion.model.pet.PETModel method) (eddymotion.model.PETModel method) (eddymotion.model.TrivialModel method)

R

random_iterator() (in module eddymotion.utils)

S

serialize_dmri() (in module eddymotion.testing.simulations) serialize_dwi() (in module eddymotion.testing.simulations) serialize_gtab() (in module eddymotion.testing.simulations) set_transform() (eddymotion.data.dmri.DWI method) (eddymotion.data.pet.PET method) simulate_multifiber_voxels() (in module eddymotion.testing.simulations) simulate_one_fiber_multivoxel() (in module eddymotion.testing.simulations)

simulate_three_fiber_multivoxel() (in module eddymotion.testing.simulations) simulate_two_fiber_multivoxel() (in module eddymotion.testing.simulations) simulate_voxels() (in module eddymotion.testing.simulations) single_fiber_voxel() (in module eddymotion.testing.simulations) spherical_covariance() (in module eddymotion.model.gpr) SphericalKriging (class in eddymotion.model.gpr) SUPPORTED_OPTIMIZERS (in module eddymotion.model.gpr)

T

THETA_EPSILON (in module eddymotion.model.gpr) to_filename() (eddymotion.data.dmri.DWI method) (eddymotion.data.pet.PET method) to_nifti() (eddymotion.data.dmri.DWI method) (eddymotion.data.pet.PET method)

total_duration (eddymotion.data.pet.PET attribute) TrivialModel (class in eddymotion.model) (class in eddymotion.model.base)