Index

_

__call__() (nifreeze.model.gpr.ExponentialKriging method) (nifreeze.model.gpr.SphericalKriging method)

__len__() (nifreeze.data.dmri.DWI method) (nifreeze.data.pet.PET method)

A

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

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

B

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

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

C

calculate_sphere_pts() (in module nifreeze.viz.signals) centralsym_iterator() (in module nifreeze.utils) compute_dmri_convex_hull() (in module nifreeze.viz.signals) compute_pairwise_angles() (in module nifreeze.model.gpr) CONFIGURABLE_OPTIONS (in module nifreeze.model.gpr) create_diffusion_encoding_gradient_dirs() (in module nifreeze.testing.simulations) create_random_diffusivity_eigenvalues() (in module nifreeze.testing.simulations)

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

D

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

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

E

em_affines (nifreeze.data.dmri.DWI attribute) (nifreeze.data.pet.PET attribute) estimate() (nifreeze.estimator.Estimator static method)

Estimator (class in nifreeze.estimator) exponential_covariance() (in module nifreeze.model.gpr) ExponentialKriging (class in nifreeze.model.gpr)

F

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

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

G

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

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

H

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

hyperparameter_l (nifreeze.model.gpr.ExponentialKriging property) (nifreeze.model.gpr.SphericalKriging property)

I

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

is_stationary() (nifreeze.model.gpr.ExponentialKriging method) (nifreeze.model.gpr.SphericalKriging method)

L

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

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

M

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

N

nifreeze.cli module nifreeze.cli.parser module nifreeze.cli.run module nifreeze.data module nifreeze.data.dmri module nifreeze.data.filtering module nifreeze.data.pet module nifreeze.data.splitting module nifreeze.data.utils module nifreeze.estimator module nifreeze.exceptions module nifreeze.model module

nifreeze.model.base module nifreeze.model.dmri module nifreeze.model.gpr module nifreeze.model.pet module nifreeze.registration module nifreeze.registration.ants module nifreeze.registration.utils module nifreeze.testing module nifreeze.testing.simulations module nifreeze.utils module nifreeze.viz module nifreeze.viz.signals module NONGRADIENT_METHODS (in module nifreeze.model.gpr)

P

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

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

R

random_iterator() (in module nifreeze.utils)

S

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

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

T

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

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