Index

_

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

__len__() (nifreeze.data.base.BaseDataset method)

A

add_b0() (in module nifreeze.testing.simulations) advanced_clip() (in module nifreeze.data.filtering) affine (nifreeze.data.base.BaseDataset attribute) (nifreeze.data.base.ImageGrid attribute) AFFINE_ABSENCE_ERROR_MSG (in module nifreeze.data.base) AFFINE_NDIM_ERROR_MSG (in module nifreeze.data.base) AFFINE_OBJECT_ERROR_MSG (in module nifreeze.data.base) AFFINE_SHAPE_ERROR_MSG (in module nifreeze.data.base) applicable_schemes (nifreeze.model.DKIModel attribute) (nifreeze.model.dmri.BaseDWIModel attribute) (nifreeze.model.dmri.DKIModel attribute) (nifreeze.model.dmri.DTIModel attribute) (nifreeze.model.dmri.GPModel attribute) (nifreeze.model.DTIModel attribute) (nifreeze.model.GPModel attribute)

apply_affines() (in module nifreeze.data.utils) ARRAY_ATTRIBUTE_NDIM_ERROR_MSG (in module nifreeze.data.pet.base) ARRAY_ATTRIBUTE_OBJECT_ERROR_MSG (in module nifreeze.data.pet.base) ATTRIBUTE_ABSENCE_ERROR_MSG (in module nifreeze.data.pet.base) ATTRIBUTE_VOLUME_DIMENSIONALITY_MISMATCH_ERROR_MSG (in module nifreeze.data.pet.base) AverageDWIModel (class in nifreeze.model) (class in nifreeze.model.dmri)

B

BASalientEntity (class in nifreeze.analysis.measure_agreement) BASalientEntityColor (class in nifreeze.viz.bland_altman) BaseDataset (class in nifreeze.data.base) BaseDWIModel (class in nifreeze.model.dmri) BaseModel (class in nifreeze.model.base) BasePETModel (class in nifreeze.model.pet) BOUNDS_2FIBERS_DOMINANT_VF1 (in module nifreeze.testing.simulations) BOUNDS_2FIBERS_NONDOMINANT_VF1 (in module nifreeze.testing.simulations) BOUNDS_3FIBERS_VF1 (in module nifreeze.testing.simulations) BOUNDS_3FIBERS_VF2 (in module nifreeze.testing.simulations) BOUNDS_LAMBDA1 (in module nifreeze.testing.simulations) BOUNDS_LAMBDA23 (in module nifreeze.testing.simulations) brainmask (nifreeze.data.base.BaseDataset attribute)

BRAINMASK_SHAPE_MISMATCH_ERROR_MSG (in module nifreeze.data.base) BSPLINE_CTRL_POINT_SUFFICIENCY_ERROR_MESSAGE (in module nifreeze.model.pet) BSPLINE_ORDER_SUFFICIENCY_ERROR_MESSAGE (in module nifreeze.model.pet) BSplinePETModel (class in nifreeze.model) (class in nifreeze.model.pet) BVAL_ATOL (in module nifreeze.data.filtering) bvals (nifreeze.data.dmri.base.DWI property) (nifreeze.data.dmri.DWI property) BVALS_KWARG (in module nifreeze.utils.iterators) bvecs (nifreeze.data.dmri.base.DWI property) (nifreeze.data.dmri.DWI property) bzero (nifreeze.data.dmri.base.DWI attribute) (nifreeze.data.dmri.DWI attribute) BZERO_SHAPE_MISMATCH_ERROR_MSG (in module nifreeze.data.dmri.base)

C

calculate_sphere_pts() (in module nifreeze.viz.signals) centralsym_iterator() (in module nifreeze.utils.iterators) CLIPPING_DEGENERATE_RANGE_ERROR_MSG (in module nifreeze.data.filtering) CLIPPING_EMPTY_SELECTION_ERROR_MSG (in module nifreeze.data.filtering) CLIPPING_INVALID_THRESHOLDS_ERROR_MSG (in module nifreeze.data.filtering) CLIPPING_NONFINITE_THRESHOLDS_ERROR_MSG (in module nifreeze.data.filtering) ClippingValueError compute_bland_altman_features() (in module nifreeze.analysis.measure_agreement) compute_dmri_convex_hull() (in module nifreeze.viz.signals) compute_fd_from_motion() (in module nifreeze.registration.utils) compute_fd_from_transform() (in module nifreeze.registration.utils) compute_pairwise_angles() (in module nifreeze.model.gpr) compute_percentage_change() (in module nifreeze.analysis.motion)

compute_pet_noise_sd() (in module nifreeze.testing.simulations) compute_temporal_markers() (in module nifreeze.data.pet.utils) compute_uptake_statistic() (in module nifreeze.data.pet.utils) compute_z_score() (in module nifreeze.analysis.measure_agreement) 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

datahdr (nifreeze.data.base.BaseDataset attribute) dataobj (nifreeze.data.base.BaseDataset attribute) DATAOBJ_ABSENCE_ERROR_MSG (in module nifreeze.data.base) DATAOBJ_NDIM_ERROR_MSG (in module nifreeze.data.base) DATAOBJ_OBJECT_ERROR_MSG (in module nifreeze.data.base) DEFAULT_BSPLINE_N_CTRL (in module nifreeze.model.pet) DEFAULT_BSPLINE_ORDER (in module nifreeze.model.pet) DEFAULT_CLIP_PERCENTILE (in module nifreeze.data.filtering) DEFAULT_DTYPE (in module nifreeze.data.filtering) DEFAULT_GRADIENT_ATOL (in module nifreeze.data.dmri.utils) DEFAULT_HIGHB_THRESHOLD (in module nifreeze.data.dmri.utils) DEFAULT_LOWB_THRESHOLD (in module nifreeze.data.dmri.utils) DEFAULT_MAX_S0 (in module nifreeze.data.dmri.utils) DEFAULT_MIN_S0 (in module nifreeze.data.dmri.utils) DEFAULT_MULTISHELL_BIN_COUNT_THR (in module nifreeze.data.dmri.utils) DEFAULT_NUM_BINS (in module nifreeze.data.dmri.utils) DEFAULT_ROUND_DECIMALS (in module nifreeze.utils.iterators) DEFAULT_S0_CLIP_PERCENTILE (in module nifreeze.model.dmri) DEFAULT_SPHERE_RECURSION_LEVEL (in module nifreeze.model.gqi) DEFAULT_TIMEPOINT_TOL (in module nifreeze.model.pet)

diag() (nifreeze.model.gpr.ExponentialKriging method) (nifreeze.model.gpr.MultiShellKernel method) (nifreeze.model.gpr.SphericalKriging method) DiffusionGPR (class in nifreeze.model.gpr) DiffusionKurtosisModel (class in nifreeze.model.dki) displacements_within_mask() (in module nifreeze.registration.utils) DKIModel (class in nifreeze.model) (class in nifreeze.model.dmri) DTI_MIN_ORIENTATIONS (in module nifreeze.data.dmri.utils) DTIModel (class in nifreeze.model) (class in nifreeze.model.dmri) DWI (class in nifreeze.data.dmri) (class in nifreeze.data.dmri.base) DWI_B0_MULTIPLE_VOLUMES_WARN_MSG (in module nifreeze.data.dmri.base) DWI_DKI_SHELL_ERROR_MSG (in module nifreeze.model.dmri) DWI_GTAB_ERROR_MSG (in module nifreeze.model.dmri) DWI_OBJECT_ERROR_MSG (in module nifreeze.model.dmri) DWI_REDUNDANT_B0_WARN_MSG (in module nifreeze.data.dmri.base) dwi_select_shells() (in module nifreeze.data.filtering) DWI_SIZE_ERROR_MSG (in module nifreeze.model.dmri)

E

eddy_xfms (nifreeze.data.dmri.base.DWI attribute) (nifreeze.data.dmri.DWI attribute) Estimator (class in nifreeze.estimator) excludes_b0 (nifreeze.model.dmri.BaseDWIModel attribute) (nifreeze.model.dmri.GQIModel attribute)

ExpectationModel (class in nifreeze.model) (class in nifreeze.model.base) exponential_covariance() (in module nifreeze.model.gpr) ExponentialKriging (class in nifreeze.model.gpr) extract_motion_parameters() (in module nifreeze.registration.utils)

F

Filter (class in nifreeze.estimator) find_shelling_scheme() (in module nifreeze.data.dmri.utils) fit() (nifreeze.model.dki.DiffusionKurtosisModel method) (nifreeze.model.gqi.GeneralizedQSamplingModel method) fit_predict() (nifreeze.model.AverageDWIModel method) (nifreeze.model.base.BaseModel method) (nifreeze.model.base.ExpectationModel method) (nifreeze.model.base.TrivialModel method) (nifreeze.model.BSplinePETModel method) (nifreeze.model.dmri.AverageDWIModel method) (nifreeze.model.dmri.BaseDWIModel method) (nifreeze.model.dmri.GPModel method) (nifreeze.model.ExpectationModel method) (nifreeze.model.GPModel method) (nifreeze.model.pet.BasePETModel method) (nifreeze.model.pet.BSplinePETModel method) (nifreeze.model.TrivialModel method)

format_array_like() (in module nifreeze.data.pet.base) format_gradients() (in module nifreeze.data.dmri.utils) format_scalar_like() (in module nifreeze.data.pet.base) FRAME_TIME_START_KEY (in module nifreeze.data.pet.io) FREE_WATER_DIFFUSIVITY_6D (in module nifreeze.model.gqi) from_filename() (nifreeze.data.base.BaseDataset class method) (nifreeze.data.dmri.base.DWI class method) (nifreeze.data.dmri.DWI class method) (nifreeze.data.pet.base.PET class method) (nifreeze.data.pet.PET class method) from_nii() (in module nifreeze.data.dmri) (in module nifreeze.data.dmri.io) (in module nifreeze.data.pet) (in module nifreeze.data.pet.io)

G

GeneralizedQSamplingFit (class in nifreeze.model.gqi) GeneralizedQSamplingModel (class in nifreeze.model.gqi) generate_command() (in module nifreeze.registration.ants) get_data() (in module nifreeze.utils.ndimage) get_filename() (nifreeze.data.base.BaseDataset method) get_params() (nifreeze.model.gpr.MultiShellKernel method) get_query_vectors() (in module nifreeze.testing.simulations) get_reliability_mask() (in module nifreeze.analysis.measure_agreement) get_shells() (nifreeze.data.dmri.base.DWI method) (nifreeze.data.dmri.DWI method) GPModel (class in nifreeze.model) (class in nifreeze.model.dmri)

gqi_kernel() (in module nifreeze.model.gqi) GQIModel (class in nifreeze.model.dmri) GRADIENT_ABSENCE_ERROR_MSG (in module nifreeze.data.dmri.utils) GRADIENT_BVAL_BVEC_PRIORITY_WARN_MSG (in module nifreeze.data.dmri.io) GRADIENT_DATA_MISSING_ERROR_MSG (in module nifreeze.data.dmri.io) GRADIENT_EXPECTED_COLUMNS_ERROR_MSG (in module nifreeze.data.dmri.utils) GRADIENT_NDIM_ERROR_MSG (in module nifreeze.data.dmri.utils) GRADIENT_OBJECT_ERROR_MSG (in module nifreeze.data.dmri.utils) GRADIENT_VOLUME_DIMENSIONALITY_MISMATCH_ERROR (in module nifreeze.data.dmri.utils) gradients (nifreeze.data.dmri.base.DWI attribute) (nifreeze.data.dmri.DWI attribute) grand_mean_normalization() (in module nifreeze.data.filtering) 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) hyperparameters (nifreeze.model.gpr.MultiShellKernel property)

I

identify_bland_altman_salient_data() (in module nifreeze.analysis.measure_agreement) identify_spikes() (in module nifreeze.analysis.motion) ImageGrid (class in nifreeze.data.base) init() (nifreeze.model.base.ModelFactory static method) (nifreeze.model.ModelFactory static method)

INVERSE_LAMBDA (in module nifreeze.model.gqi) is_fitted (nifreeze.model.pet.BasePETModel property) is_stationary() (nifreeze.model.gpr.ExponentialKriging method) (nifreeze.model.gpr.SphericalKriging method) ITERATOR_MULTIPLICITY_ERROR_MSG (in module nifreeze.utils.iterators) ITERATOR_SIZE_ERROR_MSG (in module nifreeze.utils.iterators)

K

k1 (nifreeze.model.gpr.MultiShellKernel attribute)

k2 (nifreeze.model.gpr.MultiShellKernel attribute)

L

LEFT_COLOR (nifreeze.viz.bland_altman.BASalientEntityColor attribute) LEFT_INDICES (nifreeze.analysis.measure_agreement.BASalientEntity attribute) LEFT_MASK (nifreeze.analysis.measure_agreement.BASalientEntity attribute)

linear_iterator() (in module nifreeze.utils.iterators) load() (in module nifreeze.data) load_api() (in module nifreeze.utils.ndimage) lovo_split() (in module nifreeze.data.splitting)

M

main() (in module nifreeze.cli.run) MASK_ABSENCE_WARN_MSG (in module nifreeze.model.base) midframe (nifreeze.data.pet.base.PET attribute) (nifreeze.data.pet.PET attribute) MIN_N_TIMEPOINTS (in module nifreeze.model.pet) MIN_TIMEPOINTS_ERROR_MSG (in module nifreeze.model.pet) MODALITY_SPECIFIC_SIZE_KEYS (in module nifreeze.utils.iterators) ModelFactory (class in nifreeze.model) (class in nifreeze.model.base) ModelNotFittedError module nifreeze.analysis nifreeze.analysis.filtering nifreeze.analysis.measure_agreement nifreeze.analysis.motion nifreeze.cli nifreeze.cli.parser nifreeze.cli.run nifreeze.data nifreeze.data.base nifreeze.data.dmri nifreeze.data.dmri.base nifreeze.data.dmri.io nifreeze.data.dmri.utils nifreeze.data.filtering nifreeze.data.pet nifreeze.data.pet.base nifreeze.data.pet.io nifreeze.data.pet.utils nifreeze.data.splitting nifreeze.data.utils nifreeze.estimator nifreeze.exceptions nifreeze.model nifreeze.model.base nifreeze.model.dki nifreeze.model.dmri nifreeze.model.gpr nifreeze.model.gqi nifreeze.model.pet nifreeze.registration nifreeze.registration.ants nifreeze.registration.utils nifreeze.testing nifreeze.testing.simulations nifreeze.utils nifreeze.utils.iterators nifreeze.utils.ndimage nifreeze.viz nifreeze.viz.bland_altman nifreeze.viz.motion_viz nifreeze.viz.signals

monotonic_value_iterator() (in module nifreeze.utils.iterators) motion_affines (nifreeze.data.base.BaseDataset attribute) MultiShellKernel (class in nifreeze.model.gpr)

N

nifreeze.analysis module nifreeze.analysis.filtering module nifreeze.analysis.measure_agreement module nifreeze.analysis.motion module nifreeze.cli module nifreeze.cli.parser module nifreeze.cli.run module nifreeze.data module nifreeze.data.base module nifreeze.data.dmri module nifreeze.data.dmri.base module nifreeze.data.dmri.io module nifreeze.data.dmri.utils module nifreeze.data.filtering module nifreeze.data.pet module nifreeze.data.pet.base module nifreeze.data.pet.io module nifreeze.data.pet.utils module nifreeze.data.splitting module nifreeze.data.utils module nifreeze.estimator module

nifreeze.exceptions module nifreeze.model module nifreeze.model.base module nifreeze.model.dki module nifreeze.model.dmri module nifreeze.model.gpr module nifreeze.model.gqi 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.utils.iterators module nifreeze.utils.ndimage module nifreeze.viz module nifreeze.viz.bland_altman module nifreeze.viz.motion_viz module nifreeze.viz.signals module normalize() (in module nifreeze.analysis.filtering)

O

odf() (nifreeze.model.gqi.GeneralizedQSamplingFit method)

optimizer (nifreeze.model.gpr.DiffusionGPR attribute)

P

parse_args() (in module nifreeze.cli.parser) PET (class in nifreeze.data.pet) (class in nifreeze.data.pet.base) PET_MIDFRAME_ERROR_MSG (in module nifreeze.model.pet) PET_OBJECT_ERROR_MSG (in module nifreeze.model.pet) plot_bland_altman() (in module nifreeze.viz.bland_altman) plot_correlation() (in module nifreeze.viz.signals) plot_error() (in module nifreeze.viz.signals) plot_estimation_carpet() (in module nifreeze.viz.signals)

plot_framewise_displacement() (in module nifreeze.viz.motion_viz) plot_motion_overlay() (in module nifreeze.viz.motion_viz) plot_prediction_surface() (in module nifreeze.viz.signals) plot_signal_data() (in module nifreeze.viz.signals) plot_surface() (in module nifreeze.viz.signals) plot_volumewise_motion() (in module nifreeze.viz.motion_viz) predict() (nifreeze.model.gqi.GeneralizedQSamplingFit method) PREDICTED_MAP_ERROR_MSG (in module nifreeze.model.base) prediction_kernel() (in module nifreeze.model.gqi)

R

RADIUS (in module nifreeze.registration.utils) random_iterator() (in module nifreeze.utils.iterators) REGISTRATION_MALFORMED_SETTINGS_ERROR_MSG (in module nifreeze.registration.ants) RELIABILITY_INDICES (nifreeze.analysis.measure_agreement.BASalientEntity attribute) RELIABILITY_MASK (nifreeze.analysis.measure_agreement.BASalientEntity attribute) RELIABLE_COLOR (nifreeze.viz.bland_altman.BASalientEntityColor attribute) requires_multishell (nifreeze.model.DKIModel attribute) (nifreeze.model.dmri.BaseDWIModel attribute) (nifreeze.model.dmri.DKIModel attribute)

RIGHT_COLOR (nifreeze.viz.bland_altman.BASalientEntityColor attribute) RIGHT_INDICES (nifreeze.analysis.measure_agreement.BASalientEntity attribute) RIGHT_MASK (nifreeze.analysis.measure_agreement.BASalientEntity attribute) robust_minmax_normalization() (in module nifreeze.data.filtering) run() (nifreeze.estimator.Estimator method) (nifreeze.estimator.Filter method)

S

SCALAR_ATTRIBUTE_ERROR_MSG (in module nifreeze.data.pet.base) 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.base.BaseDataset method) (nifreeze.data.pet.base.PET method) (nifreeze.data.pet.PET method) shape (nifreeze.data.base.ImageGrid attribute) shape3d (nifreeze.data.base.BaseDataset property) 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) SINGLE_FIT_CANARY_MSG (in module nifreeze.model.base)

single_fit_is_canary (nifreeze.model.base.BaseModel attribute) (nifreeze.model.dmri.GPModel attribute) (nifreeze.model.dmri.GQIModel attribute) (nifreeze.model.GPModel attribute) SingleFitCanaryWarning size3d (nifreeze.data.base.BaseDataset property) SIZE_KEYS (in module nifreeze.utils.iterators) SIZE_KWARG (in module nifreeze.utils.iterators) spherical_covariance() (in module nifreeze.model.gpr) SphericalKriging (class in nifreeze.model.gpr) srtm() (in module nifreeze.testing.simulations) START_INDEX_DATA_LENGTH_ERROR_MSG (in module nifreeze.utils.iterators) START_INDEX_KWARG (in module nifreeze.utils.iterators) START_INDEX_POSITIVITY_ERROR_MSG (in module nifreeze.utils.iterators) STOP_INDEX_DATA_LENGTH_ERROR_MSG (in module nifreeze.utils.iterators) STOP_INDEX_KWARG (in module nifreeze.utils.iterators) STOP_INDEX_ORDERING_ERROR_MSG (in module nifreeze.utils.iterators)

T

TEMPORAL_ATTRIBUTE_INCONSISTENCY_ERROR_MSG (in module nifreeze.data.pet.base) TEMPORAL_FILE_KEY_ERROR_MSG (in module nifreeze.data.pet.io) to_filename() (nifreeze.data.base.BaseDataset method) (nifreeze.data.dmri.base.DWI method) (nifreeze.data.dmri.DWI method) (nifreeze.data.pet.base.PET method) (nifreeze.data.pet.PET method) to_nifti() (in module nifreeze.data.base) (in module nifreeze.data.dmri.io) (nifreeze.data.base.BaseDataset method) (nifreeze.data.dmri.base.DWI method) (nifreeze.data.dmri.DWI method)

total_duration (nifreeze.data.pet.base.PET attribute) (nifreeze.data.pet.PET attribute) transform_fsl_bvec() (in module nifreeze.data.dmri.utils) TrivialModel (class in nifreeze.model) (class in nifreeze.model.base)

U

UNSUPPORTED_MODEL_ERROR_MSG (in module nifreeze.model.base)

UPTAKE_KWARG (in module nifreeze.utils.iterators)

V

validate_1d_array() (in module nifreeze.data.pet.base) validate_affine() (in module nifreeze.data.base)

validate_dataobj() (in module nifreeze.data.base) validate_gradients() (in module nifreeze.data.dmri.base)