Index

_

__call__() (nifreeze.model.gpr.ExponentialKriging 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) 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_A (in module nifreeze.model.gpr) BOUNDS_LAMBDA (in module nifreeze.model.gpr) brainmask (nifreeze.data.base.BaseDataset attribute) BRAINMASK_SHAPE_MISMATCH_ERROR_MSG (in module nifreeze.data.base)

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) 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_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) 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

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_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_TIMEPOINT_TOL (in module nifreeze.model.pet)

diag() (nifreeze.model.gpr.ExponentialKriging method) (nifreeze.model.gpr.SphericalKriging method) DiffusionGPR (class in nifreeze.model.gpr) 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_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) equatorial_maximum() (in module nifreeze.model.gqi) equatorial_zone_vertices() (in module nifreeze.model.gqi) Estimator (class in nifreeze.estimator)

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.gqi.GeneralizedQSamplingFit 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.ExpectationModel 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) 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_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)

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)

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

K

KWARG_ERROR_MSG (in module nifreeze.utils.iterators)

L

LBFGS_CONFIGURABLE_OPTIONS (in module nifreeze.model.gpr) 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) lofo_split() (nifreeze.data.pet.base.PET method) (nifreeze.data.pet.PET method) 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) 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.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)

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.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 NONGRADIENT_METHODS (in module nifreeze.model.gpr) normalize() (in module nifreeze.analysis.filtering) normalize_qa() (in module nifreeze.model.gqi) npa() (in module nifreeze.model.gqi)

O

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

odf_sum() (in module nifreeze.model.gqi) optimizer (nifreeze.model.gpr.DiffusionGPR attribute)

P

parse_args() (in module nifreeze.cli.parser) patch_maximum() (in module nifreeze.model.gqi) patch_sum() (in module nifreeze.model.gqi) patch_vertices() (in module nifreeze.model.gqi) 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) PETMotionEstimator (class in nifreeze.estimator) 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) polar_zone_vertices() (in module nifreeze.model.gqi) predict() (nifreeze.model.gqi.GeneralizedQSamplingFit method) (nifreeze.model.gqi.GeneralizedQSamplingModel 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)

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) (nifreeze.estimator.PETMotionEstimator 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) size3d (nifreeze.data.base.BaseDataset property) SIZE_KEYS (in module nifreeze.utils.iterators) spherical_covariance() (in module nifreeze.model.gpr) SphericalKriging (class in nifreeze.model.gpr) squared_radial_component() (in module nifreeze.model.gqi) START_INDEX_RANGE_ERROR_MSG (in module nifreeze.model.pet) SUPPORTED_OPTIMIZERS (in module nifreeze.model.gpr)

T

TEMPORAL_ATTRIBUTE_INCONSISTENCY_ERROR_MSG (in module nifreeze.data.pet.base) TEMPORAL_FILE_KEY_ERROR_MSG (in module nifreeze.data.pet.io) THETA_EPSILON (in module nifreeze.model.gpr) 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) triple_odf_maxima() (in module nifreeze.model.gqi) TrivialModel (class in nifreeze.model) (class in nifreeze.model.base)

U

UNKNOWN_OPTIMIZER_ERROR_MSG (in module nifreeze.model.gpr) UNSUPPORTED_MODEL_ERROR_MSG (in module nifreeze.model.base)

upper_hemi_map() (in module nifreeze.model.gqi) 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)