Index

A

add_subjects() (brainiak.funcalign.fastsrm.FastSRM method)

apply_signal() (in module brainiak.utils.fmrisim) array_correlation() (in module brainiak.utils.utils)

B

Ball (class in brainiak.searchlight.searchlight) beta0_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) beta0_null_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) beta_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) bGP_ (brainiak.reprsimil.brsa.BRSA attribute) bias_ (brainiak.funcalign.sssrm.SSSRM attribute) bootstrap_isc() (in module brainiak.isc) brainiak module brainiak.eventseg module brainiak.eventseg.event module brainiak.factoranalysis module brainiak.factoranalysis.htfa module brainiak.factoranalysis.tfa module brainiak.factoranalysis.tfa_extension module brainiak.fcma module brainiak.fcma.classifier module brainiak.fcma.fcma_extension module brainiak.fcma.mvpa_voxelselector module brainiak.fcma.preprocessing module brainiak.fcma.util module brainiak.fcma.voxelselector module brainiak.funcalign module brainiak.funcalign.fastsrm module brainiak.funcalign.rsrm module brainiak.funcalign.srm module brainiak.funcalign.sssrm module

brainiak.hyperparamopt module brainiak.hyperparamopt.hpo module brainiak.image module brainiak.io module brainiak.isc module brainiak.matnormal module brainiak.matnormal.covs module brainiak.matnormal.matnormal_likelihoods module brainiak.matnormal.mnrsa module brainiak.matnormal.regression module brainiak.matnormal.utils module brainiak.reconstruct module brainiak.reconstruct.iem module brainiak.reprsimil module brainiak.reprsimil.brsa module brainiak.searchlight module brainiak.searchlight.searchlight module brainiak.utils module brainiak.utils.fmrisim module brainiak.utils.fmrisim_real_time_generator module brainiak.utils.kronecker_solvers module brainiak.utils.utils module broadcast() (brainiak.searchlight.searchlight.Searchlight method) BRSA (class in brainiak.reprsimil.brsa)

C

C_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) calc_noise() (in module brainiak.utils.fmrisim) calc_weighted_event_var() (brainiak.eventseg.event.EventSegment method) calibrate() (brainiak.matnormal.regression.MatnormalRegression method) center_mass_exp() (in module brainiak.utils.utils) channels (brainiak.reconstruct.iem.InvertedEncoding2D attribute) channels_ (brainiak.reconstruct.iem.InvertedEncoding1D attribute) circ_dist() (in module brainiak.utils.utils) classes_ (brainiak.funcalign.sssrm.SSSRM attribute) Classifier (class in brainiak.fcma.classifier) clean() (brainiak.funcalign.fastsrm.FastSRM method) column_types (brainiak.utils.utils.ReadDesign attribute) comm (brainiak.funcalign.srm.SRM attribute) compute_correlation() (in module brainiak.fcma.util) compute_signal_change() (in module brainiak.utils.fmrisim)

compute_summary_statistic() (in module brainiak.isc) concatenate_not_none() (in module brainiak.utils.utils) ConditionSpec (class in brainiak.image) convolve_hrf() (in module brainiak.utils.fmrisim) cov2corr() (in module brainiak.utils.utils) CovAR1 (class in brainiak.matnormal.covs) CovBase (class in brainiak.matnormal.covs) CovDiagonal (class in brainiak.matnormal.covs) CovDiagonalGammaPrior (class in brainiak.matnormal.covs) CovIdentity (class in brainiak.matnormal.covs) CovIsotropic (class in brainiak.matnormal.covs) CovKroneckerFactored (class in brainiak.matnormal.covs) CovUnconstrainedCholesky (class in brainiak.matnormal.covs) CovUnconstrainedCholeskyWishartReg (class in brainiak.matnormal.covs) CovUnconstrainedInvCholesky (class in brainiak.matnormal.covs) Cube (class in brainiak.searchlight.searchlight)

D

decision_function() (brainiak.fcma.classifier.Classifier method) define_basis_functions_sqgrid() (brainiak.reconstruct.iem.InvertedEncoding2D method) define_basis_functions_trigrid() (brainiak.reconstruct.iem.InvertedEncoding2D method) design (brainiak.utils.utils.ReadDesign attribute)

design_task (brainiak.utils.utils.ReadDesign attribute) DetSRM (class in brainiak.funcalign.srm) Diamond (class in brainiak.searchlight.searchlight) distribute() (brainiak.searchlight.searchlight.Searchlight method)

E

event_pat_ (brainiak.eventseg.event.EventSegment attribute) event_var_ (brainiak.eventseg.event.EventSegment attribute) EventSegment (class in brainiak.eventseg.event)

export_3_column() (in module brainiak.utils.fmrisim) export_epoch_file() (in module brainiak.utils.fmrisim) extract_labels() (brainiak.image.SingleConditionSpec method)

F

F_ (brainiak.factoranalysis.tfa.TFA attribute) factor() (in module brainiak.factoranalysis.tfa_extension) FastSRM (class in brainiak.funcalign.fastsrm) find_events() (brainiak.eventseg.event.EventSegment method) fit() (brainiak.eventseg.event.EventSegment method) (brainiak.factoranalysis.htfa.HTFA method) (brainiak.factoranalysis.tfa.TFA method) (brainiak.fcma.classifier.Classifier method) (brainiak.funcalign.fastsrm.FastSRM method) (brainiak.funcalign.rsrm.RSRM method) (brainiak.funcalign.srm.DetSRM method) (brainiak.funcalign.srm.SRM method) (brainiak.funcalign.sssrm.SSSRM method) (brainiak.matnormal.mnrsa.MNRSA method) (brainiak.matnormal.regression.MatnormalRegression method) (brainiak.reconstruct.iem.InvertedEncoding1D method) (brainiak.reconstruct.iem.InvertedEncoding2D method) (brainiak.reprsimil.brsa.BRSA method) (brainiak.reprsimil.brsa.GBRSA method)

fit_transform() (brainiak.funcalign.fastsrm.FastSRM method) flatten_cholesky_unique() (in module brainiak.matnormal.utils) fmin() (in module brainiak.hyperparamopt.hpo) from_masked_images() (brainiak.image.MaskedMultiSubjectData class method) from_sym_2_tri() (in module brainiak.utils.utils) from_tri_2_sym() (in module brainiak.utils.utils)

G

GBRSA (class in brainiak.reprsimil.brsa) gen_design() (in module brainiak.utils.utils) generate_1d_gaussian_rfs() (in module brainiak.utils.fmrisim) generate_1d_rf_responses() (in module brainiak.utils.fmrisim) generate_data() (in module brainiak.utils.fmrisim_real_time_generator) generate_epochs_info() (in module brainiak.fcma.preprocessing) generate_noise() (in module brainiak.utils.fmrisim) generate_signal() (in module brainiak.utils.fmrisim) generate_stimfunction() (in module brainiak.utils.fmrisim) get_bounds() (brainiak.factoranalysis.tfa.TFA method) get_centers() (brainiak.factoranalysis.tfa.TFA method) get_centers_mean_cov() (brainiak.factoranalysis.tfa.TFA method) get_factors() (brainiak.factoranalysis.tfa.TFA method) get_map_offset() (brainiak.factoranalysis.tfa.TFA method) get_optimize_vars() (brainiak.matnormal.covs.CovAR1 method) (brainiak.matnormal.covs.CovBase method) (brainiak.matnormal.covs.CovDiagonal method) (brainiak.matnormal.covs.CovIdentity method) (brainiak.matnormal.covs.CovIsotropic method) (brainiak.matnormal.covs.CovKroneckerFactored method) (brainiak.matnormal.covs.CovUnconstrainedCholesky method) (brainiak.matnormal.covs.CovUnconstrainedInvCholesky method)

get_params() (brainiak.reconstruct.iem.InvertedEncoding1D method) (brainiak.reconstruct.iem.InvertedEncoding2D method) get_template() (brainiak.factoranalysis.tfa.TFA method) get_unique_R() (brainiak.factoranalysis.tfa.TFA method) get_weights() (brainiak.factoranalysis.tfa.TFA method) get_widths() (brainiak.factoranalysis.tfa.TFA method) get_widths_mean_var() (brainiak.factoranalysis.tfa.TFA method) global_posterior_ (brainiak.factoranalysis.htfa.HTFA attribute) global_prior_ (brainiak.factoranalysis.htfa.HTFA attribute)

H

HTFA (class in brainiak.factoranalysis.htfa)

I

init_centers_widths() (brainiak.factoranalysis.tfa.TFA method) init_prior() (brainiak.factoranalysis.tfa.TFA method) inverse_transform() (brainiak.funcalign.fastsrm.FastSRM method)

InvertedEncoding1D (class in brainiak.reconstruct.iem) InvertedEncoding2D (class in brainiak.reconstruct.iem) isc() (in module brainiak.isc) isfc() (in module brainiak.isc)

L

L() (brainiak.matnormal.covs.CovKroneckerFactored property) (brainiak.matnormal.covs.CovUnconstrainedCholesky property) (brainiak.matnormal.mnrsa.MNRSA property) L_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) lGPinten_ (brainiak.reprsimil.brsa.BRSA attribute) lGPspace_ (brainiak.reprsimil.brsa.BRSA attribute) Linv() (brainiak.matnormal.covs.CovUnconstrainedInvCholesky property) ll_ (brainiak.eventseg.event.EventSegment attribute) load_boolean_mask() (in module brainiak.io) load_images() (in module brainiak.io) load_images_from_dir() (in module brainiak.io) load_labels() (in module brainiak.io)

local_posterior_ (brainiak.factoranalysis.htfa.HTFA attribute) (brainiak.factoranalysis.tfa.TFA attribute) local_weights_ (brainiak.factoranalysis.htfa.HTFA attribute) logdet() (brainiak.matnormal.covs.CovAR1 property) (brainiak.matnormal.covs.CovBase property) (brainiak.matnormal.covs.CovDiagonal property) (brainiak.matnormal.covs.CovIdentity property) (brainiak.matnormal.covs.CovIsotropic property) (brainiak.matnormal.covs.CovKroneckerFactored property) (brainiak.matnormal.covs.CovUnconstrainedCholesky property) (brainiak.matnormal.covs.CovUnconstrainedInvCholesky property) logp() (brainiak.matnormal.mnrsa.MNRSA method) (brainiak.matnormal.regression.MatnormalRegression method)

M

make_val_and_grad() (in module brainiak.matnormal.utils) mask_ (brainiak.searchlight.searchlight.Shape attribute) mask_brain() (in module brainiak.utils.fmrisim) mask_image() (in module brainiak.image) mask_images() (in module brainiak.image) MaskedMultiSubjectData (class in brainiak.image) matnorm_logp() (in module brainiak.matnormal.matnormal_likelihoods) matnorm_logp_conditional_col() (in module brainiak.matnormal.matnormal_likelihoods) matnorm_logp_conditional_row() (in module brainiak.matnormal.matnormal_likelihoods) matnorm_logp_marginal_col() (in module brainiak.matnormal.matnormal_likelihoods) matnorm_logp_marginal_row() (in module brainiak.matnormal.matnormal_likelihoods) MatnormalRegression (class in brainiak.matnormal.regression) MNRSA (class in brainiak.matnormal.mnrsa) model_prior() (brainiak.eventseg.event.EventSegment method) module brainiak brainiak.eventseg brainiak.eventseg.event brainiak.factoranalysis brainiak.factoranalysis.htfa brainiak.factoranalysis.tfa brainiak.factoranalysis.tfa_extension brainiak.fcma brainiak.fcma.classifier brainiak.fcma.fcma_extension brainiak.fcma.mvpa_voxelselector brainiak.fcma.preprocessing brainiak.fcma.util brainiak.fcma.voxelselector brainiak.funcalign brainiak.funcalign.fastsrm brainiak.funcalign.rsrm brainiak.funcalign.srm brainiak.funcalign.sssrm brainiak.hyperparamopt brainiak.hyperparamopt.hpo brainiak.image brainiak.io brainiak.isc brainiak.matnormal brainiak.matnormal.covs brainiak.matnormal.matnormal_likelihoods brainiak.matnormal.mnrsa brainiak.matnormal.regression brainiak.matnormal.utils brainiak.reconstruct brainiak.reconstruct.iem brainiak.reprsimil brainiak.reprsimil.brsa brainiak.searchlight brainiak.searchlight.searchlight brainiak.utils brainiak.utils.fmrisim brainiak.utils.fmrisim_real_time_generator brainiak.utils.kronecker_solvers brainiak.utils.utils

mu_ (brainiak.funcalign.srm.SRM attribute) multimask_images() (in module brainiak.image) MVPAVoxelSelector (class in brainiak.fcma.mvpa_voxelselector)

N

n_basis (brainiak.utils.utils.ReadDesign attribute) n_col (brainiak.utils.utils.ReadDesign attribute) n_nureg_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) n_orth (brainiak.utils.utils.ReadDesign attribute) n_stim (brainiak.utils.utils.ReadDesign attribute) Ncomp_SVHT_MG_DLD_approx() (in module brainiak.reprsimil.brsa)

NORANDOM (brainiak.fcma.preprocessing.RandomType attribute) normalization() (in module brainiak.fcma.fcma_extension) nSNR_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) num_digits_ (brainiak.fcma.classifier.Classifier attribute) num_features_ (brainiak.fcma.classifier.Classifier attribute) num_samples_ (brainiak.fcma.classifier.Classifier attribute) num_voxels_ (brainiak.fcma.classifier.Classifier attribute)

P

P (brainiak.eventseg.event.EventSegment attribute) p_from_null() (in module brainiak.utils.utils) pack_trainable_vars() (in module brainiak.matnormal.utils) permutation_isc() (in module brainiak.isc) phase_randomize() (in module brainiak.utils.utils) phaseshift_isc() (in module brainiak.isc) predict() (brainiak.eventseg.event.EventSegment method) (brainiak.fcma.classifier.Classifier method) (brainiak.funcalign.sssrm.SSSRM method) (brainiak.matnormal.regression.MatnormalRegression method) (brainiak.reconstruct.iem.InvertedEncoding1D method) (brainiak.reconstruct.iem.InvertedEncoding2D method)

predict_feature_responses() (brainiak.reconstruct.iem.InvertedEncoding2D method) prepare_fcma_data() (in module brainiak.fcma.preprocessing) prepare_mvpa_data() (in module brainiak.fcma.preprocessing) prepare_searchlight_mvpa_data() (in module brainiak.fcma.preprocessing) prior_GP_var_half_cauchy() (in module brainiak.reprsimil.brsa) prior_GP_var_inv_gamma() (in module brainiak.reprsimil.brsa)

R

r_ (brainiak.funcalign.rsrm.RSRM attribute) random_state_ (brainiak.funcalign.rsrm.RSRM attribute) (brainiak.funcalign.srm.DetSRM attribute) (brainiak.funcalign.srm.SRM attribute) (brainiak.funcalign.sssrm.SSSRM attribute) (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) RandomType (class in brainiak.fcma.preprocessing) read_afni() (brainiak.utils.utils.ReadDesign method) ReadDesign (class in brainiak.utils.utils)

recon() (in module brainiak.factoranalysis.tfa_extension) REPRODUCIBLE (brainiak.fcma.preprocessing.RandomType attribute) rho2_ (brainiak.funcalign.srm.SRM attribute) rho_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) rmn() (in module brainiak.matnormal.utils) RSRM (class in brainiak.funcalign.rsrm) run() (brainiak.fcma.mvpa_voxelselector.MVPAVoxelSelector method) (brainiak.fcma.voxelselector.VoxelSelector method) run_block_function() (brainiak.searchlight.searchlight.Searchlight method) run_searchlight() (brainiak.searchlight.searchlight.Searchlight method)

S

s_ (brainiak.funcalign.rsrm.RSRM attribute) (brainiak.funcalign.srm.DetSRM attribute) (brainiak.funcalign.srm.SRM attribute) (brainiak.funcalign.sssrm.SSSRM attribute) save() (brainiak.funcalign.srm.SRM method) save_as_nifti_file() (in module brainiak.io) scaled_I() (in module brainiak.matnormal.utils) score() (brainiak.fcma.classifier.Classifier method) (brainiak.reconstruct.iem.InvertedEncoding1D method) (brainiak.reconstruct.iem.InvertedEncoding2D method) (brainiak.reprsimil.brsa.BRSA method) (brainiak.reprsimil.brsa.GBRSA method) score_against_reconstructed() (brainiak.reconstruct.iem.InvertedEncoding2D method) Searchlight (class in brainiak.searchlight.searchlight) segments_ (brainiak.eventseg.event.EventSegment attribute) set_centers() (brainiak.factoranalysis.tfa.TFA method) set_centers_mean_cov() (brainiak.factoranalysis.tfa.TFA method) set_event_patterns() (brainiak.eventseg.event.EventSegment method) set_K() (brainiak.factoranalysis.tfa.TFA method) set_params() (brainiak.reconstruct.iem.InvertedEncoding1D method) (brainiak.reconstruct.iem.InvertedEncoding2D method) set_prior() (brainiak.factoranalysis.tfa.TFA method)

set_seed() (brainiak.factoranalysis.tfa.TFA method) set_widths() (brainiak.factoranalysis.tfa.TFA method) set_widths_mean_var() (brainiak.factoranalysis.tfa.TFA method) Shape (class in brainiak.searchlight.searchlight) sigma_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) sigma_s_ (brainiak.funcalign.srm.SRM attribute) SingleConditionSpec (class in brainiak.image) solve() (brainiak.matnormal.covs.CovAR1 method) (brainiak.matnormal.covs.CovBase method) (brainiak.matnormal.covs.CovDiagonal method) (brainiak.matnormal.covs.CovIdentity method) (brainiak.matnormal.covs.CovIsotropic method) (brainiak.matnormal.covs.CovKroneckerFactored method) (brainiak.matnormal.covs.CovUnconstrainedCholesky method) (brainiak.matnormal.covs.CovUnconstrainedInvCholesky method) solve_det_conditional() (in module brainiak.matnormal.matnormal_likelihoods) solve_det_marginal() (in module brainiak.matnormal.matnormal_likelihoods) squareform_isfc() (in module brainiak.isc) SRM (class in brainiak.funcalign.srm) SSSRM (class in brainiak.funcalign.sssrm) StimLabels (brainiak.utils.utils.ReadDesign attribute) sumexp_stable() (in module brainiak.utils.utils)

T

test_data_ (brainiak.fcma.classifier.Classifier attribute) test_raw_data_ (brainiak.fcma.classifier.Classifier attribute) tf_kron_mult() (in module brainiak.utils.kronecker_solvers) tf_masked_triangular_solve() (in module brainiak.utils.kronecker_solvers) TFA (class in brainiak.factoranalysis.tfa) theta_ (brainiak.funcalign.sssrm.SSSRM attribute) timeshift_isc() (in module brainiak.isc) training_data_ (brainiak.fcma.classifier.Classifier attribute) transform() (brainiak.funcalign.fastsrm.FastSRM method) (brainiak.funcalign.rsrm.RSRM method) (brainiak.funcalign.srm.DetSRM method) (brainiak.funcalign.srm.SRM method) (brainiak.funcalign.sssrm.SSSRM method) (brainiak.reprsimil.brsa.BRSA method) (brainiak.reprsimil.brsa.GBRSA method)

transform_subject() (brainiak.funcalign.rsrm.RSRM method) (brainiak.funcalign.srm.DetSRM method) (brainiak.funcalign.srm.SRM method)

U

U_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) unflatten_cholesky_unique() (in module brainiak.matnormal.utils)

unpack_trainable_vars() (in module brainiak.matnormal.utils) UNREPRODUCIBLE (brainiak.fcma.preprocessing.RandomType attribute) usable_cpu_count() (in module brainiak.utils.utils)

V

VoxelSelector (class in brainiak.fcma.voxelselector)

W

W_ (brainiak.factoranalysis.tfa.TFA attribute) w_ (brainiak.funcalign.rsrm.RSRM attribute) (brainiak.funcalign.srm.DetSRM attribute) (brainiak.funcalign.srm.SRM attribute) (brainiak.funcalign.sssrm.SSSRM attribute)

W_ (brainiak.reconstruct.iem.InvertedEncoding1D attribute) (brainiak.reconstruct.iem.InvertedEncoding2D attribute)

X

X0_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute) X0_null_ (brainiak.reprsimil.brsa.BRSA attribute) (brainiak.reprsimil.brsa.GBRSA attribute)

x_tx() (in module brainiak.matnormal.utils) xx_t() (in module brainiak.matnormal.utils)