Index

A

above() (LabelBlock method) add_dense() (ColumnStore method) add_sparse() (ColumnStore method) ALE (class in nimare.meta.cbma.ale) ALEKernel (class in nimare.meta.kernel) ALESubtraction (class in nimare.meta.cbma.ale) analyses (Study property) (Studyset property) analyses_with_points() (View method) Analysis (class in nimare.studyset) analysis (Image property) analysis_flags() (View method)

analysis_level_stores() (StudysetStore method) annotations (Analysis property) (Dataset property) (Studyset property) annotations_df (Dataset property) (Studyset property) AnnotationSet (class in nimare.studyset) as_input() (Coordinates method) (Images method) (Labels method) (PerAnalysis method) (Texts method) authors (Study property)

B

BalancedALESubtraction (class in nimare.meta.cbma.ale) basepath (Studyset property)

beta brainmap_decode() (in module nimare.decode.discrete) BrainMapDecoder (class in nimare.decode.discrete)

C

CBMAEstimator (class in nimare.meta.cbma.base) CBMAWorkflow() (in module nimare.workflows.cbma) check_invariants (class in nimare.studyset) chi2_to_nlogp() (in module nimare.transforms) clear_map_cache() (in module nimare.ml) coefficient_image() (in module nimare.ml) CogAtLemmatizer (class in nimare.annotate.cogat) col() (LabelBlock method) column() (LabelBlock method) ColumnStore (class in nimare.studyset) combine_analyses() (Studyset method) Comparison (class in nimare.studyset) compute_log_likelihood() (GCLDAModel method) conditions (Analysis property) conjunction_analysis() (in module nimare.workflows.misc) Context (class in nimare.studyset) ContrastWorkflow() (in module nimare.workflows.cbma) convert_dataset_to_nimads_dict() (in module nimare.io) convert_dataset_to_studyset() (in module nimare.io) convert_neurostore_json_to_parquet (class in nimare.studyset) convert_neurosynth_to_dataset() (in module nimare.io) convert_neurosynth_to_dict() (in module nimare.io) convert_neurosynth_to_json() (in module nimare.io) convert_neurovault_to_dataset() (in module nimare.io) convert_nimads_to_dataset() (in module nimare.io) convert_nimads_to_sleuth() (in module nimare.io) convert_sleuth_to_dataset() (in module nimare.io) convert_sleuth_to_dict() (in module nimare.io) convert_sleuth_to_json() (in module nimare.io) convert_sleuth_to_studyset() (in module nimare.io) coordinate_block() (Studyset method) (View method)

CoordinateBlock (class in nimare.studyset) Coordinates (class in nimare.studyset) coordinates (Dataset property) (Point property) (Studyset property) copy() (AnnotationSet method) (ColumnStore method) (Dataset method) (MetaResult method) (Studyset method) correct_fdr_indep() (FDRCorrector method) (MKDAChi2 method) correct_fdr_negcorr() (FDRCorrector method) correct_fwe_bonferroni() (FWECorrector method) correct_fwe_montecarlo() (ALE method) (ALESubtraction method) (BalancedALESubtraction method) (CBMAEstimator method) (KDA method) (MKDAChi2 method) (MKDADensity method) (PairwiseCBMAEstimator method) (PermutedOLS method) (SCALE method) correct_fwe_predictive() (ALE method) CorrelationDecoder (class in nimare.decode.continuous) CorrelationDistributionDecoder (class in nimare.decode.continuous) counts() (TextBlock method) create_coordinate_dataset() (in module nimare.generate) create_coordinate_studyset() (in module nimare.generate) create_neurovault_dataset() (in module nimare.generate) create_neurovault_studyset() (in module nimare.generate)

D

d_to_g() (in module nimare.transforms) Dataset (class in nimare.dataset) Decoder (class in nimare.decode.base) dense() (LabelBlock method) DerSimonianLaird (class in nimare.meta.ibma) describe_fields() (in module nimare.ml) description (Analysis property) (Study property)

description_ (MetaResult property) doi (Study property) download_abstracts() (in module nimare.extract) download_cognitive_atlas() (in module nimare.extract) download_nidm_pain() (in module nimare.extract) drop_keys() (View method) DroppedInput (class in nimare.results) dtype() (AnnotationSet method)

E

entries() (ColumnStore method) Estimator (class in nimare.estimator)

exclude_study_ids() (Studyset method) expand_counts() (in module nimare.annotate.cogat) extract_cogat() (in module nimare.annotate.cogat)

F

FDRCorrector (class in nimare.correct) fetch_neuroquery() (in module nimare.extract) fetch_neurostore() (in module nimare.extract) fetch_neurostore_releases() (in module nimare.extract) fetch_neurostore_studyset() (in module nimare.io) fetch_neurosynth() (in module nimare.extract) filename (Image property) filter_annotations() (Studyset method) filter_ids() (Studyset method) filter_metadata() (Studyset method) filter_study_ids() (Studyset method) Fishers (class in nimare.meta.ibma) fit() (ALE method) (ALESubtraction method) (BalancedALESubtraction method) (BrainMapDecoder method) (CBMAEstimator method) (CorrelationDecoder method) (CorrelationDistributionDecoder method) (Decoder method) (DerSimonianLaird method) (Estimator method) (Fishers method) (FixedEffectsHedges method) (GCLDAModel method) (Hedges method) (IBMAEstimator method) (KDA method) (LDAModel method) (MAKernel method) (MaskerTransformer method) (MKDAChi2 method) (MKDADensity method) (NeurosynthDecoder method) (PairwiseCBMAEstimator method) (PermutedOLS method) (ROIAssociationDecoder method) (SampleSizeBasedLikelihood method) (SCALE method) (Stouffers method) (VarianceBasedLikelihood method) (WeightedLeastSquares method)

fit_transform() (MAKernel method) (MaskerTransformer method) FixedEffectsHedges (class in nimare.meta.ibma) FocusCounter (class in nimare.diagnostics) FocusFilter (class in nimare.diagnostics) frame() (View method) freeze() (ColumnStore method) from_dataset() (Studyset class method) from_nimads (class in nimare.studyset) from_nimads() (Studyset class method) from_parquet (class in nimare.studyset) from_parquet() (Studyset class method) from_sleuth() (Studyset class method) full_id (Analysis property) FWECorrector (class in nimare.correct)

G

gclda_decode_map() (in module nimare.decode.continuous) gclda_decode_roi() (in module nimare.decode.discrete) gclda_encode() (in module nimare.decode.encode) GCLDAModel (class in nimare.annotate.gclda) generate_counts() (in module nimare.annotate.text) get() (ColumnStore method) (Dataset method) get_analyses_by_annotations() (Studyset method) get_analyses_by_coordinate() (Studyset method) get_analyses_by_label() (Studyset method) get_analyses_by_mask() (Studyset method) get_analyses_by_metadata() (Studyset method) get_annotations() (Studyset method) get_data_dirs() (in module nimare.extract.utils) get_feature_names_out() (MAKernel method) (MaskerTransformer method) get_images() (Dataset method) (Studyset method) get_labels() (Dataset method) (Studyset method) get_map() (MetaResult method) get_masker() (in module nimare.utils) get_metadata() (Analysis method) (Dataset method) (Studyset method) get_metadata_routing() (MAKernel method) (MaskerTransformer method) get_numeric() (ColumnStore method) get_params() (ALE method) (ALEKernel method) (ALESubtraction method) (BalancedALESubtraction method) (BrainMapDecoder method) (CBMAEstimator method) (CorrelationDecoder method) (CorrelationDistributionDecoder method) (Dataset method) (Decoder method) (DerSimonianLaird method) (Estimator method) (FDRCorrector method) (Fishers method) (FixedEffectsHedges method) (FocusCounter method) (FocusFilter method) (FWECorrector method) (GCLDAModel method) (Hedges method) (IBMAEstimator method) (ImagesToCoordinates method) (ImageTransformer method) (Jackknife method) (KDA method) (KDAKernel method) (KernelTransformer method) (LDAModel method) (MAKernel method) (MaskerTransformer method) (MetaResult method) (MKDAChi2 method) (MKDADensity method) (MKDAKernel method) (NeurosynthDecoder method) (NiMAREBase method) (PairwiseCBMAEstimator method) (PermutedOLS method) (ResampledStability method) (ROIAssociationDecoder method) (SampleSizeBasedLikelihood method) (SCALE method) (StandardizeField method) (Stouffers method) (StudyWeights method) (VarianceBasedLikelihood method) (WeightedLeastSquares method)

get_points() (Studyset method) get_probability_distributions() (GCLDAModel method) get_resource_path() (in module nimare.utils) get_studies_by_coordinate() (Dataset method) (Studyset method) get_studies_by_label() (Dataset method) (Studyset method) get_studies_by_mask() (Dataset method) (Studyset method) get_template() (in module nimare.utils) get_texts() (Dataset method) (Studyset method) group() (CoordinateBlock method) group_of_point() (CoordinateBlock method) group_sizes() (CoordinateBlock method)

H

harmonized() (Studyset method)

Hedges (class in nimare.meta.ibma)

I

IBMAEstimator (class in nimare.meta.ibma) IBMAWorkflow() (in module nimare.workflows.ibma) id (Analysis property) (Point property) (Study property) (Studyset property) ids (Dataset property) (Studyset property) ijk() (CoordinateBlock method) Image (class in nimare.studyset) image_block() (Studyset method) (View method)

image_rows (Studyset property) ImageBlock (class in nimare.studyset) images (Analysis property) Images (class in nimare.studyset) images (Dataset property) (Studyset property) ImagesToCoordinates (class in nimare.transforms) ImageTransformer (class in nimare.transforms) inspect() (FDRCorrector class method) (FWECorrector class method) inverse_transform() (MaskerTransformer method)

J

Jackknife (class in nimare.diagnostics)

K

KDA (class in nimare.meta.cbma.mkda) KDAKernel (class in nimare.meta.kernel) keep_images() (Studyset method) KernelTransformer (class in nimare.meta.kernel)

keys (View property) keys() (AnnotationSet method) (ColumnStore method) kind (Point property)

L

label_block() (Studyset method) (View method) LabelBlock (class in nimare.studyset) labels (Analysis property) Labels (class in nimare.studyset) LDAModel (class in nimare.annotate.lda) load() (ALE class method) (ALEKernel class method) (ALESubtraction class method) (BalancedALESubtraction class method) (BrainMapDecoder class method) (CBMAEstimator class method) (CorrelationDecoder class method) (CorrelationDistributionDecoder class method) (Dataset class method) (Decoder class method) (DerSimonianLaird class method) (Estimator class method) (FDRCorrector class method) (Fishers class method) (FixedEffectsHedges class method) (FocusCounter class method) (FocusFilter class method) (FWECorrector class method) (GCLDAModel class method) (Hedges class method) (IBMAEstimator class method) (ImagesToCoordinates class method) (ImageTransformer class method) (Jackknife class method) (KDA class method) (KDAKernel class method) (KernelTransformer class method) (LDAModel class method) (MetaResult class method) (MKDAChi2 class method) (MKDADensity class method) (MKDAKernel class method) (NeurosynthDecoder class method) (NiMAREBase class method) (PairwiseCBMAEstimator class method) (PermutedOLS class method) (ResampledStability class method) (ROIAssociationDecoder class method) (SampleSizeBasedLikelihood class method) (SCALE class method) (StandardizeField class method) (Stouffers class method) (Studyset static method) (StudyWeights class method) (VarianceBasedLikelihood class method) (WeightedLeastSquares class method)

load_imgs() (CorrelationDecoder method)

M

macm_workflow() (in module nimare.workflows) make_nimare_column_transformer() (in module nimare.ml) MAKernel (class in nimare.ml) masker (Dataset property) (Studyset property) MaskerTransformer (class in nimare.ml) materialize_points() (Studyset method) merge() (Dataset method) (Studyset method) metadata (Analysis property) (Dataset property) (Image property) (Study property) (Studyset property) MetaResult (class in nimare.results) MKDAChi2 (class in nimare.meta.cbma.mkda) MKDADensity (class in nimare.meta.cbma.mkda) MKDAKernel (class in nimare.meta.kernel) mm2vox() (in module nimare.utils) mni2tal() (in module nimare.utils) module nimare.annotate nimare.annotate.cogat nimare.annotate.gclda nimare.annotate.lda nimare.annotate.text nimare.annotate.utils nimare.base nimare.correct nimare.dataset nimare.decode nimare.decode.base nimare.decode.continuous nimare.decode.discrete nimare.decode.encode nimare.diagnostics nimare.extract nimare.generate nimare.io nimare.meta nimare.meta.cbma.ale nimare.meta.cbma.base nimare.meta.cbma.mkda nimare.meta.cbma.weights nimare.meta.cbmr nimare.meta.ibma nimare.meta.kernel nimare.ml nimare.reports nimare.results nimare.stats nimare.studyset nimare.transforms nimare.utils nimare.workflows

N

n1 (Comparison property) n_analyses (StudysetStore property) n_fixed_effects_ (StudyWeights attribute) n_groups (CoordinateBlock property) n_images (StudysetStore property) n_imputed_ (StudyWeights attribute) n_points (StudysetStore property) n_studies (StudysetStore property) name (Analysis property) (Study property) (Studyset property) neurosynth_decode() (in module nimare.decode.discrete) NeurosynthDecoder (class in nimare.decode.discrete) nimare.annotate module nimare.annotate.cogat module nimare.annotate.gclda module nimare.annotate.lda module nimare.annotate.text module nimare.annotate.utils module nimare.base module nimare.correct module nimare.dataset module nimare.decode module nimare.decode.base module nimare.decode.continuous module nimare.decode.discrete module nimare.decode.encode module nimare.diagnostics module nimare.extract module

nimare.generate module nimare.io module nimare.meta module nimare.meta.cbma.ale module nimare.meta.cbma.base module nimare.meta.cbma.mkda module nimare.meta.cbma.weights module nimare.meta.cbmr module nimare.meta.ibma module nimare.meta.kernel module nimare.ml module nimare.reports module nimare.results module nimare.stats module nimare.studyset module nimare.transforms module nimare.utils module nimare.workflows module NiMAREBase (class in nimare.base) nlogp_bonferroni() (in module nimare.stats) nlogp_fdr() (in module nimare.stats) nlogp_to_z() (in module nimare.transforms) normalize_collection (class in nimare.studyset) normalize_weights() (in module nimare.meta.cbma.weights) null_to_p() (in module nimare.stats) nullhist_to_p() (in module nimare.stats)

O

one_way() (in module nimare.stats)

P

p_to_z() (in module nimare.transforms) PairwiseCBMAEstimator (class in nimare.meta.cbma.base) PairwiseCBMAWorkflow() (in module nimare.workflows.cbma) pearson() (in module nimare.stats) PerAnalysis (class in nimare.studyset) permute() (Comparison method) PermutedOLS (class in nimare.meta.ibma) pmid (Study property)

Point (class in nimare.studyset) point_flags() (View method) point_level_stores() (StudysetStore method) points (Analysis property) points_in_mask() (View method) points_near() (View method) pooled() (Comparison method) position_of_row() (View method) publication (Study property)

R

raw_weights() (StudyWeights method) reorder() (ColumnStore method) ResampledStability (class in nimare.diagnostics) resolve() (Coordinates method) (Images method) (Labels method) (PerAnalysis method) (Studyset method) (Texts method) (View method) resolve_transforms() (in module nimare.transforms)

resolve_weighting() (in module nimare.meta.cbma.weights) resolved_masker() (Context method) ROIAssociationDecoder (class in nimare.decode.discrete) row (Analysis property) (Image property) (Point property) (Study property) row_of_id() (Studyset method) row_of_key() (View method) rows() (ColumnStore method) run_reports() (in module nimare.reports)

S

sample_sizes() (Studyset method) sample_sizes_to_dof() (in module nimare.transforms) sample_sizes_to_sample_size() (in module nimare.transforms) SampleSizeBasedLikelihood (class in nimare.meta.ibma) samplevar_dataset_to_varcope() (in module nimare.transforms) save() (ALE method) (ALEKernel method) (ALESubtraction method) (BalancedALESubtraction method) (BrainMapDecoder method) (CBMAEstimator method) (CorrelationDecoder method) (CorrelationDistributionDecoder method) (Dataset method) (Decoder method) (DerSimonianLaird method) (Estimator method) (FDRCorrector method) (Fishers method) (FixedEffectsHedges method) (FocusCounter method) (FocusFilter method) (FWECorrector method) (GCLDAModel method) (Hedges method) (IBMAEstimator method) (ImagesToCoordinates method) (ImageTransformer method) (Jackknife method) (KDA method) (KDAKernel method) (KernelTransformer method) (LDAModel method) (MetaResult method) (MKDAChi2 method) (MKDADensity method) (MKDAKernel method) (NeurosynthDecoder method) (NiMAREBase method) (PairwiseCBMAEstimator method) (PermutedOLS method) (ResampledStability method) (ROIAssociationDecoder method) (SampleSizeBasedLikelihood method) (SCALE method) (StandardizeField method) (Stouffers method) (Studyset method) (StudyWeights method) (VarianceBasedLikelihood method) (WeightedLeastSquares method) save_maps() (MetaResult method) save_tables() (MetaResult method) SCALE (class in nimare.meta.cbma.ale) sd_to_varcope() (in module nimare.transforms) se_to_varcope() (in module nimare.transforms) select() (View method) select_analyses() (Studyset method) select_keys() (View method) select_points() (Studyset method) (View method) select_studies() (View method) set_output() (MAKernel method) (MaskerTransformer method) set_params() (ALE method) (ALEKernel method) (ALESubtraction method) (BalancedALESubtraction method) (BrainMapDecoder method) (CBMAEstimator method) (CorrelationDecoder method) (CorrelationDistributionDecoder method) (Dataset method) (Decoder method) (DerSimonianLaird method) (Estimator method) (FDRCorrector method) (Fishers method) (FixedEffectsHedges method) (FocusCounter method) (FocusFilter method) (FWECorrector method) (GCLDAModel method) (Hedges method) (IBMAEstimator method) (ImagesToCoordinates method) (ImageTransformer method) (Jackknife method) (KDA method) (KDAKernel method) (KernelTransformer method) (LDAModel method) (MAKernel method) (MaskerTransformer method) (MetaResult method) (MKDAChi2 method) (MKDADensity method) (MKDAKernel method) (NeurosynthDecoder method) (NiMAREBase method) (PairwiseCBMAEstimator method) (PermutedOLS method) (ResampledStability method) (ROIAssociationDecoder method) (SampleSizeBasedLikelihood method) (SCALE method) (StandardizeField method) (Stouffers method) (StudyWeights method) (VarianceBasedLikelihood method) (WeightedLeastSquares method)

share_masked_image_cache() (DerSimonianLaird method) (Fishers method) (FixedEffectsHedges method) (Hedges method) (IBMAEstimator method) (PermutedOLS method) (SampleSizeBasedLikelihood method) (Stouffers method) (VarianceBasedLikelihood method) (WeightedLeastSquares method) short_keys (View property) slice() (Dataset method) (Studyset method) space (Image property) (Point property) (Studyset property) StandardizeField (class in nimare.transforms) store (Studyset property) Stouffers (class in nimare.meta.ibma) studies (Studyset property) study (Analysis property) Study (class in nimare.studyset) study_ids (Studyset property) study_keys (View property) study_level_stores() (StudysetStore method) Studyset (class in nimare.studyset) StudysetStore (class in nimare.studyset) StudyWeights (class in nimare.meta.cbma.weights) subset() (ColumnStore method)

T

t_and_beta_to_varcope() (in module nimare.transforms) t_and_varcope_to_beta() (in module nimare.transforms) t_to_d() (in module nimare.transforms) t_to_nlogp() (in module nimare.transforms) t_to_z() (in module nimare.transforms) tal2mni() (in module nimare.utils) text_block() (Studyset method) (View method) TextBlock (class in nimare.studyset) texts (Analysis property) Texts (class in nimare.studyset) texts (Dataset property) (Studyset property) threshold_image() (in module nimare.transforms) to_bunch() (Studyset method) to_dataset() (Studyset method) to_dict() (Studyset method) to_nimads() (Studyset method) to_parquet() (Studyset method) transform() (ALEKernel method) (BrainMapDecoder method) (CogAtLemmatizer method) (CorrelationDecoder method) (CorrelationDistributionDecoder method) (FDRCorrector method) (FocusCounter method) (FocusFilter method) (FWECorrector method) (ImagesToCoordinates method) (ImageTransformer method) (Jackknife method) (KDAKernel method) (KernelTransformer method) (MAKernel method) (MaskerTransformer method) (MKDAKernel method) (NeurosynthDecoder method) (ResampledStability method) (ROIAssociationDecoder method) (StandardizeField method)

transform_images() (in module nimare.transforms) two_way() (in module nimare.stats) two_way_counts() (in module nimare.stats)

U

unique_rows() (in module nimare.utils) update_path() (Dataset method) (Studyset method)

url (Image property)

V

validity() (Coordinates method) (Images method) (Labels method) (PerAnalysis method) (Texts method) value_type (Image property)

values (Point property) values() (PerAnalysis method) varcope VarianceBasedLikelihood (class in nimare.meta.ibma) View (class in nimare.studyset) view (Studyset property) vox2mm() (in module nimare.utils)

W

WeightedLeastSquares (class in nimare.meta.ibma) weights (Analysis property) with_() (Context method) with_annotation() (Studyset method) with_annotation_payload() (Studyset method) with_annotations_df() (Studyset method) with_context() (Studyset method) (View method)

with_images() (Studyset method) with_metadata() (Studyset method) with_points() (Studyset method) with_texts() (Studyset method) write_nimads (class in nimare.studyset) write_parquet (class in nimare.studyset)

X

x (Point property)

Y

y (Point property)

year (Study property)

Z

z (Point property) z_to_nlogp() (in module nimare.transforms)

z_to_p() (in module nimare.transforms) z_to_t() (in module nimare.transforms)