NiMARE
0.3.0
Contents:
About NiMARE
Installation
API
Examples
Contributing to NiMARE
NiMARE Developer Guide
Command Line Interface
Outputs of NiMARE
NiMARE Methods
What’s New
Glossary
NiMARE
NiMARE: Neuroimaging Meta-Analysis Research Environment
Edit on GitHub
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Z
A
ALE (class in nimare.meta.cbma.ale)
ALEKernel (class in nimare.meta.kernel)
ALESubtraction (class in nimare.meta.cbma.ale)
Analysis (class in nimare.nimads)
Annotation (class in nimare.nimads)
annotations (Dataset property)
(Studyset property)
B
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)
CBMREstimator (class in nimare.meta.cbmr)
CBMRInference (class in nimare.meta.cbmr)
CogAtLemmatizer (class in nimare.annotate.cogat)
combine_analyses() (Studyset method)
compute_log_likelihood() (GCLDAModel method)
Condition (class in nimare.nimads)
conjunction_analysis() (in module nimare.workflows.misc)
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_sleuth_to_dataset() (in module nimare.io)
convert_sleuth_to_dict() (in module nimare.io)
convert_sleuth_to_json() (in module nimare.io)
coordinates (Dataset property)
copy() (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)
(CBMAEstimator method)
(KDA method)
(MKDAChi2 method)
(MKDADensity method)
(PairwiseCBMAEstimator method)
(PermutedOLS method)
(SCALE method)
CorrelationDecoder (class in nimare.decode.continuous)
CorrelationDistributionDecoder (class in nimare.decode.continuous)
create_contrast() (CBMRInference method)
create_coordinate_dataset() (in module nimare.generate)
create_neurovault_dataset() (in module nimare.generate)
create_regular_expressions() (CBMRInference method)
D
Dataset (class in nimare.dataset)
Decoder (class in nimare.decode.base)
DerSimonianLaird (class in nimare.meta.ibma)
description_ (MetaResult property)
display() (CBMRInference method)
download_abstracts() (in module nimare.extract)
download_cognitive_atlas() (in module nimare.extract)
download_nidm_pain() (in module nimare.extract)
E
Estimator (class in nimare.estimator)
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_neurosynth() (in module nimare.extract)
Fishers (class in nimare.meta.ibma)
fit() (ALE method)
(ALESubtraction method)
(BrainMapDecoder method)
(CBMAEstimator method)
(CBMREstimator method)
(CBMRInference method)
(CorrelationDecoder method)
(CorrelationDistributionDecoder method)
(Decoder method)
(DerSimonianLaird method)
(Estimator method)
(Fishers method)
(GCLDAModel method)
(Hedges method)
(IBMAEstimator method)
(KDA method)
(LDAModel 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() (CBMRInference method)
FocusCounter (class in nimare.diagnostics)
FocusFilter (class in nimare.diagnostics)
from_nimads() (Studyset class method)
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() (Dataset method)
get_analyses() (Study method)
get_analyses_by_annotations() (Studyset method)
get_analyses_by_coordinates() (Studyset method)
get_analyses_by_images() (Studyset method)
get_analyses_by_mask() (Studyset method)
get_analyses_by_metadata() (Studyset method)
get_analyses_by_texts() (Studyset method)
get_annotations() (Studyset method)
get_data_dirs() (in module nimare.extract.utils)
get_images() (Dataset method)
(Studyset method)
get_labels() (Dataset method)
get_map() (MetaResult method)
get_masker() (in module nimare.utils)
get_metadata() (Dataset method)
(Studyset method)
get_params() (ALE method)
(ALEKernel method)
(ALESubtraction method)
(BrainMapDecoder method)
(CBMAEstimator method)
(CBMREstimator method)
(CorrelationDecoder method)
(CorrelationDistributionDecoder method)
(Dataset method)
(Decoder method)
(DerSimonianLaird method)
(Estimator method)
(FDRCorrector method)
(Fishers 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)
(ROIAssociationDecoder method)
(SampleSizeBasedLikelihood method)
(SCALE method)
(Stouffers 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)
get_studies_by_label() (Dataset method)
get_studies_by_mask() (Dataset method)
get_template() (in module nimare.utils)
get_texts() (Dataset method)
(Studyset method)
H
Hedges (class in nimare.meta.ibma)
I
IBMAEstimator (class in nimare.meta.ibma)
IBMAWorkflow() (in module nimare.workflows.ibma)
ids (Dataset property)
Image (class in nimare.nimads)
images (Dataset property)
ImagesToCoordinates (class in nimare.transforms)
ImageTransformer (class in nimare.transforms)
inspect() (FDRCorrector class method)
(FWECorrector class method)
J
Jackknife (class in nimare.diagnostics)
K
KDA (class in nimare.meta.cbma.mkda)
KDAKernel (class in nimare.meta.kernel)
KernelTransformer (class in nimare.meta.kernel)
L
LDAModel (class in nimare.annotate.lda)
load() (ALE class method)
(ALEKernel class method)
(ALESubtraction class method)
(BrainMapDecoder class method)
(CBMAEstimator class method)
(CBMREstimator 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)
(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)
(ROIAssociationDecoder class method)
(SampleSizeBasedLikelihood class method)
(SCALE class method)
(Stouffers class method)
(Studyset method)
(VarianceBasedLikelihood class method)
(WeightedLeastSquares class method)
load_imgs() (CorrelationDecoder method)
M
macm_workflow() (in module nimare.workflows)
masker (Dataset property)
merge() (Dataset method)
(Studyset method)
metadata (Dataset 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.cbmr
nimare.meta.ibma
nimare.meta.kernel
nimare.nimads
nimare.reports
nimare.results
nimare.stats
nimare.transforms
nimare.utils
nimare.workflows
N
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.cbmr
module
nimare.meta.ibma
module
nimare.meta.kernel
module
nimare.nimads
module
nimare.reports
module
nimare.results
module
nimare.stats
module
nimare.transforms
module
nimare.utils
module
nimare.workflows
module
NiMAREBase (class in nimare.base)
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)
PermutedOLS (class in nimare.meta.ibma)
Point (class in nimare.nimads)
R
resolve_transforms() (in module nimare.transforms)
ROIAssociationDecoder (class in nimare.decode.discrete)
run_reports() (in module nimare.reports)
S
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)
(BrainMapDecoder method)
(CBMAEstimator method)
(CBMREstimator method)
(CorrelationDecoder method)
(CorrelationDistributionDecoder method)
(Dataset method)
(Decoder method)
(DerSimonianLaird method)
(Estimator method)
(FDRCorrector method)
(Fishers 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)
(ROIAssociationDecoder method)
(SampleSizeBasedLikelihood method)
(SCALE method)
(Stouffers method)
(Studyset 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)
set_params() (ALE method)
(ALEKernel method)
(ALESubtraction method)
(BrainMapDecoder method)
(CBMAEstimator method)
(CBMREstimator method)
(CorrelationDecoder method)
(CorrelationDistributionDecoder method)
(Dataset method)
(Decoder method)
(DerSimonianLaird method)
(Estimator method)
(FDRCorrector method)
(Fishers 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)
(ROIAssociationDecoder method)
(SampleSizeBasedLikelihood method)
(SCALE method)
(Stouffers method)
(VarianceBasedLikelihood method)
(WeightedLeastSquares method)
slice() (Dataset method)
(Studyset method)
Stouffers (class in nimare.meta.ibma)
Study (class in nimare.nimads)
Studyset (class in nimare.nimads)
T
t_and_beta_to_varcope() (in module nimare.transforms)
t_and_varcope_to_beta() (in module nimare.transforms)
t_to_z() (in module nimare.transforms)
tal2mni() (in module nimare.utils)
texts (Dataset property)
to_dataset() (Studyset method)
to_dict() (Analysis method)
(Annotation method)
(Condition method)
(Image method)
(Point method)
(Study method)
(Studyset method)
to_nimads() (Studyset method)
transform() (ALEKernel method)
(BrainMapDecoder method)
(CBMRInference 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)
(MKDAKernel method)
(NeurosynthDecoder method)
(ROIAssociationDecoder method)
transform_images() (in module nimare.transforms)
two_way() (in module nimare.stats)
U
unique_rows() (in module nimare.utils)
update_image_path() (Studyset method)
update_path() (Dataset method)
V
varcope
VarianceBasedLikelihood (class in nimare.meta.ibma)
vox2mm() (in module nimare.utils)
W
WeightedLeastSquares (class in nimare.meta.ibma)
Z
z_to_p() (in module nimare.transforms)
z_to_t() (in module nimare.transforms)