├── .codecov.yml ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── config.yml │ └── feature_request.md ├── config.yml ├── pull_request_template.md ├── release.yml └── workflows │ ├── benchmark.yml │ ├── linting.yml │ ├── python-publish.yml │ ├── testing.yml │ └── update-changelog.yml ├── .gitignore ├── .readthedocs.yaml ├── .zenodo.json ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── asv.conf.json ├── benchmarks ├── __init__.py ├── bench_cbma.py └── bench_ibma.py.bak ├── docs ├── Makefile ├── _static │ ├── ecosystem.png │ ├── nimare.css │ ├── nimare_banner.png │ ├── nimare_favicon.png │ ├── nimare_overview.png │ └── theme_overrides.css ├── _templates │ ├── class.rst │ ├── function.rst │ ├── indexsidebar.html │ ├── layout.html │ ├── module.rst │ └── navbar.html ├── about.rst ├── api.rst ├── cbma.rst ├── changelog.rst ├── cli.rst ├── conf.py ├── contributing.rst ├── decoding.rst ├── dev_guide.rst ├── fetching.rst ├── glossary.rst ├── index.rst ├── installation.rst ├── links.rst ├── make.bat ├── methods.rst ├── outputs.rst └── sphinxext │ └── github_link.py ├── examples ├── 01_datasets │ ├── 01_plot_dataset_io.py │ ├── 02_download_neurosynth.py │ ├── 03_plot_neurovault_io.py │ ├── 04_transform_images_to_coordinates.py │ ├── 05_plot_nimads.py │ ├── 06_plot_dataset_json.py │ └── README.txt ├── 02_meta-analyses │ ├── 01_plot_cbma.py │ ├── 02_plot_ibma.py │ ├── 03_plot_kernel_transformers.py │ ├── 04_plot_estimators.py │ ├── 05_plot_correctors.py │ ├── 06_plot_compare_ibma_and_cbma.py │ ├── 07_macm.py │ ├── 08_plot_cbma_subtraction_conjunction.py │ ├── 09_plot_simulated_data.py │ ├── 10_plot_cbma_workflow.py │ ├── 11_plot_cbmr.py │ ├── 12_plot_ibma_workflow.py │ └── README.txt ├── 03_annotation │ ├── 01_plot_tfidf.py │ ├── 02_plot_cognitive_atlas.py │ ├── 03_plot_lda.py │ ├── 04_plot_gclda.py │ └── README.txt ├── 04_decoding │ ├── 01_plot_discrete_decoders.py │ └── README.txt ├── README.txt └── misc-notebooks │ ├── nidm_pain_meta-analyses.ipynb │ └── save_nidm_to_dset.ipynb ├── nimare ├── __init__.py ├── _version.py ├── annotate │ ├── __init__.py │ ├── cogat.py │ ├── gclda.py │ ├── lda.py │ ├── text.py │ └── utils.py ├── base.py ├── cli.py ├── correct.py ├── dataset.py ├── decode │ ├── __init__.py │ ├── base.py │ ├── continuous.py │ ├── discrete.py │ ├── encode.py │ └── utils.py ├── diagnostics.py ├── estimator.py ├── exceptions.py ├── extract │ ├── __init__.py │ ├── extract.py │ └── utils.py ├── generate.py ├── io.py ├── meta │ ├── __init__.py │ ├── cbma │ │ ├── __init__.py │ │ ├── ale.py │ │ ├── base.py │ │ └── mkda.py │ ├── cbmr.py │ ├── ibma.py │ ├── kernel.py │ ├── models.py │ └── utils.py ├── nimads.py ├── reports │ ├── __init__.py │ ├── base.py │ ├── default.yml │ ├── figures.py │ └── report.tpl ├── resources │ ├── __init__.py │ ├── atlases │ │ ├── Harvard-Oxford-LICENSE │ │ └── HarvardOxford-cort-maxprob-thr25-2mm.nii.gz │ ├── cognitive_atlas │ │ ├── cogat_aliases.csv │ │ └── cogat_relationships.csv │ ├── database_file_manifest.json │ ├── english_spellings.csv │ ├── filenames.json │ ├── neurosynth_laird_studies.json │ ├── neurosynth_stoplist.txt │ ├── nidm_pain_dset.json │ ├── references.bib │ ├── semantic_knowledge_children.txt │ ├── semantic_relatedness_children.txt │ └── templates │ │ ├── MNI152_2x2x2_brainmask.nii.gz │ │ ├── tpl-MNI152NLin6Asym_res-01_T1w.nii.gz │ │ ├── tpl-MNI152NLin6Asym_res-01_desc-brain_mask.nii.gz │ │ ├── tpl-MNI152NLin6Asym_res-02_T1w.nii.gz │ │ └── tpl-MNI152NLin6Asym_res-02_desc-brain_mask.nii.gz ├── results.py ├── stats.py ├── tests │ ├── __init__.py │ ├── conftest.py │ ├── data │ │ ├── amygdala_roi.nii.gz │ │ ├── data-neurosynth_version-7_coordinates.tsv.gz │ │ ├── data-neurosynth_version-7_metadata.tsv.gz │ │ ├── data-neurosynth_version-7_vocab-terms_source-abstract_type-tfidf_features.npz │ │ ├── data-neurosynth_version-7_vocab-terms_vocabulary.txt │ │ ├── neurosynth_dset.json │ │ ├── neurosynth_laird_studies.json │ │ ├── nidm_pain_dset.json │ │ ├── nimads_annotation.json │ │ ├── nimads_studyset.json │ │ ├── sample_size_nimads_studyset.json │ │ ├── test_baseline.txt │ │ ├── test_pain_dataset.json │ │ ├── test_pain_dataset │ │ │ ├── atlas.nii.gz │ │ │ ├── mask.nii.gz │ │ │ ├── pain_01_beta.nii.gz │ │ │ ├── pain_01_se.nii.gz │ │ │ ├── pain_01_t.nii.gz │ │ │ ├── pain_01_varcope.nii.gz │ │ │ ├── pain_01_z.nii.gz │ │ │ ├── pain_02_beta.nii.gz │ │ │ ├── pain_02_se.nii.gz │ │ │ ├── pain_02_t.nii.gz │ │ │ ├── pain_02_varcope.nii.gz │ │ │ ├── pain_02_z.nii.gz │ │ │ ├── pain_03_beta.nii.gz │ │ │ ├── pain_03_se.nii.gz │ │ │ ├── pain_03_t.nii.gz │ │ │ ├── pain_03_varcope.nii.gz │ │ │ ├── pain_03_z.nii.gz │ │ │ ├── pain_04_beta.nii.gz │ │ │ ├── pain_04_se.nii.gz │ │ │ ├── pain_04_t.nii.gz │ │ │ ├── pain_04_varcope.nii.gz │ │ │ ├── pain_04_z.nii.gz │ │ │ ├── pain_05_beta.nii.gz │ │ │ ├── pain_05_se.nii.gz │ │ │ ├── pain_05_t.nii.gz │ │ │ ├── pain_05_varcope.nii.gz │ │ │ ├── pain_05_z.nii.gz │ │ │ ├── pain_06_beta.nii.gz │ │ │ ├── pain_06_se.nii.gz │ │ │ ├── pain_06_t.nii.gz │ │ │ ├── pain_06_varcope.nii.gz │ │ │ ├── pain_06_z.nii.gz │ │ │ ├── pain_07_beta.nii.gz │ │ │ ├── pain_07_se.nii.gz │ │ │ ├── pain_07_t.nii.gz │ │ │ ├── pain_07_varcope.nii.gz │ │ │ ├── pain_07_z.nii.gz │ │ │ ├── pain_08_beta.nii.gz │ │ │ ├── pain_08_se.nii.gz │ │ │ ├── pain_08_t.nii.gz │ │ │ ├── pain_08_varcope.nii.gz │ │ │ ├── pain_08_z.nii.gz │ │ │ ├── pain_09_beta.nii.gz │ │ │ ├── pain_09_se.nii.gz │ │ │ ├── pain_09_t.nii.gz │ │ │ ├── pain_09_varcope.nii.gz │ │ │ ├── pain_09_z.nii.gz │ │ │ ├── pain_10_beta.nii.gz │ │ │ ├── pain_10_se.nii.gz │ │ │ ├── pain_10_t.nii.gz │ │ │ ├── pain_10_varcope.nii.gz │ │ │ ├── pain_10_z.nii.gz │ │ │ ├── pain_11_beta.nii.gz │ │ │ ├── pain_11_se.nii.gz │ │ │ ├── pain_11_t.nii.gz │ │ │ ├── pain_11_varcope.nii.gz │ │ │ ├── pain_11_z.nii.gz │ │ │ ├── pain_12_beta.nii.gz │ │ │ ├── pain_12_se.nii.gz │ │ │ ├── pain_12_t.nii.gz │ │ │ ├── pain_12_varcope.nii.gz │ │ │ ├── pain_12_z.nii.gz │ │ │ ├── pain_13_beta.nii.gz │ │ │ ├── pain_13_se.nii.gz │ │ │ ├── pain_13_t.nii.gz │ │ │ ├── pain_13_varcope.nii.gz │ │ │ ├── pain_13_z.nii.gz │ │ │ ├── pain_14_beta.nii.gz │ │ │ ├── pain_14_se.nii.gz │ │ │ ├── pain_14_t.nii.gz │ │ │ ├── pain_14_varcope.nii.gz │ │ │ ├── pain_14_z.nii.gz │ │ │ ├── pain_15_beta.nii.gz │ │ │ ├── pain_15_se.nii.gz │ │ │ ├── pain_15_t.nii.gz │ │ │ ├── pain_15_varcope.nii.gz │ │ │ ├── pain_15_z.nii.gz │ │ │ ├── pain_16_beta.nii.gz │ │ │ ├── pain_16_se.nii.gz │ │ │ ├── pain_16_t.nii.gz │ │ │ ├── pain_16_varcope.nii.gz │ │ │ ├── pain_16_z.nii.gz │ │ │ ├── pain_17_beta.nii.gz │ │ │ ├── pain_17_se.nii.gz │ │ │ ├── pain_17_t.nii.gz │ │ │ ├── pain_17_varcope.nii.gz │ │ │ ├── pain_17_z.nii.gz │ │ │ ├── pain_18_beta.nii.gz │ │ │ ├── pain_18_se.nii.gz │ │ │ ├── pain_18_t.nii.gz │ │ │ ├── pain_18_varcope.nii.gz │ │ │ ├── pain_18_z.nii.gz │ │ │ ├── pain_19_beta.nii.gz │ │ │ ├── pain_19_se.nii.gz │ │ │ ├── pain_19_t.nii.gz │ │ │ ├── pain_19_varcope.nii.gz │ │ │ ├── pain_19_z.nii.gz │ │ │ ├── pain_20-1_2.0x2.0x2.0_varcope.nii.gz │ │ │ ├── pain_20_beta.nii.gz │ │ │ ├── pain_20_se.nii.gz │ │ │ ├── pain_20_t.nii.gz │ │ │ ├── pain_20_varcope.nii.gz │ │ │ ├── pain_20_z.nii.gz │ │ │ ├── pain_21-1_2.0x2.0x2.0_z.nii.gz │ │ │ ├── pain_21_beta.nii.gz │ │ │ ├── pain_21_se.nii.gz │ │ │ ├── pain_21_t.nii.gz │ │ │ ├── pain_21_varcope.nii.gz │ │ │ └── pain_21_z.nii.gz │ │ ├── test_pain_dataset_multiple_contrasts.json │ │ ├── test_sleuth_file.txt │ │ ├── test_sleuth_file2.txt │ │ ├── test_sleuth_file3.txt │ │ ├── test_sleuth_file4.txt │ │ └── test_sleuth_file5.txt │ ├── test_annotate_cogat.py │ ├── test_annotate_gclda.py │ ├── test_annotate_lda.py │ ├── test_dataset.py │ ├── test_decode_continuous.py │ ├── test_decode_discrete.py │ ├── test_diagnostics.py │ ├── test_estimator_performance.py │ ├── test_extract.py │ ├── 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