API === .. _api_meta_ref: :mod:`nimare.meta`: Meta-analytic algorithms -------------------------------------------------- For more information about the components of coordinate-based meta-analysis in NiMARE, see :doc:`cbma`. .. automodule:: nimare.meta :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: module.rst meta.ibma meta.cbma.ale meta.cbma.mkda meta.cbma.base meta.kernel meta.cbmr .. _api_results_ref: :mod:`nimare.results`: Meta-analytic results ------------------------------------------------------ .. automodule:: nimare.results :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: class.rst results.MetaResult .. _api_correct_ref: :mod:`nimare.correct`: Multiple comparisons correction ------------------------------------------------------ .. automodule:: nimare.correct :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: class.rst correct.FWECorrector correct.FDRCorrector .. _api_diagnostics_ref: :mod:`nimare.diagnostics`: Diagnostics ------------------------------------------------------ .. automodule:: nimare.diagnostics :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: class.rst diagnostics.FocusFilter diagnostics.Jackknife diagnostics.FocusCounter diagnostics.ResampledStability .. _api_annotate_ref: :mod:`nimare.annotate`: Automated annotation -------------------------------------------------- .. automodule:: nimare.annotate :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: module.rst annotate.cogat annotate.gclda annotate.lda annotate.text annotate.utils .. _api_decode_ref: :mod:`nimare.decode`: Functional characterization analysis ----------------------------------------------------------- For more information about functional characterization analysis, see :doc:`decoding`. .. automodule:: nimare.decode :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: module.rst decode.discrete decode.continuous decode.encode decode.base .. _api_io_ref: :mod:`nimare.io`: Tools for ingesting data in other formats ----------------------------------------------------------- .. automodule:: nimare.io :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: function.rst io.convert_neurosynth_to_dict io.convert_neurosynth_to_json io.convert_neurosynth_to_dataset io.fetch_neurostore_studyset io.convert_nimads_to_dataset io.convert_nimads_to_sleuth io.convert_dataset_to_nimads_dict io.convert_dataset_to_studyset io.convert_sleuth_to_dict io.convert_sleuth_to_json io.convert_sleuth_to_dataset io.convert_sleuth_to_studyset io.convert_neurovault_to_dataset .. _api_nimads_ref: :mod:`nimare.nimads`: NeuroImaging Meta-Analysis Data Structure --------------------------------------------------------------- The NIMADS :class:`~nimare.nimads.Studyset` is the primary collection type for all NiMARE workflows. .. automodule:: nimare.nimads :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: class.rst nimads.convert_neurostore_json_to_parquet nimads.Studyset nimads.Annotation nimads.Study nimads.Analysis nimads.Condition nimads.Image nimads.Point .. _api_dataset_ref: :mod:`nimare.dataset`: Legacy Dataset IO -------------------------------------------------- .. automodule:: nimare.dataset :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: class.rst dataset.Dataset .. _api_transforms_ref: :mod:`nimare.transforms`: Data transforms ----------------------------------------------------- .. automodule:: nimare.transforms :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: class.rst transforms.ImageTransformer transforms.ImagesToCoordinates transforms.StandardizeField :template: function.rst transforms.threshold_image transforms.transform_images transforms.resolve_transforms transforms.sample_sizes_to_dof transforms.sample_sizes_to_sample_size transforms.sd_to_varcope transforms.se_to_varcope transforms.samplevar_dataset_to_varcope transforms.t_and_varcope_to_beta transforms.t_and_beta_to_varcope transforms.t_to_d transforms.d_to_g transforms.p_to_z transforms.t_to_z transforms.z_to_t transforms.z_to_p .. _api_extract_ref: :mod:`nimare.extract`: Dataset and model fetching ----------------------------------------------------- For more information about fetching data from the internet, see :ref:`fetching tools`. .. automodule:: nimare.extract :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: function.rst extract.fetch_neuroquery extract.fetch_neurosynth extract.download_nidm_pain extract.download_cognitive_atlas extract.download_abstracts extract.utils.get_data_dirs .. _api_stats_ref: :mod:`nimare.stats`: Statistical functions ----------------------------------------------------- .. automodule:: nimare.stats :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: function.rst stats.one_way stats.two_way_counts stats.two_way stats.pearson stats.null_to_p stats.nullhist_to_p .. _api_generate_ref: :mod:`nimare.generate`: Data generation functions ----------------------------------------------------- .. automodule:: nimare.generate :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: function.rst generate.create_coordinate_dataset generate.create_coordinate_studyset generate.create_neurovault_dataset generate.create_neurovault_studyset .. _api_utils_ref: :mod:`nimare.utils`: Utility functions and submodules ----------------------------------------------------- .. automodule:: nimare.utils :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: function.rst utils.get_template utils.get_masker utils.get_resource_path utils.vox2mm utils.mm2vox utils.tal2mni utils.mni2tal utils.unique_rows .. _api_workflows_ref: :mod:`nimare.workflows`: Common workflows -------------------------------------------------- .. automodule:: nimare.workflows :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: function.rst workflows.macm_workflow workflows.cbma.CBMAWorkflow workflows.cbma.ContrastWorkflow workflows.cbma.PairwiseCBMAWorkflow workflows.ibma.IBMAWorkflow workflows.misc.conjunction_analysis :mod:`nimare.reports`: NiMARE report -------------------------------------------------- .. automodule:: nimare.reports :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: function.rst reports.run_reports .. _api_base_ref: :mod:`nimare.base`: Base classes -------------------------------------------------- .. automodule:: nimare.base :no-members: :no-inherited-members: .. currentmodule:: nimare .. autosummary:: :toctree: generated/ :template: class.rst base.NiMAREBase estimator.Estimator