API¶
nimare.dataset
: Dataset IO¶
Classes for representing datasets of images and/or coordinates.
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Storage container for a coordinate- and/or image-based meta-analytic dataset/database. |
nimare.meta
: Meta-analytic algorithms¶
Coordinate-, image-, and effect-size-based meta-analysis estimators.
Effect-size meta-analysis functions |
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Image-based meta-analysis estimators |
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Methods for estimating thresholded cluster maps from neuroimaging contrasts (Contrasts) from sets of foci and optional additional information (e.g., sample size and test statistic values). |
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CBMA methods from the activation likelihood estimation (ALE) family |
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CBMA methods from the multilevel kernel density analysis (MKDA) family |
nimare.results
: Meta-analytic results¶
Base classes for datasets.
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Base class for meta-analytic results. |
nimare.correct
: Multiple comparisons correction¶
Multiple comparisons correction methods
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Perform family-wise error rate correction on a meta-analysis. |
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Perform false discovery rate correction on a meta-analysis. |
nimare.annotate
: Automated annotation¶
Automated annotation tools
Automated annotation of Cognitive Atlas labels. |
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Automated annotation of Cognitive Paradigm Ontology labels. |
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Utility functions for ontology tools. |
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Topic modeling with deep Boltzmann machines. |
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Topic modeling with generalized correspondence latent Dirichlet allocation. |
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Topic modeling with latent Dirichlet allocation via MALLET. |
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Generate a Text2Brain vector model. |
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GloVe model-based annotation. |
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Text extraction tools. |
nimare.decode
: Functional characterization analysis¶
Functional decoding tools
Methods for decoding subsets of voxels (e.g., ROIs) or experiments (e.g., from meta-analytic clustering on a database) into text. |
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Methods for decoding unthresholded brain maps into text. |
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Methods for encoding text into brain maps. |
nimare.parcellate
: Meta-analytic parcellation¶
Meta-analytic parcellation tools
Coactivation-based parcellation |
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Meta-analytic activation modeling-based parcellation (MAMP). |
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Meta-analytic parcellation based on text (MAPBOT). |
nimare.io
: Input/Output¶
Input/Output operations.
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Convert Neurosynth database files to a dictionary. |
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Convert Neurosynth dataset text file to a NiMARE json file. |
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Convert Neurosynth database files into dictionary and create NiMARE Dataset with dictionary. |
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Convert Sleuth text file to a dictionary. |
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Convert Sleuth output text file into json. |
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Convert Sleuth output text file into dictionary and create NiMARE Dataset with dictionary. |
nimare.extract
: Dataset and model fetching¶
Dataset and trained model downloading functions
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Download NIDM Results for 21 pain studies from NeuroVault for tests. |
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Download the MALLET toolbox for LDA topic modeling. |
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Download Cognitive Atlas ontology and combine Concepts, Tasks, and Disorders to create ID and relationship DataFrames. |
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Download the abstracts for a list of PubMed IDs. |
Download the trained Peaks2Maps model from OHBM 2018. |
nimare.stats
: Statistical functions¶
Various statistical helper functions
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One-way chi-square test of independence. |
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Two-way chi-square test of independence. |
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Correlate row vector x with each row vector in 2D array y, quickly. |
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Return p-value for test value against null array. |
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Determine FDR threshold given a p value array and desired false discovery rate q. |
nimare.transforms
: Data transforms¶
Miscellaneous spatial and statistical transforms
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Convert p-values to (unsigned) z-values. |
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Convert standard deviation to sampling variance. |
Convert standard error values to sampling variance. |
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Convert “sample variance” (variance of the individual observations in a single sample) to “sampling variance” (variance of sampling distribution for the parameter). |
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Convert t-statistic to parameter estimate using sampling variance. |
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Convert t-statistics to z-statistics. |
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Convert matrix subscripts to coordinates. |
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Convert coordinates to matrix subscripts. |
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Python version of BrainMap’s tal2icbm_other.m. |
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Python version of BrainMap’s icbm_other2tal.m. |
nimare.utils
: Utility functions and submodules¶
Utilities
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Load template file. |
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Get an initialized, fitted nilearn Masker instance from passed argument. |
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Wraps all non-list or tuple objects in a list; provides a simple way to accept flexible arguments. |
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Numpy rounds X.5 values to nearest even integer. |
Returns the path to general resources, terminated with separator. |
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From https://www.geeksforgeeks.org/longest-common-substring-array-strings/ |
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Convert UK spellings to US based on a converter. |
nimare.workflows
: Common workflows¶
Common meta-analytic workflows
Workflow for running an ALE meta-analysis from a Sleuth text file. |
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Workflow for running a contrast permutation meta-analysis on a set of images. |
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Perform MACM with ALE algorithm. |
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Workflow for contrast permutation meta-analysis on images constructed from coordinates using the Peaks2Maps kernel. |
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Workflow for running a SCALE meta-analysis from a Sleuth text file. |
nimare.base
: Base classes¶
Base classes for datasets.
Base class for NiMARE. |
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Estimators take in Datasets and return MetaResults |
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Transformers take in Datasets and return Datasets |