├── .github └── workflows │ ├── auto_deploy_docs_pypi_onrelease.yml │ ├── auto_formatting_tests_and_coverage.yml │ ├── manual_deploy_docs_only.yml │ └── manual_deploy_pypi_only.yml ├── .gitignore ├── .vscode └── extensions.json ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── _templates │ └── layout.html ├── api.rst ├── conf.py ├── index.rst └── install.rst ├── examples ├── 01_DataOperations │ ├── README.txt │ ├── plot_adjacency.py │ ├── plot_design_matrix.py │ ├── plot_download.py │ ├── plot_mask.py │ ├── plot_mni_prefs.py │ └── plot_neurovault_io.py ├── 02_Analysis │ ├── README.txt │ ├── plot_decomposition.py │ ├── plot_hyperalignment.py │ ├── plot_multivariate_classification.py │ ├── plot_multivariate_prediction.py │ ├── plot_similarity_example.py │ └── plot_univariate_regression.py └── README.txt ├── nltools ├── __init__.py ├── analysis.py ├── cross_validation.py ├── data │ ├── __init__.py │ ├── adjacency.py │ ├── brain_data.py │ └── design_matrix.py ├── datasets.py ├── external │ ├── __init__.py │ ├── hrf.py │ └── srm.py ├── file_reader.py ├── mask.py ├── plotting.py ├── prefs.py ├── resources │ ├── MNI152_T1_2mm.nii.gz │ ├── MNI152_T1_2mm_brain.nii.gz │ ├── MNI152_T1_2mm_brain_mask.nii.gz │ ├── MNI152_T1_2mm_brain_mask_no_ventricles.nii.gz │ ├── MNI152_T1_3mm.nii.gz │ ├── MNI152_T1_3mm_brain.nii.gz │ ├── MNI152_T1_3mm_brain_mask.nii.gz │ ├── MNI152_T1_3mm_brain_mask_no_ventricles.nii.gz │ ├── covariates_example.csv │ ├── gm_mask_2mm.nii.gz │ ├── gm_mask_3mm.nii.gz │ ├── onsets_example.txt │ └── onsets_example_with_dur.txt ├── simulator.py ├── stats.py ├── tests │ ├── conftest.py │ ├── matplotlibrc │ ├── new_brain.h5 │ ├── new_double.h5 │ ├── new_single.h5 │ ├── old_brain.h5 │ ├── old_double.h5 │ ├── old_single.h5 │ ├── test_adjacency.py │ ├── test_analysis.py │ ├── test_brain_data.py │ ├── test_cross_validation.py │ ├── test_design_matrix.py │ ├── test_file_reader.py │ ├── test_groupby.py │ ├── test_mask.py │ ├── test_prefs.py │ ├── test_simulator.py │ ├── test_stats.py │ └── test_utils.py ├── utils.py └── version.py ├── optional-dependencies.txt ├── pytest.ini ├── requirements-dev.txt ├── requirements.txt ├── setup.cfg └── setup.py /.github/workflows/auto_deploy_docs_pypi_onrelease.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cosanlab/nltools/HEAD/.github/workflows/auto_deploy_docs_pypi_onrelease.yml -------------------------------------------------------------------------------- /.github/workflows/auto_formatting_tests_and_coverage.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cosanlab/nltools/HEAD/.github/workflows/auto_formatting_tests_and_coverage.yml -------------------------------------------------------------------------------- /.github/workflows/manual_deploy_docs_only.yml: -------------------------------------------------------------------------------- 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