├── .gitignore ├── .readthedocs.yml ├── .ropeproject └── config.py ├── LICENSE.md ├── README.rst ├── docs ├── Makefile ├── _build │ ├── doctrees │ │ ├── api.doctree │ │ ├── auto_examples │ │ │ └── index.doctree │ │ ├── environment.pickle │ │ ├── generated │ │ │ ├── neuroharmony.ComBat.doctree │ │ │ ├── neuroharmony.Neuroharmony.doctree │ │ │ ├── neuroharmony.combine_freesurfer.doctree │ │ │ ├── neuroharmony.combine_mriqc.doctree │ │ │ ├── neuroharmony.exclude_single_subject_groups.doctree │ │ │ ├── neuroharmony.fetch_mri_data.doctree │ │ │ ├── neuroharmony.fetch_sample.doctree │ │ │ ├── neuroharmony.fetch_trained_model.doctree │ │ │ └── neuroharmony.ks_test_grid.doctree │ │ ├── index.doctree │ │ └── neuroharmony.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _downloads │ │ ├── 322a6134779c4f652acb55119731e8e7 │ │ │ └── auto_examples_jupyter.zip │ │ └── a5b660def9789dd2f4756a8ef648a4f4 │ │ │ └── auto_examples_python.zip │ │ ├── _images │ │ └── article.png │ │ ├── _modules │ │ ├── index.html │ │ └── neuroharmony │ │ │ ├── data │ │ │ ├── collect_tools.html │ │ │ └── combine_tools.html │ │ │ └── models │ │ │ ├── harmonization.html │ │ │ └── metrics.html │ │ ├── _sources │ │ ├── api.rst.txt │ │ ├── auto_examples │ │ │ └── index.rst.txt │ │ ├── generated │ │ │ ├── neuroharmony.ComBat.rst.txt │ │ │ ├── neuroharmony.Neuroharmony.rst.txt │ │ │ ├── neuroharmony.combine_freesurfer.rst.txt │ │ │ ├── neuroharmony.combine_mriqc.rst.txt │ │ │ ├── neuroharmony.exclude_single_subject_groups.rst.txt │ │ │ ├── neuroharmony.fetch_mri_data.rst.txt │ │ │ ├── neuroharmony.fetch_sample.rst.txt │ │ │ ├── neuroharmony.fetch_trained_model.rst.txt │ │ │ └── neuroharmony.ks_test_grid.rst.txt │ │ ├── index.rst.txt │ │ └── neuroharmony.rst.txt │ │ ├── _static │ │ ├── article.png │ │ ├── basic.css │ │ ├── broken_example.png │ │ ├── css │ │ │ ├── badge_only.css │ │ │ ├── fonts │ │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ │ ├── fontawesome-webfont.eot │ │ │ │ ├── fontawesome-webfont.svg │ │ │ │ ├── fontawesome-webfont.ttf │ │ │ │ ├── fontawesome-webfont.woff │ │ │ │ ├── fontawesome-webfont.woff2 │ │ │ │ ├── lato-bold-italic.woff │ │ │ │ ├── lato-bold-italic.woff2 │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-normal-italic.woff │ │ │ │ ├── lato-normal-italic.woff2 │ │ │ │ ├── lato-normal.woff │ │ │ │ └── lato-normal.woff2 │ │ │ ├── project-template.css │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── fonts │ │ │ ├── FontAwesome.otf │ │ │ ├── Lato │ │ │ │ ├── lato-bold.eot │ │ │ │ ├── lato-bold.ttf │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ ├── lato-italic.eot │ │ │ │ ├── lato-italic.ttf │ │ │ │ ├── lato-italic.woff │ │ │ │ ├── lato-italic.woff2 │ │ │ │ ├── lato-regular.eot │ │ │ │ ├── lato-regular.ttf │ │ │ │ ├── lato-regular.woff │ │ │ │ └── lato-regular.woff2 │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ ├── Roboto-Slab-Light.woff │ │ │ ├── Roboto-Slab-Light.woff2 │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ ├── Roboto-Slab-Thin.woff │ │ │ ├── Roboto-Slab-Thin.woff2 │ │ │ ├── RobotoSlab │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ ├── fontawesome-webfont.woff2 │ │ │ ├── lato-bold-italic.woff │ │ │ ├── lato-bold-italic.woff2 │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-normal-italic.woff │ │ │ ├── lato-normal-italic.woff2 │ │ │ ├── lato-normal.woff │ │ │ └── lato-normal.woff2 │ │ ├── gallery-binder.css │ │ ├── gallery-dataframe.css │ │ ├── gallery.css │ │ ├── jquery-3.5.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── badge_only.js │ │ │ ├── copybutton.js │ │ │ ├── html5shiv-printshiv.min.js │ │ │ ├── html5shiv.min.js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── no_image.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ └── underscore.js │ │ ├── api.html │ │ ├── auto_examples │ │ └── index.html │ │ ├── generated │ │ ├── neuroharmony.ComBat.html │ │ ├── neuroharmony.Neuroharmony.html │ │ ├── neuroharmony.combine_freesurfer.html │ │ ├── neuroharmony.combine_mriqc.html │ │ ├── neuroharmony.exclude_single_subject_groups.html │ │ ├── neuroharmony.fetch_mri_data.html │ │ ├── neuroharmony.fetch_sample.html │ │ ├── neuroharmony.fetch_trained_model.html │ │ └── neuroharmony.ks_test_grid.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── neuroharmony.html │ │ ├── objects.inv │ │ ├── search.html │ │ └── searchindex.js ├── _static │ ├── article.png │ ├── css │ │ └── project-template.css │ └── js │ │ └── copybutton.js ├── _templates │ ├── class.rst │ ├── function.rst │ └── numpydoc_docstring.py ├── api.rst ├── auto_examples │ ├── auto_examples_jupyter.zip │ ├── auto_examples_python.zip │ ├── index.rst │ ├── searchindex.bak │ ├── searchindex.dat │ └── searchindex.dir ├── conf.py ├── generated │ ├── neuroharmony.ComBat.examples │ ├── neuroharmony.ComBat.fit.examples │ ├── neuroharmony.ComBat.fit_transform.examples │ ├── neuroharmony.ComBat.rst │ ├── neuroharmony.ComBat.transform.examples │ ├── neuroharmony.Neuroharmony.examples │ ├── neuroharmony.Neuroharmony.fit.examples │ ├── neuroharmony.Neuroharmony.fit_transform.examples │ ├── neuroharmony.Neuroharmony.rst │ ├── neuroharmony.Neuroharmony.transform.examples │ ├── neuroharmony.combine_freesurfer.examples │ ├── neuroharmony.combine_freesurfer.rst │ ├── neuroharmony.combine_mriqc.examples │ ├── neuroharmony.combine_mriqc.rst │ ├── neuroharmony.exclude_single_subject_groups.examples │ ├── neuroharmony.exclude_single_subject_groups.rst │ ├── neuroharmony.fetch_mri_data.examples │ ├── neuroharmony.fetch_mri_data.rst │ ├── neuroharmony.fetch_sample.examples │ ├── neuroharmony.fetch_sample.rst │ ├── neuroharmony.fetch_trained_model.examples │ ├── neuroharmony.fetch_trained_model.rst │ ├── neuroharmony.ks_test_grid.examples │ └── neuroharmony.ks_test_grid.rst ├── index.rst ├── make.bat ├── neuroharmony.rst └── requirements.txt ├── examples ├── README.txt └── use_trained_model.py ├── neuroharmony ├── __init__.py ├── data │ ├── __init__.py │ ├── collect_tools.py │ ├── combine_tools.py │ └── rois.py └── models │ ├── __init__.py │ ├── harmonization.py │ ├── metrics.py │ ├── mriqc.py │ └── neuroCombat.py ├── pytest.ini ├── requirements.txt ├── setup.cfg ├── setup.py └── tests ├── __init__.py ├── test_collect.py ├── test_combat_harmonization.py ├── test_combine.py └── test_neuroharmony.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/garciadias/Neuroharmony/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/garciadias/Neuroharmony/HEAD/.readthedocs.yml -------------------------------------------------------------------------------- /.ropeproject/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/garciadias/Neuroharmony/HEAD/.ropeproject/config.py -------------------------------------------------------------------------------- /LICENSE.md: 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