├── .gitignore ├── LICENSE ├── README.rst ├── cortex ├── __init__.py ├── analysis │ ├── __init__.py │ ├── load_mri.py │ ├── mri │ │ ├── __init__.py │ │ └── rois.py │ └── read_fmri.py ├── datasets │ ├── __init__.py │ ├── basic │ │ ├── __init__.py │ │ ├── caltech.py │ │ ├── cifar.py │ │ ├── euclidean.py │ │ ├── horses.py │ │ ├── mnist.py │ │ └── uci.py │ └── neuroimaging │ │ ├── __init__.py │ │ ├── fmri.py │ │ ├── mri.py │ │ ├── nifti_viewer.py │ │ ├── simTB.py │ │ ├── snp.py │ │ └── tests │ │ └── _test_snp.py ├── demos │ ├── __init__.py │ ├── demos_basic │ │ ├── __init__.py │ │ ├── classifier.py │ │ ├── classifier_mnist.yaml │ │ ├── eval_rbm.py │ │ ├── rbm_cifar.yaml │ │ ├── rbm_mnist.py │ │ ├── rbm_mnist.yaml │ │ ├── reweighted_vae.yaml │ │ ├── tests │ │ │ └── test_demos.py │ │ ├── vae.py │ │ └── vae_mnist.yaml │ └── demos_neuroimaging │ │ ├── __init__.py │ │ ├── rbm_ni.py │ │ ├── rbm_olin.yaml │ │ ├── rbm_vbm.yaml │ │ ├── vae.py │ │ └── vae_mri.yaml ├── inference │ ├── __init__.py │ ├── air.py │ ├── gdir.py │ ├── irvi.py │ ├── rws.py │ └── tests │ │ └── test_gdir.py ├── models │ ├── __init__.py │ ├── darn.py │ ├── deep_helmholtz.py │ ├── distributions.py │ ├── gru.py │ ├── helmholtz.py │ ├── layers.py │ ├── lstm.py │ ├── mlp.py │ ├── rbm.py │ ├── rnn.py │ └── tests │ │ ├── __init__.py │ │ ├── _test_gru.py │ │ ├── test_darn.py │ │ ├── test_mlp.py │ │ ├── test_rbm.py │ │ ├── test_rnn.py │ │ └── test_vae.py └── utils │ ├── __init__.py │ ├── extra.py │ ├── learning_scheduler.py │ ├── logger.py │ ├── monitor.py │ ├── op.py │ ├── preprocessor.py │ ├── tools.py │ ├── training.py │ ├── vis_utils.py │ └── viz_h │ ├── Visualization.ipynb │ └── tsne.py ├── doc ├── Makefile ├── _build │ ├── doctrees │ │ ├── cortex.doctree │ │ ├── demos.doctree │ │ ├── environment.pickle │ │ ├── index.doctree │ │ ├── modules.doctree │ │ ├── setup.doctree │ │ └── source │ │ │ ├── cortex.analysis.doctree │ │ │ ├── cortex.analysis.mri.doctree │ │ │ ├── cortex.datasets.basic.doctree │ │ │ ├── cortex.datasets.doctree │ │ │ ├── cortex.datasets.neuroimaging.doctree │ │ │ ├── cortex.demos.demos_basic.doctree │ │ │ ├── cortex.demos.demos_neuroimaging.doctree │ │ │ ├── cortex.demos.doctree │ │ │ ├── cortex.doctree │ │ │ ├── cortex.inference.doctree │ │ │ ├── cortex.models.doctree │ │ │ ├── cortex.models.tests.doctree │ │ │ ├── cortex.utils.doctree │ │ │ └── modules.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _modules │ │ ├── cortex.html │ │ ├── cortex │ │ │ ├── analysis │ │ │ │ ├── load_mri.html │ │ │ │ ├── mri │ │ │ │ │ └── rois.html │ │ │ │ └── read_fmri.html │ │ │ ├── datasets.html │ │ │ ├── datasets │ │ │ │ ├── basic │ │ │ │ │ ├── caltech.html │ │ │ │ │ ├── cifar.html │ │ │ │ │ ├── euclidean.html │ │ │ │ │ ├── horses.html │ │ │ │ │ ├── mnist.html │ │ │ │ │ └── uci.html │ │ │ │ ├── neuroimaging.html │ │ │ │ └── neuroimaging │ │ │ │ │ ├── fmri.html │ │ │ │ │ ├── mri.html │ │ │ │ │ ├── nifti_viewer.html │ │ │ │ │ ├── simTB.html │ │ │ │ │ └── snp.html │ │ │ ├── demos.html │ │ │ ├── demos │ │ │ │ ├── demos_basic.html │ │ │ │ ├── demos_basic │ │ │ │ │ ├── classifier.html │ │ │ │ │ ├── eval_rbm.html │ │ │ │ │ ├── rbm_mnist.html │ │ │ │ │ └── vae.html │ │ │ │ ├── demos_neuroimaging.html │ │ │ │ └── demos_neuroimaging │ │ │ │ │ ├── rbm_ni.html │ │ │ │ │ └── vae.html │ │ │ ├── inference.html │ │ │ ├── inference │ │ │ │ ├── air.html │ │ │ │ ├── gdir.html │ │ │ │ ├── irvi.html │ │ │ │ └── rws.html │ │ │ ├── models.html │ │ │ ├── models │ │ │ │ ├── darn.html │ │ │ │ ├── deep_helmholtz.html │ │ │ │ ├── distributions.html │ │ │ │ ├── gru.html │ │ │ │ ├── helmholtz.html │ │ │ │ ├── layers.html │ │ │ │ ├── lstm.html │ │ │ │ ├── mlp.html │ │ │ │ ├── rbm.html │ │ │ │ ├── rnn.html │ │ │ │ └── tests │ │ │ │ │ ├── test_darn.html │ │ │ │ │ ├── test_lfmlp.html │ │ │ │ │ ├── test_mlp.html │ │ │ │ │ ├── test_rbm.html │ │ │ │ │ ├── test_rnn.html │ │ │ │ │ └── test_vae.html │ │ │ └── utils │ │ │ │ ├── costs.html │ │ │ │ ├── extra.html │ │ │ │ ├── learning_scheduler.html │ │ │ │ ├── logger.html │ │ │ │ ├── monitor.html │ │ │ │ ├── op.html │ │ │ │ ├── preprocessor.html │ │ │ │ ├── tools.html │ │ │ │ ├── training.html │ │ │ │ └── vis_utils.html │ │ └── index.html │ │ ├── _sources │ │ ├── cortex.txt │ │ ├── demos.txt │ │ ├── index.txt │ │ ├── modules.txt │ │ ├── setup.txt │ │ └── source │ │ │ ├── cortex.analysis.mri.txt │ │ │ ├── cortex.analysis.txt │ │ │ ├── cortex.datasets.basic.txt │ │ │ ├── cortex.datasets.neuroimaging.txt │ │ │ ├── cortex.datasets.txt │ │ │ ├── cortex.demos.demos_basic.txt │ │ │ ├── cortex.demos.demos_neuroimaging.txt │ │ │ ├── cortex.demos.txt │ │ │ ├── cortex.inference.txt │ │ │ ├── cortex.models.tests.txt │ │ │ ├── cortex.models.txt │ │ │ ├── cortex.txt │ │ │ ├── cortex.utils.txt │ │ │ └── modules.txt │ │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── basic.css │ │ ├── classic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── jquery-1.11.1.js │ │ ├── jquery.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── sidebar.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── cortex.html │ │ ├── demos.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── modules.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ ├── setup.html │ │ └── source │ │ ├── cortex.analysis.html │ │ ├── cortex.analysis.mri.html │ │ ├── cortex.datasets.basic.html │ │ ├── cortex.datasets.html │ │ ├── cortex.datasets.neuroimaging.html │ │ ├── cortex.demos.demos_basic.html │ │ ├── cortex.demos.demos_neuroimaging.html │ │ ├── cortex.demos.html │ │ ├── cortex.html │ │ ├── cortex.inference.html │ │ ├── cortex.models.html │ │ ├── cortex.models.tests.html │ │ ├── cortex.utils.html │ │ └── modules.html ├── conf.py ├── demos.rst ├── index.rst ├── make.bat ├── setup.rst └── source │ ├── 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