├── .conda └── meta.yaml ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── support-request.md └── workflows │ ├── publish.yml │ ├── style.yml │ └── testbuild.yml ├── .gitignore ├── .readthedocs.yml ├── AUTHORS ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── demos ├── 118_images_files │ ├── 118_animate_RDM.npy │ └── 118_animate_labels.npy ├── 92imageData │ ├── 92_behavRDMs.mat │ ├── 92_brainRDMs.mat │ ├── 92_modelRDMs.mat │ ├── Kriegeskorte_Neuron2008_supplementalData.mat │ ├── faceAnimateInaniClustersRDM.mat │ ├── rdm92_HMAXnatImPatch.mat │ ├── rdm92_V1model.mat │ └── simTruePatterns.mat ├── TemporalSampleData │ ├── meg_sample_data.pkl │ └── preproc_mne_sample_data.py ├── demo_annotated_rdm_plot.ipynb ├── demo_bootstrap.ipynb ├── demo_dataset.ipynb ├── demo_dissimilarities.ipynb ├── demo_eeg.ipynb ├── demo_eeg_data │ ├── Meadows_nsd100annotations_v_v1_devoted-caiman_2_annotations.csv │ ├── annotate.png │ ├── shared0140_nsd11797.png │ ├── shared0936_nsd67830.png │ └── shared0944_nsd68742.png ├── demo_flexible_models.ipynb ├── demo_fmri_custom.ipynb ├── demo_fmri_files │ ├── mur32_stims.png │ └── mur32_tasks.png ├── demo_fmri_nilearn.ipynb ├── demo_fmri_patterns.ipynb ├── demo_fmri_spm.ipynb ├── demo_meg_mne.ipynb ├── demo_model_family.ipynb ├── demo_model_map.ipynb ├── demo_rdm_comparison_scatterplot.ipynb ├── demo_rdm_visualisation_92images.ipynb ├── demo_riemannian.ipynb ├── demo_searchlight_volume.ipynb ├── demo_spikes.ipynb ├── demo_temporal.ipynb ├── demo_unbalanced.ipynb ├── paper_examples │ ├── sim_crossval.ipynb │ ├── sim_crossval.py │ └── sim_mahalanobis.ipynb ├── prepare_demo_fmri_patterns.py └── rdms_inferring │ ├── modelRDMs_A2020.mat │ └── noisyModelRDMs_A2020.mat ├── devops ├── gha.py ├── style_assistant.py └── typing_assistant.py ├── docs ├── Makefile ├── README.md ├── requirements.txt └── source │ ├── TemporalSampleData │ ├── meg_sample_data.pkl │ └── preproc_mne_sample_data.py │ ├── _static │ ├── SoftwareFlowChart.png │ ├── rsatoolbox_workflow.pdf │ └── rsatoolbox_workflow.png │ ├── comparing.rst │ ├── conf.py │ ├── datasets.rst │ ├── demo_annotated_rdm_plot.nblink │ ├── demo_bootstrap.nblink │ ├── demo_dataset.nblink │ ├── demo_dissimilarities.nblink │ ├── demo_eeg.nblink │ ├── demo_flexible_models.nblink │ ├── demo_fmri_files │ ├── mur32_stims.png │ └── mur32_tasks.png │ ├── demo_fmri_nilearn.nblink │ ├── demo_fmri_patterns.nblink │ ├── demo_fmri_spm.nblink │ ├── demo_meg_mne.nblink │ ├── demo_rdm_vis.nblink │ ├── demo_riemannian.nblink │ ├── demo_searchlight.nblink │ ├── demo_spikes.nblink │ ├── demo_temporal.nblink │ ├── demo_unbalanced.nblink │ ├── demos.rst │ ├── distances.rst │ ├── getting_started.rst │ ├── index.rst │ ├── inference.rst │ ├── literature_cited.rst │ ├── model_fitting.rst │ ├── model_specification.rst │ ├── operations.rst │ ├── overview.rst │ ├── rescale_partials.rst │ ├── rsatoolbox.data.base.rst │ ├── rsatoolbox.data.computations.rst │ ├── rsatoolbox.data.dataset.rst │ ├── rsatoolbox.data.noise.rst │ ├── rsatoolbox.data.ops.rst │ ├── rsatoolbox.data.rst │ ├── rsatoolbox.inference.boot_testset.rst │ ├── rsatoolbox.inference.bootstrap.rst │ ├── rsatoolbox.inference.crossvalsets.rst │ ├── rsatoolbox.inference.evaluate.rst │ ├── rsatoolbox.inference.noise_ceiling.rst │ ├── rsatoolbox.inference.result.rst │ ├── rsatoolbox.inference.rst │ ├── rsatoolbox.io.bids.rst │ ├── rsatoolbox.io.fmriprep.rst │ ├── rsatoolbox.io.hdf5.rst │ ├── rsatoolbox.io.meadows.rst │ ├── rsatoolbox.io.mne.rst │ ├── rsatoolbox.io.optional.rst │ ├── rsatoolbox.io.pandas.rst │ ├── rsatoolbox.io.pkl.rst │ ├── rsatoolbox.io.rst │ ├── rsatoolbox.io.spm.rst │ ├── rsatoolbox.model.fitter.rst │ ├── rsatoolbox.model.model.rst │ ├── rsatoolbox.model.rst │ ├── rsatoolbox.rdm.calc.rst │ ├── rsatoolbox.rdm.calc_unbalanced.rst │ ├── rsatoolbox.rdm.combine.rst │ ├── rsatoolbox.rdm.compare.rst │ ├── rsatoolbox.rdm.pairs.rst │ ├── rsatoolbox.rdm.rdms.rst │ ├── rsatoolbox.rdm.rst │ ├── rsatoolbox.rdm.transform.rst │ ├── rsatoolbox.rst │ ├── rsatoolbox.simulation.rst │ ├── rsatoolbox.simulation.sim.rst │ ├── rsatoolbox.util.data_utils.rst │ ├── rsatoolbox.util.descriptor_utils.rst │ ├── rsatoolbox.util.file_io.rst │ ├── rsatoolbox.util.inference_util.rst │ ├── rsatoolbox.util.matrix.rst │ ├── rsatoolbox.util.pooling.rst │ ├── rsatoolbox.util.rdm_utils.rst │ ├── rsatoolbox.util.rst │ ├── rsatoolbox.util.searchlight.rst │ ├── rsatoolbox.util.weighted_mds.rst │ ├── rsatoolbox.vis.colors.rst │ ├── rsatoolbox.vis.icon.rst │ ├── rsatoolbox.vis.model_plot.rst │ ├── rsatoolbox.vis.rdm_plot.rst │ ├── rsatoolbox.vis.rst │ ├── rsatoolbox.vis.scatter_plot.rst │ ├── rsatoolbox.vis.timecourse.rst │ ├── temp_rdm.png │ └── visualization.rst ├── pyproject.toml ├── requirements.txt ├── ruff.toml ├── setup.py ├── src └── rsatoolbox │ ├── __init__.py │ ├── cengine │ ├── __init__.pxd │ ├── __init__.py │ └── similarity.pyx │ ├── data │ ├── __init__.py │ ├── base.py │ ├── computations.py │ ├── dataset.py │ ├── noise.py │ └── ops.py │ ├── inference │ ├── __init__.py │ ├── boot_testset.py │ ├── bootstrap.py │ ├── crossvalsets.py │ ├── evaluate.py │ ├── noise_ceiling.py │ └── result.py │ ├── io │ ├── __init__.py │ ├── bids.py │ ├── fmriprep.py │ ├── hdf5.py │ ├── hrf.py │ ├── meadows.py │ ├── mne.py │ ├── optional.py │ ├── pandas.py │ ├── petnames.py │ ├── pkl.py │ └── spm.py │ ├── model │ ├── __init__.py │ ├── fitter.py │ ├── model.py │ └── model_family.py │ ├── py.typed │ ├── rdm │ ├── __init__.py │ ├── calc.py │ ├── calc_unbalanced.py │ ├── combine.py │ ├── compare.py │ ├── pairs.py │ ├── rdms.py │ └── transform.py │ ├── resources.py │ ├── simulation │ ├── __init__.py │ └── sim.py │ ├── test.py │ ├── util │ ├── __init__.py │ ├── build_rdm.py │ ├── data_utils.py │ ├── descriptor_utils.py │ ├── file_io.py │ ├── inference_util.py │ ├── matrix.py │ ├── pooling.py │ ├── rdm_utils.py │ ├── searchlight.py │ └── weighted_mds.py │ └── vis │ ├── __init__.py │ ├── colors.py │ ├── icon.py │ ├── model_map.py │ ├── model_plot.py │ ├── modelfamily_graph.py │ ├── rdm.mplstyle │ ├── rdm_comparison.py │ ├── rdm_plot.py │ ├── scatter_plot.py │ └── timecourse.py ├── tests ├── __init__.py ├── data │ ├── Meadows_myExp_v_v1_arrangement_1D.mat │ ├── Meadows_myExp_v_v1_cuddly-bunny_3_1D.mat │ ├── Meadows_myExp_v_v1_cuddly-bunny_3_tree.json │ ├── Meadows_twoMaTasks_v_v1_informed-mole_tree.json │ └── README.md ├── requirements.txt ├── test_c.py ├── test_calc_rdm.py ├── test_calc_unbalanced.py ├── test_colors.py ├── test_compare_rdm.py ├── test_crossval.py ├── test_data.py ├── test_data_ops_merge.py ├── test_data_utils.py ├── test_dataset_dataframe.py ├── test_demo.py ├── test_descriptor_utils.py ├── test_inference.py ├── test_io_bids.py ├── test_io_fmriprep.py ├── test_io_hdf5.py ├── test_io_meadows.py ├── test_io_mne.py ├── test_io_pkl.py ├── test_io_spm.py ├── test_model.py ├── test_noise_ceiling.py ├── 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