├── .github └── workflows │ ├── build_docs.yml │ └── run_tests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CITATION.cff ├── LICENSE.md ├── README.md ├── cedalion.def ├── docs ├── CHANGELOG.md ├── LICENSE.md ├── Makefile ├── _static │ ├── IBS_Logo_sm.png │ └── css │ │ └── rtd_fixes.css ├── _templates │ ├── custom-class-template.rst │ └── custom-module-template.rst ├── community │ ├── contributing_code.md │ ├── contributors.md │ ├── index.md │ └── toolboxes.md ├── conf.py ├── data_io │ └── index.rst ├── environments.md ├── examples.rst ├── examples │ └── Makefile ├── getting_started │ ├── colab_setup.md │ ├── contributing_code │ │ ├── contributing_code.md │ │ ├── dirs_parent.png │ │ └── dirs_src.png │ ├── index.md │ └── installation.md ├── image_reco │ └── index.rst ├── img │ ├── IBS_clr_small.png │ ├── cedalion_frontpage.png │ ├── colab │ │ ├── colab_cell.png │ │ ├── colab_fileaccess.png │ │ ├── colab_fileupload.jpg │ │ └── gdrive_prompt.png │ ├── image_recon_multiview.gif │ ├── image_recon_multiview_scalp.gif │ ├── image_recon_view.gif │ ├── image_recon_view_still.png │ ├── recording │ │ ├── dataarray_indexing_overview.png │ │ ├── ndarray.png │ │ └── rec_container_overview.png │ ├── scalp_plot_ts.gif │ ├── special_thanks.png │ └── time_series_guiexample.png ├── index.md ├── machine_learning │ └── index.rst ├── make.bat ├── physio │ └── index.rst ├── plot_vis │ └── index.rst ├── references.bib ├── references.rst ├── sigproc │ └── index.rst └── synth │ └── index.rst ├── environment_dev.yml ├── environment_doc.yml ├── examples ├── augmentation │ ├── 61_synthetic_artifacts_example.ipynb │ └── 62_synthetic_hrfs_example.ipynb ├── getting_started_io │ ├── 00_test_installation.ipynb │ ├── 10_xarray_datastructs_fnirs.ipynb │ ├── 11_recording_container.ipynb │ ├── 13_data_structures_intro.ipynb │ └── 34_store_hrfs_in_snirf_file.ipynb ├── head_models │ ├── 40_image_reconstruction.ipynb │ ├── 41_photogrammetric_optode_coregistration.ipynb │ ├── 42_1010_system.ipynb │ ├── 43_crs_and_headmodel.ipynb │ ├── 44_head_models.ipynb │ ├── 45_parcel_sensitivity.ipynb │ └── 46_precompute_fluence.ipynb ├── machine_learning │ ├── 50_finger_tapping_lda_classification.ipynb │ └── 51_multimodal_source_decomposition_on_synthetic_fNIRS-EEG_data.ipynb ├── misc │ ├── 14_xarray_indexing.ipynb │ ├── PCArecurse_motion_correct.ipynb │ ├── align_ninja_to_colin.ipynb │ ├── finger_tapping_full_pipeline.ipynb │ ├── head_models.ipynb │ └── registration.ipynb ├── modeling │ ├── 31_glm_basis_functions.ipynb │ ├── 32_glm_fingertapping_example.ipynb │ ├── 33_glm_illustrative_example.ipynb │ ├── 34_glm_fingertapping_nans.ipynb │ └── 35_statsmodels_overview.ipynb ├── physio │ └── 71_ampd_heartbeat.ipynb ├── plots_visualization │ └── 12_plots_example.ipynb ├── signal_quality │ ├── 20_scalp_coupling_index.ipynb │ ├── 21_data_quality_and_pruning.ipynb │ ├── 22_motion_artefacts_and_correction.ipynb │ ├── 23_sampling_corrections.ipynb │ └── 24_downweighting_noisy_channels.ipynb ├── sketch.ipynb └── splineSG_motion_correct.ipynb ├── install_nirfaster.sh ├── pyproject.toml ├── scripts ├── build_docs.sh ├── colab_setup.py ├── prefetch_docs_datasets.py └── run_tasks.py ├── src └── cedalion │ ├── __init__.py │ ├── data │ ├── 10-5-System_Mastoids_EGI129.tsv │ ├── __init__.py │ ├── measfunc_table.npy │ ├── ninja_cap_probe │ │ ├── fullhead_56x144_System2_landmarks.tsv │ │ ├── fullhead_56x144_System2_measlist.tsv │ │ └── fullhead_56x144_System2_optodes.tsv │ ├── ninja_uhd_cap_probe │ │ ├── fullhead_164x496_landmarks.tsv │ │ ├── fullhead_164x496_measlist.tsv │ │ └── fullhead_164x496_optodes.tsv │ └── prahl_absorption_spectrum.tsv │ ├── dataclasses │ ├── __init__.py │ ├── accessors.py │ ├── geometry.py │ ├── recording.py │ └── schemas.py │ ├── datasets.py │ ├── errors.py │ ├── geometry │ ├── __init__.py │ ├── landmarks.py │ ├── photogrammetry │ │ ├── __init__.py │ │ └── processors.py │ ├── registration.py │ ├── segmentation.py │ └── utils.py │ ├── imagereco │ ├── __init__.py │ ├── forward_model.py │ ├── solver.py │ ├── tissue_properties.py │ └── utils.py │ ├── io │ ├── __init__.py │ ├── anatomy.py │ ├── bids.py │ ├── forward_model.py │ ├── nirs.py │ ├── photogrammetry.py │ ├── probe_geometry.py │ └── snirf.py │ ├── math │ ├── __init__.py │ ├── ar_irls.py │ ├── ar_model.py │ ├── resample.py │ └── stats_helpers.py │ ├── models │ ├── __init__.py │ └── glm │ │ ├── __init__.py │ │ ├── basis_functions.py │ │ ├── design_matrix.py │ │ └── solve.py │ ├── nirs.py │ ├── physunits.py │ ├── plots.py │ ├── sigdecomp │ ├── ERBM.py │ ├── ICA_EBM.py │ ├── __init__.py │ ├── dummy.py │ ├── measfunc_table.npy │ ├── multimodal │ │ ├── cca_models.py │ │ ├── mspoc.py │ │ ├── tcca_models.py │ │ └── utils_multimodal_models.py │ └── spoc.py │ ├── sigproc │ ├── __init__.py │ ├── epochs.py │ ├── frequency.py │ ├── motion_correct.py │ ├── physio.py │ ├── quality.py │ └── tasks.py │ ├── sim │ ├── __init__.py │ ├── synthetic_artifact.py │ ├── synthetic_hrf.py │ └── synthetic_utils.py │ ├── tasks.py │ ├── testing.py │ ├── typing.py │ ├── utils.py │ ├── validators.py │ ├── vis │ ├── __init__.py │ ├── plot_probe.py │ ├── plot_sensitivity_matrix.py │ └── time_series.py │ ├── vtktutils.py │ └── xrutils.py └── tests ├── test_bids.py ├── test_dataclasses_geometry.py ├── test_geodesics.py ├── test_imagereco_forward_model.py ├── test_imagereco_solver.py ├── test_io_forward_model.py ├── test_io_nirs.py ├── test_io_photogrammetry.py ├── test_io_probe_geometry.py ├── test_io_snirf.py ├── test_labeled_points.py ├── test_model_glm_design_matrix.py ├── test_nirs.py ├── test_points_accessors.py ├── test_sigdecomp.py ├── test_sigdecomp_dummy.py ├── test_sigdecomp_multimodal_cca.py ├── test_sigdecomp_multimodal_mspoc.py ├── test_sigdecomp_multimodal_utils.py ├── test_sigproc_epochs.py ├── test_sigproc_frequency.py ├── test_sigproc_motion_correct.py ├── test_sigproc_quality.py ├── test_synthetic_hrf.py ├── test_utils.py ├── test_vtkutils.py └── test_xrutils.py 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