LICENSE
README.md
pyproject.toml
doc/Makefile
doc/conf.py
doc/documentation.rst
doc/faq.rst
doc/index.rst
doc/install.rst
doc/requirements.txt
doc/using_bmrc.rst
doc/models/dynemo.rst
doc/models/hmm.rst
doc/models/images/dynemo-cost-function.pdf
doc/models/images/dynemo-full-model.jpeg
doc/models/images/dynemo-generative-model.jpeg
doc/models/images/hmm-cost-function.pdf
doc/models/images/hmm-fisher-kernel.pdf
doc/models/images/hmm-generative-model.png
doc/tutorials/1-1_data_loading.py
doc/tutorials/1-2_data_prepare_meg.py
doc/tutorials/1-3_data_prepare_fmri.py
doc/tutorials/1-4_data_time_delay_embedding.py
doc/tutorials/2-1_static_spectra_analysis.py
doc/tutorials/2-2_static_power_analysis.py
doc/tutorials/2-3_static_aec_analysis.py
doc/tutorials/3-1_sliding_window_analysis.py
doc/tutorials/3-2_hmm_training.py
doc/tutorials/3-3_dynemo_training.py
doc/tutorials/3-4_hmm_dynemo_get_inf_params.py
doc/tutorials/4-1_hmm_multitaper_spectra.py
doc/tutorials/4-2_hmm_plotting_meg_networks.py
doc/tutorials/4-3_hmm_summary_stats.py
doc/tutorials/4-4_hmm_fmri_dual_estimation.py
doc/tutorials/4-5_hmm_plotting_fmri_networks.py
doc/tutorials/5-1_dynemo_regression_spectra.py
doc/tutorials/5-2_dynemo_plotting_networks.py
doc/tutorials/5-3_dynemo_mixing_coefs.py
doc/tutorials/6-1_group_contrast.py
doc/tutorials/6-2_group_network_response.py
doc/tutorials/README.rst
envs/README.md
envs/bmrc.yml
envs/fsl.yml
envs/hbaws.yml
envs/osld-2.0-bmrc.yml
envs/osld-2.0-hbaws.yml
envs/osld-2.0.yml
envs/osld-tf-cuda.yml
envs/osld-tf-macos.yml
envs/osld-tf.yml
envs/osld.yml
examples/README.md
examples/decoding/README.md
examples/decoding/get_data.py
examples/decoding/prediction_pipeline.py
examples/decoding/hmm/1_calc_hmm_features.py
examples/decoding/hmm/2_predict_continuous_value.py
examples/decoding/hmm/3_predict_class_label.py
examples/decoding/hmm/README.md
examples/decoding/static/1_calc_static_features.py
examples/decoding/static/2_predict_continuous_value.py
examples/decoding/static/3_predict_class_label.py
examples/decoding/static/README.md
examples/fmri/README.md
examples/fmri/biobank/0_submit_jobs.py
examples/fmri/biobank/1_find_data_files.py
examples/fmri/biobank/2_train_hmm.py
examples/fmri/biobank/3_print_free_energy.py
examples/fmri/biobank/4_dual_estimation.py
examples/fmri/biobank/5_plot_results.py
examples/fmri/biobank/README.md
examples/fmri/hcp/0_submit_jobs.py
examples/fmri/hcp/1_find_data_files.py
examples/fmri/hcp/2_train_hmm.py
examples/fmri/hcp/3_print_free_energy.py
examples/fmri/hcp/4_dual_estimation.py
examples/fmri/hcp/5_plot_results.py
examples/fmri/hcp/README.md
examples/meg/README.md
examples/meg/ae-hmm_rest/0_get_data.py
examples/meg/ae-hmm_rest/1_train_hmm.py
examples/meg/ae-hmm_rest/2_print_free_energy.py
examples/meg/ae-hmm_rest/3_get_inf_params.py
examples/meg/ae-hmm_rest/4_dual_estimation.py
examples/meg/ae-hmm_rest/5_calc_summary_stats.py
examples/meg/ae-hmm_rest/6_plot_networks.py
examples/meg/ae-hmm_rest/README.md
examples/meg/projects/camcan/1_prepare_data.py
examples/meg/projects/camcan/2_submit_jobs.py
examples/meg/projects/camcan/2_train_hmm.py
examples/meg/projects/camcan/3_print_free_energy.py
examples/meg/projects/camcan/4_get_inf_params.py
examples/meg/projects/camcan/5_calc_post_hoc.py
examples/meg/projects/camcan/README.md
examples/meg/projects/notts_movie_opm/dynemo_full-pipeline.py
examples/meg/projects/notts_movie_opm/hmm_full-pipeline.py
examples/meg/projects/notts_movie_opm/static.py
examples/meg/projects/uk_meg_notts/hmm_hierarchical_clustering.py
examples/meg/projects/uk_meg_notts/hmm_tinda.py
examples/meg/tde-dynemo_rest/0_get_data.py
examples/meg/tde-dynemo_rest/1_train_dynemo.py
examples/meg/tde-dynemo_rest/2_print_free_energy.py
examples/meg/tde-dynemo_rest/3_get_inf_params.py
examples/meg/tde-dynemo_rest/4_calc_regression_spectra.py
examples/meg/tde-dynemo_rest/5_calc_summary_stats.py
examples/meg/tde-dynemo_rest/6_plot_networks.py
examples/meg/tde-dynemo_rest/README.md
examples/meg/tde-hmm_rest/0_get_data.py
examples/meg/tde-hmm_rest/1_train_hmm.py
examples/meg/tde-hmm_rest/2_print_free_energy.py
examples/meg/tde-hmm_rest/3_get_inf_params.py
examples/meg/tde-hmm_rest/4_calc_multitaper.py
examples/meg/tde-hmm_rest/5_calc_summary_stats.py
examples/meg/tde-hmm_rest/6_plot_networks.py
examples/meg/tde-hmm_rest/README.md
examples/meg/tde-hmm_task/0_get_data.py
examples/meg/tde-hmm_task/1_train_hmm.py
examples/meg/tde-hmm_task/2_print_free_energy.py
examples/meg/tde-hmm_task/3_get_inf_params.py
examples/meg/tde-hmm_task/4_calc_multitaper.py
examples/meg/tde-hmm_task/5_plot_networks.py
examples/meg/tde-hmm_task/6_evoked_response.py
examples/meg/tde-hmm_task/README.md
examples/plotting/README.md
examples/plotting/aec_abs.py
examples/plotting/aec_sep.py
examples/plotting/basic.py
examples/plotting/coherence_networks_spectra.py
examples/plotting/coherence_networks_spectra_nnmf.py
examples/plotting/giles_parcellation.py
examples/plotting/mean_activity_maps.py
examples/plotting/mean_activity_maps_workbench.py
examples/plotting/power_maps_spectra.py
examples/plotting/power_maps_tde_cov.py
examples/plotting/sensor_topoplot.py
examples/simulation/README.md
examples/simulation/dive_hmm-mvn.py
examples/simulation/dynemo_hmm-mvn.py
examples/simulation/dynemo_hmm-mvn_high-n-modes.py
examples/simulation/dynemo_long-range-dep1.py
examples/simulation/dynemo_long-range-dep2.py
examples/simulation/dynemo_soft-mixing.py
examples/simulation/dyneste_hmm-mvn.py
examples/simulation/dyneste_long-range-dep.py
examples/simulation/hive_hmm-mvn.py
examples/simulation/hmm-poi_hmm-poi.py
examples/simulation/hmm_hmm-mvn.py
examples/simulation/hmm_hmm-mvn_fisher-kernel.py
examples/simulation/mdynemo_hmm-mvn.py
examples/static/calc_power_spectra.py
examples/static/calc_spectra.py
examples/static/plot_aec_maps.py
examples/static/plot_coh_maps.py
examples/static/plot_fc_maps.py
examples/static/plot_power_maps.py
examples/statistics/README.md
examples/statistics/evoked_response.py
examples/statistics/group_difference.py
examples/tinda/README.md
examples/tinda/cycle_duration.py
examples/tinda/hmm_simulation.py
examples/toolbox_paper/README.md
examples/toolbox_paper/ctf_rest/README.md
examples/toolbox_paper/ctf_rest/get_data.py
examples/toolbox_paper/ctf_rest/static_networks.py
examples/toolbox_paper/ctf_rest/tde_dynemo_networks.py
examples/toolbox_paper/ctf_rest/tde_hmm_bursts.py
examples/toolbox_paper/ctf_rest/tde_hmm_networks.py
examples/toolbox_paper/ctf_rest/preproc/1_preprocess.py
examples/toolbox_paper/ctf_rest/preproc/2_fix_smri_files.py
examples/toolbox_paper/ctf_rest/preproc/3_source_reconstruct.py
examples/toolbox_paper/ctf_rest/preproc/4_sign_flip.py
examples/toolbox_paper/ctf_rest/preproc/5_save_data_bursts.py
examples/toolbox_paper/ctf_rest/preproc/6_save_data_networks.py
examples/toolbox_paper/ctf_rest/preproc/README.md
examples/toolbox_paper/elekta_task/README.md
examples/toolbox_paper/elekta_task/ae_hmm.py
examples/toolbox_paper/elekta_task/get_data.py
examples/toolbox_paper/elekta_task/tde_hmm.py
examples/toolbox_paper/elekta_task/preproc/1_preprocess.py
examples/toolbox_paper/elekta_task/preproc/2_source_reconstruct.py
examples/toolbox_paper/elekta_task/preproc/3_sign_flip.py
examples/toolbox_paper/elekta_task/preproc/README.md
osl_dynamics/__init__.py
osl_dynamics/array_ops.py
osl_dynamics.egg-info/PKG-INFO
osl_dynamics.egg-info/SOURCES.txt
osl_dynamics.egg-info/dependency_links.txt
osl_dynamics.egg-info/entry_points.txt
osl_dynamics.egg-info/top_level.txt
osl_dynamics/analysis/__init__.py
osl_dynamics/analysis/connectivity.py
osl_dynamics/analysis/fisher_kernel.py
osl_dynamics/analysis/gmm.py
osl_dynamics/analysis/modes.py
osl_dynamics/analysis/power.py
osl_dynamics/analysis/prediction.py
osl_dynamics/analysis/regression.py
osl_dynamics/analysis/spectral.py
osl_dynamics/analysis/static.py
osl_dynamics/analysis/statistics.py
osl_dynamics/analysis/tinda.py
osl_dynamics/analysis/workbench.py
osl_dynamics/config_api/__init__.py
osl_dynamics/config_api/pipeline.py
osl_dynamics/config_api/wrappers.py
osl_dynamics/data/__init__.py
osl_dynamics/data/base.py
osl_dynamics/data/processing.py
osl_dynamics/data/rw.py
osl_dynamics/data/task.py
osl_dynamics/data/tf.py
osl_dynamics/files/__init__.py
osl_dynamics/files/functions.py
osl_dynamics/files/mask/MNI152_T1_1mm_brain.nii.gz
osl_dynamics/files/mask/MNI152_T1_2mm_brain.nii.gz
osl_dynamics/files/mask/MNI152_T1_8mm_brain.nii.gz
osl_dynamics/files/mask/ParcellationPilot.L.inflated.32k_fs_LR.surf.gii
osl_dynamics/files/mask/ParcellationPilot.L.midthickness.32k_fs_LR.surf.gii
osl_dynamics/files/mask/ParcellationPilot.L.very_inflated.32k_fs_LR.surf.gii
osl_dynamics/files/mask/ParcellationPilot.R.inflated.32k_fs_LR.surf.gii
osl_dynamics/files/mask/ParcellationPilot.R.midthickness.32k_fs_LR.surf.gii
osl_dynamics/files/mask/ParcellationPilot.R.very_inflated.32k_fs_LR.surf.gii
osl_dynamics/files/mask/__init__.py
osl_dynamics/files/mask/ft_8mm_brain_mask.nii.gz
osl_dynamics/files/parcellation/Glasser50_space-MNI152NLin6_res-8x8x8.nii.gz
osl_dynamics/files/parcellation/Glasser52_binary_space-MNI152NLin6_res-8x8x8.nii.gz
osl_dynamics/files/parcellation/Yeo17_8mm.nii.gz
osl_dynamics/files/parcellation/Yeo7_8mm.nii.gz
osl_dynamics/files/parcellation/__init__.py
osl_dynamics/files/parcellation/aal_cortical_merged_8mm_stacked.nii.gz
osl_dynamics/files/parcellation/fMRI_parcellation_ds8mm.nii.gz
osl_dynamics/files/parcellation/fmri_d100_parcellation_with_3PCC_ips_reduced_2mm_ss5mm_ds8mm.nii.gz
osl_dynamics/files/parcellation/fmri_d100_parcellation_with_3PCC_ips_reduced_2mm_ss5mm_ds8mm_adj.nii.gz
osl_dynamics/files/parcellation/fmri_d100_parcellation_with_PCC_reduced_2mm_ss5mm_ds8mm.nii.gz
osl_dynamics/files/parcellation/fmri_d100_parcellation_with_PCC_tighterMay15_v2_6mm_exclusive.nii.gz
osl_dynamics/files/parcellation/fmri_d100_parcellation_with_PCC_tighterMay15_v2_8mm.nii.gz
osl_dynamics/files/parcellation/giles_39_binary.nii.gz
osl_dynamics/files/scanner/__init__.py
osl_dynamics/files/scanner/ctf275_channel_names.npy
osl_dynamics/files/scanner/neuromag306_channel_names.npy
osl_dynamics/files/scanner/layouts/4D148.lay
osl_dynamics/files/scanner/layouts/4D248.lay
osl_dynamics/files/scanner/layouts/4D248_helmet.lay
osl_dynamics/files/scanner/layouts/4D248_helmet.outline
osl_dynamics/files/scanner/layouts/CTF151.lay
osl_dynamics/files/scanner/layouts/CTF151_helmet.lay
osl_dynamics/files/scanner/layouts/CTF151_helmet.outline
osl_dynamics/files/scanner/layouts/CTF275.lay
osl_dynamics/files/scanner/layouts/CTF275_helmet.lay
osl_dynamics/files/scanner/layouts/CTF275_helmet.outline
osl_dynamics/files/scanner/layouts/neuromag122cmb.lay
osl_dynamics/files/scanner/layouts/neuromag122planar.lay
osl_dynamics/files/scanner/layouts/neuromag306all.lay
osl_dynamics/files/scanner/layouts/neuromag306all_helmet.lay
osl_dynamics/files/scanner/layouts/neuromag306all_helmet.outline
osl_dynamics/files/scanner/layouts/neuromag306cmb.lay
osl_dynamics/files/scanner/layouts/neuromag306cmb_helmet.lay
osl_dynamics/files/scanner/layouts/neuromag306cmb_helmet.outline
osl_dynamics/files/scanner/layouts/neuromag306mag.lay
osl_dynamics/files/scanner/layouts/neuromag306mag_helmet.lay
osl_dynamics/files/scanner/layouts/neuromag306mag_helmet.outline
osl_dynamics/files/scanner/layouts/neuromag306planar.lay
osl_dynamics/files/scanner/layouts/neuromag306planar_helmet.lay
osl_dynamics/files/scanner/layouts/neuromag306planar_helmet.outline
osl_dynamics/files/scene/__init__.py
osl_dynamics/files/scene/mode_scene.scene
osl_dynamics/glm/__init__.py
osl_dynamics/glm/base.py
osl_dynamics/glm/ols.py
osl_dynamics/glm/permutation.py
osl_dynamics/inference/__init__.py
osl_dynamics/inference/callbacks.py
osl_dynamics/inference/initializers.py
osl_dynamics/inference/layers.py
osl_dynamics/inference/metrics.py
osl_dynamics/inference/modes.py
osl_dynamics/inference/optimizers.py
osl_dynamics/inference/regularizers.py
osl_dynamics/inference/tf_ops.py
osl_dynamics/models/__init__.py
osl_dynamics/models/dive.py
osl_dynamics/models/dynemo.py
osl_dynamics/models/dyneste.py
osl_dynamics/models/hive.py
osl_dynamics/models/hmm.py
osl_dynamics/models/hmm_poi.py
osl_dynamics/models/inf_mod_base.py
osl_dynamics/models/mdynemo.py
osl_dynamics/models/mod_base.py
osl_dynamics/models/obs_mod.py
osl_dynamics/simulation/__init__.py
osl_dynamics/simulation/base.py
osl_dynamics/simulation/hmm.py
osl_dynamics/simulation/hsmm.py
osl_dynamics/simulation/mar.py
osl_dynamics/simulation/mvn.py
osl_dynamics/simulation/poi.py
osl_dynamics/simulation/sm.py
osl_dynamics/utils/__init__.py
osl_dynamics/utils/misc.py
osl_dynamics/utils/model.py
osl_dynamics/utils/parcellation.py
osl_dynamics/utils/plotting.py
osl_dynamics/utils/topoplots.py