├── +MEGsim ├── AB_epoch2logical.m ├── AB_get_bad_sections.m ├── AB_get_source_timecourses.m ├── AB_get_source_timecourses_recon.m ├── Contents.m ├── LCMV_beamformer.m ├── README.txt ├── assign_inputs.m ├── check_filename_is_clear.m ├── compute_recon.m ├── copy_meeg.m ├── create_new_meeg_object.m ├── do_source_recon_using_osl.m ├── find_MEG_chantypes.m ├── find_nearest_coordinate.m ├── get_oil_dipole_magnitudes.m ├── get_orientations_from_mesh.m ├── get_source_data.m ├── inverse_affine_transform_points.m ├── inverse_transform_dipole_orientation.m ├── invert_affine_transformation.m ├── isposdef.m ├── license.txt ├── make_debugging_plots.m ├── megchannels.m ├── mwpinv.m ├── neuromag_empty_room_noise_covariance.mat ├── randnorm.m ├── setup_source_recon_params.m ├── setup_source_recon_params_for_blank_recon.m ├── simulate_MEG_signal.m └── transform_dipole_orientation.m ├── +osl_conf ├── default.m ├── disable_warnings.m ├── find.m ├── get_userpath.m ├── path_backup.m ├── path_restore.m ├── read.m ├── set.m ├── unset.m └── write.m ├── +osl_util ├── bytesize.m ├── contains.m ├── filewrite.m ├── genpath_exclude.m ├── isdir.m ├── isfile.m ├── mapfun.m ├── mkdir.m ├── repstruct.m ├── structkvfun.m └── structmerge.m ├── +report ├── bad_channels.m ├── bad_segments.m ├── bad_trials.m ├── coreg.m ├── events.m ├── headpos.m ├── ica.m ├── save_figs.m ├── spectrogram.m └── trial_timings.m ├── .gitignore ├── HCP ├── HCP_MNI152_T1_8mm_brain.nii.gz ├── HCP_MNI152_T1_8mm_brain_mask.nii.gz ├── HCP_beamform.m ├── HCP_create_ft_masks.m ├── HCP_sourcemodel_to_nii.m └── README.md ├── README.md ├── africa ├── component_topoplot.m ├── osl_africa.m ├── private │ ├── compute_metrics.m │ ├── identify_artefactual_components_auto.m │ └── identify_artefactual_components_manual.m └── sensors_topoplot.m ├── channelconnectivity.m ├── cleanup.sh ├── cluster4d_batch.m ├── cluster4d_dist.m ├── detect_eyeblinks.m ├── examples ├── .gitignore ├── old │ ├── HCP_example_beamforming_script.m │ ├── HCP_example_motortask_script.m │ ├── README.md │ ├── gen_uncorrelated_signals.m │ ├── osl_example_continuous_oat.m │ ├── osl_example_group_sensorspace_oat.m │ ├── osl_example_oil.m │ ├── osl_example_preprocessing_eeg.m │ ├── osl_example_sensorspace_continuous_oat.m │ ├── osl_example_simulate_MEG_data.m │ ├── setup_group_oat_example.m │ └── setup_multisession_group_oat_example.m ├── osl_example_africa.m ├── osl_example_beamforming.m ├── osl_example_coregistration.m ├── osl_example_data_structures.m ├── osl_example_decoding.m ├── osl_example_hcp.m ├── osl_example_hmmmar.m ├── osl_example_import_CTF_resting.m ├── osl_example_intro_to_meg.m ├── osl_example_maxfilter.m ├── osl_example_oat_1_sensorspace.m ├── osl_example_oat_1_sensorspace_v2.m ├── osl_example_oat_2_sensorspace_tf.m ├── osl_example_oat_3_sourcespace.m ├── osl_example_oat_4_group.m ├── osl_example_osleyes.m ├── osl_example_oslview.m ├── osl_example_parcellation.m ├── osl_example_preprocessing_detect_artefacts.m ├── osl_example_preprocessing_manual.m ├── osl_example_preprocessing_opt.m ├── osl_example_preprocessing_simple.m ├── osl_example_roinets_1_synthetic.m ├── osl_example_roinets_2_manual.m ├── osl_example_roinets_3_group.m ├── osl_example_surrogate.m └── osl_example_workbench.m ├── eyeblink_correct_detect.m ├── eyeblink_hb_correct_remove.m ├── find_best_voxs_mean.m ├── find_erf_best_voxs_mean.m ├── functionSignatures.json ├── git-replace.sh ├── git-update.sh ├── normalise_sensor_data.m ├── oat ├── oat_cluster_perm_sensor_tf.m ├── oat_cluster_permutation_testing.m ├── oat_consolidate_results.m ├── oat_convert_trialwise_to_fieldtrip.m ├── oat_find_max_stats.m ├── oat_first_level_stats_report.m ├── oat_get_sensordata.m ├── oat_group_level_stats_report.m ├── oat_load_results.m ├── oat_merge_first_levels.m ├── oat_output_roi_stats.m ├── oat_plot_hmm_states.m ├── oat_plot_vox_stats.m ├── oat_prepare_source_recon.m ├── oat_run_first_level.m ├── oat_run_first_level_continuous.m ├── oat_run_first_level_epoched.m ├── oat_run_group_level.m ├── oat_run_source_recon.m ├── oat_run_source_recon_sensorspace.m ├── oat_run_subject_level.m ├── oat_save_nii_stats.m ├── oat_save_results.m ├── oat_save_spm_stats.m ├── oat_setup_designmatrix.m ├── oat_source_recon_report.m ├── oat_stats_combine_grads.m ├── oat_stats_multiplotER.m ├── oat_stats_multiplotFreq.m ├── oat_stats_multiplotSpec.m ├── oat_stats_multiplotTFR.m ├── osl_check_oat.m ├── osl_load_oat.m ├── osl_prepare_oat_batch.m ├── osl_reassemble_oat.m ├── osl_run_oat.m ├── osl_run_parallel_oat.m └── osl_save_oat.m ├── oil ├── oil_concat_subs.m ├── oil_ica_maps_group_stats.m ├── oil_ica_preproc.m ├── oil_perform_ica.m ├── oil_run_first_level_ica.m ├── oil_run_group_level_ica.m ├── oil_save_nii_ica_maps.m ├── oil_single_subject_maps.m ├── osl_check_oil.m ├── osl_run_oil.m ├── osl_save_oil.m └── osl_setup_oil.m ├── old ├── demo_coape_vs_acope.m ├── osl_bad_sections.m ├── osl_badchans.m ├── osl_detect_badchannel.m ├── osl_envcorr.m ├── osl_make_standalone.m ├── osl_make_surf_movie.m ├── osl_render_vols_to_surf.m ├── osl_seedcorr.m └── upgrade.sh ├── opt ├── new_opt.m ├── opt_consolidate_results.m ├── opt_gather_results.m ├── opt_load_results.m ├── opt_report_summary_plots.m ├── opt_save_results.m ├── osl_check_opt.m ├── osl_load_opt.m ├── osl_run_maxfilter.m ├── osl_run_opt.m └── standard_pipeline.m ├── osl_apply_parcellation.m ├── osl_baseline_correct.m ├── osl_braingraph.m ├── osl_change_spm_eeg_data.m ├── osl_check_eigenspectrum.m ├── osl_check_for_zeros.m ├── osl_check_installation.m ├── osl_cluster_permutation_testing.m ├── osl_clustertf.m ├── osl_concat_spm_eeg_chans.m ├── osl_concat_subs.m ├── osl_convert_script.m ├── osl_cov.m ├── osl_detect_artefacts.m ├── osl_edit_fid.m ├── osl_envelope.m ├── osl_epoch.m ├── osl_erase_trigger_artefact.m ├── osl_filelist.m ├── osl_filter.m ├── osl_forward_model.m ├── osl_get_recon_timecourse.m ├── osl_headmodel.m ├── osl_hilbenv.m ├── osl_hmm_toolbox ├── HMM_demo_simulations.m ├── conda.m ├── gumbel_infer_dynamic_model.m ├── load_results_dynamic_model_gamma.m ├── load_results_gumbel.m ├── osl_hmm_groupinference.m ├── osl_hmm_groupinference_parcels_old.m ├── osl_hmm_infer.m ├── osl_hmm_plotstatepath.m ├── osl_hmm_statemaps.m ├── osl_hmm_stats.m ├── osl_hmm_stats_by_subject.m ├── osl_hmm_subjectinference.m ├── osl_teh_prepare_data.m ├── osl_teh_prepare_raw_data.m ├── run_elife_analysis.m ├── run_ica_analysis.m ├── spm_eeg_epochs_osl.m ├── teh_epoch_multicond_statetcs.m ├── teh_epoch_statetcs.m ├── teh_graph_gmm_fit.m ├── teh_groupinference_parcels.m ├── teh_spectral_nnmf.m ├── vbrt_infer_dynamic_model.m ├── vbrt_infer_dynamic_model_gamma.m └── vbrt_infer_gumbel.m ├── osl_import.m ├── osl_inverse_mne_weights.m ├── osl_inverse_model.m ├── osl_isactive.m ├── osl_lightbox.m ├── osl_maxfilter.m ├── osl_memblocks.m ├── osl_merge_first_levels.m ├── osl_merge_meeg.m ├── osl_mnicoords2ind.m ├── osl_mnicoords2mnimask.m ├── osl_mnimask2mnicoords.m ├── osl_mniparcellation2mnicoords.m ├── osl_movavg.m ├── osl_movcorr.m ├── osl_normalise_sensor_data.m ├── osl_parc_permutation_testing.m ├── osl_prepare_oat_batch.m ├── osl_publish.m ├── osl_quick_spectra.m ├── osl_recompile_fieldtrip.m ├── osl_rejectvisual.m ├── osl_remove_jumps.m ├── osl_render4D.m ├── osl_report_add_sub_report.m ├── osl_report_add_text.m ├── osl_report_print_figs.m ├── osl_report_set_figs.m ├── osl_report_setup.m ├── osl_report_write.m ├── osl_resample_meeg.m ├── osl_resolve_sign_ambiguity.m ├── osl_shutdown.m ├── osl_simulate_MEG_data.m ├── osl_simulate_envelopes.m ├── osl_source_variance.m ├── osl_spm_resample.m ├── osl_spmfun.m ├── osl_startup.m ├── osl_stats_multiplotER.m ├── osl_stats_multiplotTFR.m ├── osl_surrogate.m ├── osl_tf_transform.m ├── osl_tracker_read_file.m ├── osl_upgrade.m ├── osldir.m ├── oslview ├── oslview.m ├── oslview.mat └── oslview_filter.m ├── plot_hmm.m ├── plot_vector.m ├── rhino ├── icp.m ├── osl_RAC.m ├── osl_pol_preproc.m ├── pointTriangleDistance.m ├── rhino.m ├── rhino_bruteforce.m ├── rhino_cperror.m ├── rhino_display.m ├── rhino_gradientdescent.m ├── rhino_icp.m ├── rhino_manual.m ├── rhino_rigidtransform.m └── rhino_select.m ├── run_multistart_hmm.m ├── setup_beamformer_designmatrix.m ├── setup_mask_indices.m ├── setup_std_masks.m ├── spm-changes ├── altered_fieldtrip_and_spm_files.md ├── ft_headmodel_localspheres.m ├── ft_read_event_4osl.m ├── ft_select_range.m ├── ft_singleplotER.m ├── ft_singleplotTFR.m ├── functionSignatures.json ├── read_trigger_4osl.m ├── spm-beamforming-toolbox │ ├── bf_copy.m │ ├── bf_data.m │ ├── bf_example_samgam_mv.m │ ├── bf_features.m │ ├── bf_features_contcov.m │ ├── bf_features_cov.m │ ├── bf_features_cov_bysamples.m │ ├── bf_features_csd.m │ ├── bf_features_regmulticov.m │ ├── bf_inverse.m │ ├── bf_inverse_deflect.m │ ├── bf_inverse_dics.m │ ├── bf_inverse_eloreta.m │ ├── bf_inverse_lcmv.m │ ├── bf_inverse_lcmv_multicov.m │ ├── bf_inverse_minimumnorm.m │ ├── bf_inverse_mne_adaptive.m │ ├── bf_load.m │ ├── bf_output.m │ ├── bf_output_image_cfGLM.m │ ├── bf_output_image_dics.m │ ├── bf_output_image_filtcorr.m │ ├── bf_output_image_gain.m │ ├── bf_output_image_mv.m │ ├── bf_output_image_pac.m │ ├── bf_output_image_powcorr.m │ ├── bf_output_image_power.m │ ├── bf_output_montage.m │ ├── bf_output_montage_osl.m │ ├── bf_output_sourcedata_robust.m │ ├── bf_pipeline_DICS_coherence.m │ ├── bf_pipeline_DICS_power.m │ ├── bf_pipeline_DeFlect.m │ ├── bf_pipeline_LCMV_all_mesh_sources.m │ ├── bf_pipeline_LCMV_imaging.m │ ├── bf_pipeline_LCMV_source_extraction.m │ ├── bf_pipeline_MVAR_activation_vs_baseline.m │ ├── bf_pipeline_MVAR_two_conditions.m │ ├── bf_pipeline_Minimum_Norm.m │ ├── bf_pipeline_eLORETA.m │ ├── bf_regularise_mantrunc.m │ ├── bf_regularise_manual.m │ ├── bf_regularise_minkatrunc.m │ ├── bf_regularise_roi.m │ ├── bf_save.m │ ├── bf_sources.m │ ├── bf_sources_grid.m │ ├── bf_sources_grid_phantom.m │ ├── bf_sources_mesh.m │ ├── bf_sources_mni_coords.m │ ├── bf_sources_voi.m │ ├── bf_std_fields.m │ ├── bf_write.m │ ├── bf_write_gifti.m │ ├── bf_write_nifti.m │ ├── bf_write_spmeeg.m │ ├── bf_write_spmeeg_osl.m │ ├── private │ │ ├── DeFleCT.m │ │ ├── MNestimator.m │ │ ├── bf_fuse_lf.m │ │ ├── ft_inverse_beamformer_dics.m │ │ ├── gen_bf_ttest.m │ │ ├── get_data_features.m │ │ ├── mkfilt_eloreta_v2.m │ │ ├── output_image_mv_cva.m │ │ ├── pinv_plus.m │ │ ├── spm_eeg_inv_get_vol_sens.m │ │ └── spm_pca_order.m │ ├── spm_beamforming.m │ ├── spm_spm-beamforming-toolbox.m │ └── tbx_cfg_bf.m ├── spm_eeg_inv_mesh_ui.m ├── spm_eeg_montage.m ├── topoplot_common.m ├── undobalancing_giles.m └── undobalancing_original.m ├── spm_eeg_convert_4osl.m ├── spm_eeg_inv_checkdatareg_3Donly.m ├── spm_pca_order.m └── util ├── add_montage.m ├── bandpass.m ├── bluewhitered.m ├── boxcox1.m ├── ca.m ├── convert_back_to_time.m ├── demean.m ├── devar.m ├── dirTree.m ├── dirichlet_entropy.m ├── event_to_sample.m ├── exportfig.m ├── fftconv.m ├── find_ROI_centres.m ├── findcluster.m ├── fix_fslview.app └── Contents │ ├── Info.plist │ ├── MacOS │ └── applet │ ├── PkgInfo │ └── Resources │ ├── Scripts │ └── main.scpt │ ├── applet.icns │ ├── applet.rsrc │ └── description.rtfd │ └── TXT.rtf ├── fix_fslview.scpt ├── flame1.m ├── flip_voxels.m ├── freezeColors.m ├── fsleyes.m ├── fslview.m ├── functionSignatures.json ├── gauss.m ├── generate_ar_surrogates.m ├── gesd.m ├── get_cols.m ├── getfullpath.m ├── getmasksize.m ├── glm_fast.m ├── glm_fast_for_meg.m ├── glm_faster_for_meg.m ├── good_samples.m ├── has_montage.m ├── herrorbar.m ├── hilbenv.m ├── hist2d.m ├── ho.m ├── initialise_fsl.m ├── initialise_spm.m ├── initialise_workbench.m ├── inside_contour.m ├── make_colorbar.m ├── matrix2vols.m ├── max2d.m ├── max3d.m ├── moving.m ├── nearest_vec.m ├── normalise.m ├── ols.m ├── openfif.m ├── opengz.m ├── opennii.m ├── ortho_overlay_act.m ├── osl_change_path.m ├── osl_colormap.m ├── osl_commit_montage.m ├── osl_gauss.m ├── 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