├── +microstate ├── +external │ ├── FastICA_25 │ │ ├── Contents.m │ │ ├── fastica.m │ │ ├── fpica.m │ │ ├── pcamat.m │ │ ├── remmean.m │ │ └── whitenv.m │ ├── HCP230 │ │ └── atlas │ │ │ └── hcp230.mat │ ├── HMM-MAR-master │ │ ├── LICENSE │ │ ├── README.md │ │ ├── cvhmmmar.m │ │ ├── eval │ │ │ ├── GammaEntropy.m │ │ │ ├── GammaavLL.m │ │ │ ├── checkhmmmar.m │ │ │ ├── evalfreeenergy.m │ │ │ ├── evalfreeenergylogistic.m │ │ │ ├── hmmerror.m │ │ │ └── loglikelihoodofH.m │ │ ├── examples │ │ │ ├── CerebralCortex2018.m │ │ │ ├── NatComms2018_fullpipeline.m │ │ │ ├── NeuroImage2016_runHMM.m │ │ │ ├── PNAS2017_fullpipeline.m │ │ │ ├── run_HMMMAR.m │ │ │ ├── run_HMMMAR_2.m │ │ │ └── run_TUDA.m │ │ ├── hmmdecode.m │ │ ├── hmmdual.m │ │ ├── hmmfe.m │ │ ├── hmmmar.m │ │ ├── hmmpred.m │ │ ├── hmmtestretest.m │ │ ├── plot │ │ │ ├── gammaRasterPlot.m │ │ │ ├── plot_Gamma.m │ │ │ └── plot_hmmspectra.m │ │ ├── simulate │ │ │ ├── simgamma.m │ │ │ ├── simgamma_ltd.m │ │ │ ├── simgauss.m │ │ │ ├── simhmmmar.m │ │ │ └── simmar.m │ │ ├── spectral │ │ │ ├── check_mar_spectra.m │ │ │ ├── hmmplv.m │ │ │ ├── hmmspectramar.m │ │ │ ├── hmmspectramt.m │ │ │ ├── hmmspectratde.m │ │ │ ├── hmmtimefreq.m │ │ │ ├── relspect.m │ │ │ ├── spectbands.m │ │ │ ├── spectdecompose.m │ │ │ ├── spectrerr.m │ │ │ └── subrutpdc.m │ │ ├── stochastic │ │ │ ├── hmmsdecode.m │ │ │ ├── hmmsinit.m │ │ │ ├── hmmsinitg.m │ │ │ ├── hmmsinith.m │ │ │ ├── hmmstrain.m │ │ │ ├── state_snew.m │ │ │ └── states_supdate.m │ │ ├── task │ │ │ ├── cluster_decoding.m │ │ │ ├── monitoring │ │ │ │ ├── getAccuracy.m │ │ │ │ ├── getBehAssociation.m │ │ │ │ └── getSynchronicity.m │ │ │ ├── standard_classification.m │ │ │ ├── standard_classifier_test.m │ │ │ ├── standard_classifier_train.m │ │ │ ├── standard_decoding.m │ │ │ ├── standard_encoding.m │ │ │ ├── tucacv.m │ │ │ ├── tucatrain.m │ │ │ ├── tudabeta.m │ │ │ ├── tudacv.m │ │ │ ├── tudadecode.m │ │ │ ├── tudaencoding.m │ │ │ ├── tudaomega.m │ │ │ ├── tudaregressbeh.m │ │ │ ├── tudasparsify.m │ │ │ ├── tudatrain.m │ │ │ └── utils │ │ │ │ ├── LDApredict.m │ │ │ │ ├── continuous_prediction_2class.m │ │ │ │ ├── convertToMultinomial.m │ │ │ │ ├── decorrelateDesignMatrix.m │ │ │ │ ├── encodertrain.m │ │ │ │ ├── fitEquivUnsupervisedModel.m │ │ │ │ ├── group_accuracy_significance.m │ │ │ │ ├── iseuclidean.m │ │ │ │ ├── multinomLogRegPred.m │ │ │ │ ├── preproc4hmm.m │ │ │ │ ├── standard_decoding_permutations.m │ │ │ │ └── tudacv_permutations.m │ │ ├── train │ │ │ ├── fb_Gamma_inference.m │ │ │ ├── hmmhsinit.m │ │ │ ├── hmmmar_init.m │ │ │ ├── hmmperturb.m │ │ │ ├── hmmrotatepca.m │ │ │ ├── hmmtrain.m │ │ │ ├── hsinference.m │ │ │ ├── hsupdate.m │ │ │ ├── id_Gamma_inference.m │ │ │ ├── initGamma_random.m │ │ │ ├── initGamma_seq.m │ │ │ ├── mlhmmmar.m │ │ │ ├── mlmar.m │ │ │ ├── obs │ │ │ │ ├── updateAlpha.m │ │ │ │ ├── updateBeta.m │ │ │ │ ├── updateOmega.m │ │ │ │ ├── updatePCAparam.m │ │ │ │ ├── updatePsi.m │ │ │ │ ├── updateSigma.m │ │ │ │ └── updateW.m │ │ │ ├── obsinference.m │ │ │ ├── obsinit.m │ │ │ ├── obslike.m │ │ │ ├── obslikelogistic.m │ │ │ └── obsupdate.m │ │ └── utils │ │ │ ├── analysis │ │ │ ├── corrStaticFC.m │ │ │ ├── evokedStateProbability.m │ │ │ ├── explainedvar_PCA.m │ │ │ ├── explainedvar_singleMAR.m │ │ │ ├── getAutoCovMat.m │ │ │ ├── getFractionalOccupancy.m │ │ │ ├── getFuncConn.m │ │ │ ├── getGammaSimilarity.m │ │ │ ├── getMARmodel.m │ │ │ ├── getMaskedTransProbMats.m │ │ │ ├── getMaxFractionalOccupancy.m │ │ │ ├── getMean.m │ │ │ ├── getStartFinish_StateVisits.m │ │ │ ├── getStateIntervalTimes.m │ │ │ ├── getStateLifeTimes.m │ │ │ ├── getStateOnsets.m │ │ │ ├── getSwitchingRate.m │ │ │ ├── getTransProbs.m │ │ │ └── permtestFC.m │ │ │ ├── general │ │ │ ├── chain_dropstates.m │ │ │ ├── clearTPM.m │ │ │ ├── dirichletdiags.m │ │ │ ├── dropstate.m │ │ │ ├── higherorder.m │ │ │ ├── hmmorder.m │ │ │ ├── loadfile.m │ │ │ ├── logisticMarginaliseHMM.m │ │ │ ├── logisticMergeHMM.m │ │ │ ├── meanResiduals.m │ │ │ ├── munkres.m │ │ │ ├── padGamma.m │ │ │ ├── padVP.m │ │ │ ├── project_PSD.m │ │ │ ├── project_hmm.m │ │ │ ├── read_spm_file.m │ │ │ ├── test_script.m │ │ │ ├── test_script_spectra.m │ │ │ └── vpath_to_stc.m │ │ │ ├── hidden_state_inference │ │ │ ├── README.md │ │ │ ├── hidden_state_inference.cpp │ │ │ ├── hidden_state_inference.doxy │ │ │ ├── hidden_state_inference.hpp │ │ │ ├── hidden_state_inference_mx.cpp │ │ │ ├── hidden_state_inference_mx.hpp │ │ │ ├── linux │ │ │ │ ├── install_on_linux.txt │ │ │ │ └── makefile │ │ │ ├── mac │ │ │ │ └── makefile │ │ │ └── src │ │ │ │ └── hidden_state_inference_mx.m │ │ │ ├── internal │ │ │ ├── checkGamma.m │ │ │ ├── checkGammaOverfitting.m │ │ │ ├── checkoptions.m │ │ │ ├── checkoptions_spectra.m │ │ │ ├── checkspelling.m │ │ │ ├── computePandPi.m │ │ │ ├── copyhmm.m │ │ │ ├── data2struct.m │ │ │ ├── formautoregr.m │ │ │ ├── formindexes.m │ │ │ ├── formorders.m │ │ │ ├── getactivestates.m │ │ │ ├── getresiduals.m │ │ │ ├── getresidualslogistic.m │ │ │ ├── rangeerror.m │ │ │ └── versCompatibilityFix.m │ │ │ ├── macro │ │ │ ├── checkdatacell.m │ │ │ ├── loadfile_sub.m │ │ │ ├── removesoptions.m │ │ │ ├── setstateoptions.m │ │ │ ├── setxx.m │ │ │ └── writefile_sub.m │ │ │ ├── math │ │ │ ├── KLtransition.m │ │ │ ├── approximateXi.m │ │ │ ├── dirichlet_kl.m │ │ │ ├── gamma_kl.m │ │ │ ├── gamma_square.m │ │ │ ├── gauss_kl.m │ │ │ ├── hmm_kl.m │ │ │ ├── log_sigmoid.m │ │ │ ├── logdet.m │ │ │ ├── logmvnpdf.m │ │ │ ├── logsumexp.m │ │ │ ├── lowmem_xcorr.m │ │ │ ├── multinomrnd.m │ │ │ ├── normalisem.m │ │ │ ├── randpermNK.m │ │ │ ├── rdiv.m │ │ │ ├── riemannian_dist.m │ │ │ ├── symm_kl_div.m │ │ │ ├── weighted_covariance.m │ │ │ └── wishart_kl.m │ │ │ ├── prediction │ │ │ ├── computeDistMatrix.m │ │ │ ├── computeDistMatrix_AVFC.m │ │ │ └── predictPhenotype.m │ │ │ ├── preproc │ │ │ ├── cleandata4hmm.m │ │ │ ├── computeValidDimensions.m │ │ │ ├── detrenddata.m │ │ │ ├── downsampledata.m │ │ │ ├── embeddata.m │ │ │ ├── embedx.m │ │ │ ├── filterdata.m │ │ │ ├── highdim_pca.m │ │ │ ├── leadingPhEigenvector.m │ │ │ ├── leakcorr.m │ │ │ ├── pcamar_decomp.m │ │ │ ├── pcapred_decomp.m │ │ │ ├── rawsignal2power.m │ │ │ └── standardisedata.m │ │ │ ├── signflip │ │ │ ├── aligntotask.m │ │ │ ├── findflip.m │ │ │ ├── flipdata.m │ │ │ ├── getAllCovMats.m │ │ │ └── getCovMats.m │ │ │ └── testing │ │ │ ├── hmmtest.m │ │ │ ├── hmmtest_epoched.m │ │ │ ├── permtest_aux.m │ │ │ ├── permtest_aux_NPC.m │ │ │ ├── permtestdiff_aux.m │ │ │ ├── permtestmass_NPC.m │ │ │ ├── spectsignificance.m │ │ │ └── specttest.m │ ├── LORETA │ │ ├── LORETA_dipole_positions.mat │ │ ├── README.txt │ │ └── sLORETA_dipole_positions.mat │ ├── boxplot_LT.m │ ├── brewermap │ │ ├── LICENSE.TXT │ │ ├── README.md │ │ ├── brewermap.m │ │ ├── brewermap_plot.m │ │ ├── brewermap_view.m │ │ └── rgb2hex.m │ └── fieldtrip │ │ └── template │ │ ├── anatomy │ │ ├── README │ │ └── inflated.mat │ │ ├── atlas │ │ ├── aal.mat │ │ ├── afni_brick0.mat │ │ ├── afni_brick1.mat │ │ └── brainnetome.mat │ │ └── layout │ │ ├── CTF151.mat │ │ ├── CTF275.mat │ │ ├── EEG1005.mat │ │ ├── biosemi256.mat │ │ └── neuromag306.mat ├── +functions │ ├── DISS.m │ ├── add_options.m │ ├── align_maps2template.m │ ├── average_stats_across_conditions.m │ ├── erp_TANOVA_plot.m │ ├── erp_chi2_plot.m │ ├── exportstruct.m │ ├── importstruct.m │ ├── layout_creator.m │ ├── layout_creator_gui.mlapp │ ├── make_options.m │ ├── map_centroids.m │ ├── map_similarity_funhandle.m │ ├── paired_tanova.m │ ├── pinknoise.m │ ├── process_append.m │ ├── select_time.m │ ├── structappend.m │ ├── tanova.m │ ├── toolbox_path.m │ └── transform_clusterstat.m ├── @cohort │ ├── cluster_global.m │ ├── cluster_globalkoptimum.m │ ├── cluster_globalmaps2individual.m │ ├── cohort.m │ ├── erp_chi2stateprobs.m │ ├── erp_clusterperm_TANOVA.m │ ├── erp_clusterperm_gfp.m │ ├── erp_grandaverage.m │ ├── plot.m │ └── stats_TANOVA.m └── @individual │ ├── calculate_gfp.m │ ├── cluster_alignmaps.m │ ├── cluster_estimatemaps.m │ ├── cluster_get_gfppeaks.m │ ├── cluster_koptimum.m │ ├── cluster_label2maps.m │ ├── define_trials.m │ ├── individual.m │ ├── networks_wpli.m │ ├── plot.m │ ├── preprocess.m │ ├── preprocess_ampenv.m │ ├── preprocess_filter.m │ ├── preprocess_orthogonalize.m │ ├── preprocess_rereference.m │ ├── preprocess_resample.m │ ├── simulate.m │ ├── simulate_data.m │ ├── simulate_seq_markov.m │ ├── simulate_seq_randomwalk.m │ ├── stats_all.m │ ├── stats_autoinformation.m │ ├── stats_complexity.m │ ├── stats_coverage.m │ ├── stats_duration.m │ ├── stats_gev.m │ ├── stats_gfp_peaksfreq.m │ ├── stats_hurst.m │ ├── stats_markov.m │ ├── stats_mutualinformation.m │ ├── stats_occurrence.m │ └── stats_syntax.m ├── .gitattributes ├── LICENSE.md ├── README.md ├── documentation.html └── examples ├── Supplementary_Scripts ├── fieldtrip_preprocess_data_example1.m ├── fieldtrip_preprocess_data_example2.m ├── supp_example2_script_withinsubject.m └── supp_example4_script_make_data.m ├── example1_EEGcanonicalmaps 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