├── Figure_1 ├── CatStructFields.m ├── extractBehavior.m └── extractTrialDurations.m ├── Figure_3 ├── collect_allTrials_2to7_minLeaves500.m ├── collect_allTrials_reconstructionMultipleTrials.m ├── map_HPC2HPC.m ├── mind_findMinLeaves.m ├── mind_fitFiringFieldsNEW_dimX_manuel.m ├── mind_fitPowerLaw_FunctionSLIM.m ├── mind_makeTiledMovie.m ├── mind_pcaTest.m ├── mind_plotManifoldGradients.m ├── mind_plotTiledFieldsSLIM.m ├── plot_HPC2HPC.m └── run_analysis_allTrials.m ├── Figure_4 ├── buildDoublets.m ├── calcDoubletManifoldCorrelation.m ├── findDoublets.m ├── findTriplets.m ├── makeOutputDoublets_Metamouse.m ├── mind_calcDoubletROC.m ├── mind_calcOptimalROC.m ├── mind_plotDoubletTrajectory.m ├── plotDoublets.m ├── plotSequenceTrialROI.m └── shuffleDoublets_v2.m ├── Figure_S2 └── peak_counterSLIM.m ├── Figure_S4 ├── collect_allTrials_reconstructionMultipleROIs_Function.m └── plot_allTrials_reconstructionMultipleROIs_Function.m ├── Figure_S5 ├── analyzeTaskManifold.m ├── fitManifold2Video.m ├── luminance2HPC.m └── plot_manifold_figure.m ├── Figure_S6 ├── mind_compareTowersAlternationVA.m ├── mind_decodePCAVariable.m ├── mind_makeVAplot.m └── mind_nonlinearDecoding_VarGroup.m ├── Figure_S7 └── plotSequenceTrialROI_multiple.m ├── Figure_S9 ├── makeOutputTriplets_Metamouse.m └── plotTriplets.m ├── Helper ├── MathWorksFileExchange │ ├── distinguishable_colors │ │ ├── distinguishable_colors.m │ │ └── license.txt │ ├── nanconv │ │ ├── license.txt │ │ └── nanconv.m │ ├── shadedErrorBar │ │ ├── LICENSE │ │ ├── README.md │ │ ├── demo_shadedErrorBar.m │ │ ├── exampleImages │ │ │ ├── basic_with_overlay.png │ │ │ ├── mod-handles.png │ │ │ └── multiple_lines.png │ │ └── shadedErrorBar.m │ └── venn │ │ ├── license.txt │ │ └── venn.m ├── NicsCode_clean │ ├── 1_Data_processing │ │ ├── circshift_within_trials.m │ │ ├── extractVariables.m │ │ ├── mind_preprocess.m │ │ └── robustSTD.m │ ├── 3_getSkaggs │ │ ├── generateMetamouse.m │ │ ├── generateMetamouseT7.m │ │ ├── getSkaggs.m │ │ ├── getSkaggs_cutdown.m │ │ ├── plot_exampleTrialsNEW.m │ │ ├── plot_getSkaggs_summarySLIM.m │ │ └── plot_metamouse_seqplot.m │ └── 6_Dependencies │ │ └── computeSkaggsInformation.m ├── TrialLengthFromD.m ├── behav │ ├── analysis │ │ ├── analysisParams.m │ │ ├── logRegressionFromConcatLog2.m │ │ ├── psychometricFit.m │ │ ├── revCorr_logistic.m │ │ └── xMousePyschometric.m │ ├── plotting │ │ └── plotPsychometricCurve_ctrl.m │ └── util │ │ ├── binointervalLP.cc │ │ ├── binointervalLP.mexa64 │ │ ├── binointervalLP.mexmaci64 │ │ ├── binointervalLP.mexw64 │ │ └── selectMouseTrials.m ├── cmap_heatmap3.mat ├── fieldwidth_colormap2.mat ├── generateCrossValSet_v2.m ├── jeff_randomizer.m ├── lputil │ └── errbar.m ├── mind-paper-bb │ ├── .DS_Store │ ├── embedAsFunction.m │ ├── embedding_code │ │ ├── LLEMap.m │ │ ├── LLEMap_gp.m │ │ ├── LLEMap_quick.m │ │ ├── LLEMap_time_block_cv.m │ │ └── tspartition.m │ ├── mindAsFunction.m │ ├── supporting_code │ │ ├── .DS_Store │ │ ├── MyPCA.m │ │ ├── get_landmarks.m │ │ ├── greedyvq.m │ │ ├── kmedoids_d.m │ │ ├── mdscale.m │ │ ├── norm_columns.m │ │ ├── norm_rows.m │ │ └── robustSTD.m │ └── tree_code_v0.3 │ │ ├── BSHNode.m │ │ ├── DForest.m │ │ ├── DTree.m │ │ ├── HPPCARegressionNode.m │ │ ├── HandleVar.m │ │ ├── PPCARegressionNode.m │ │ ├── SplitPCA.m │ │ ├── TreeNode.m │ │ └── parse_args.m ├── mind_findTopROIs.m ├── mind_makeFnameStruct.m ├── mind_nonlinearDecoding_dimX_All.m ├── mind_smoothDimensions.m ├── nieh_barSEM.m ├── nieh_barSEMpaired.m ├── nieh_ci.m ├── nieh_sem.m ├── parseModelingName.m ├── publicationscripts │ ├── FormatDefaults.m │ └── PaneledFigure.m ├── sakfunctions │ └── fiteval.m ├── submitJobs.m └── tankmousevr │ └── experiments │ ├── classes │ └── Choice.m │ └── utility │ └── toBinCenters.m ├── README ├── makeFigures_Figure1.m ├── makeFigures_Figure2.m ├── makeFigures_Figure3.m ├── makeFigures_Figure4.m ├── makeFigures_FigureS1.m ├── makeFigures_FigureS2.m ├── makeFigures_FigureS3.m ├── 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