├── LICENSE ├── README.md ├── docs ├── CNAME ├── FAQ.md ├── _config.yml ├── about.md ├── data-sharing.md ├── detailed-protocol.md └── index.md ├── myconnectome ├── __init__.py ├── config.ini ├── diffusion │ ├── __init__.py │ ├── combine_tracksummaries.py │ ├── compare_diffusion_rsfmri_connectivity.py │ ├── diffusion_clustering.py │ ├── get_seed_sizes.sh │ ├── get_track_summary.py │ ├── mk_dtispace_parcels.py │ ├── register_ecdata.py │ ├── run_all_probtrackx.py │ ├── run_all_tracksumm.py │ ├── run_bedpost.sh │ ├── run_dtifit_combined.sh │ └── setup_bedpost.sh ├── metabolomics │ ├── Make_metabolomics_table.Rmd │ ├── Metabolomics_clustering.Rmd │ ├── README.md │ ├── __init__.py │ └── mk_metabolomics_table.py ├── openfmri │ ├── README.md │ ├── check_data.py │ ├── dcmstack_convert.py │ ├── fix_bvals.py │ ├── fix_bvals_pilot.py │ ├── make_dist.py │ ├── make_dist_dcmstack.py │ ├── merge_fmap.sh │ ├── merge_washu_files.py │ ├── mk_model_files.py │ ├── package_tarfiles.py │ ├── process_stanford.py │ ├── process_washu.py │ ├── rename_washu_files.py │ └── washu_fieldmap.py ├── qa │ ├── PerBaseGCContent.csv │ ├── PerBaseNContent.csv │ ├── PerBaseSeqQuality.csv │ ├── QA_summary_anatomical.ipynb │ ├── QA_summary_diffusion.ipynb │ ├── QA_summary_func.ipynb │ ├── QA_summary_rnaseq.Rmd │ ├── QA_summary_rnaseq.ipynb │ ├── QA_summary_rsfmri.Rmd │ ├── __init__.py │ ├── cocktail party.ipynb │ ├── corr_anat.csv │ ├── corr_func.csv │ ├── myconnectome_func_qa_allsubs.csv │ ├── myconnectome_func_qa_goodsubs.csv │ ├── qa_summary.py │ ├── run_qap_anat.py │ ├── run_qap_func.py │ └── summarize_fastqc_files.py ├── rnaseq-processing │ ├── htseq_cmd.sh │ ├── index_cmd.sh │ ├── process_rnaseq.py │ ├── reorder_cmd.sh │ ├── samtools_cmd.sh │ └── tophat_cmd.sh ├── rnaseq │ ├── GOBS_MyConnectome_analysis.Rmd │ ├── MIR181_vs_affect.py │ ├── Make_rnaseq_table.Rmd │ ├── README.md │ ├── RNAseq_data_preparation.Rmd │ ├── Run_WGCNA.Rmd │ ├── Snyderome_data_preparation.Rmd │ ├── __init__.py │ ├── compare_snyderome_myconnectome.py │ ├── filter_gene_types.py │ ├── get_GOBS_cluster_eigengenes.py │ ├── get_ImmPort_eigengenes.py │ ├── get_WGCNA_DAVID_annotation.py │ ├── get_module_descriptions.py │ ├── gwas_wincorr.R │ ├── mk_gwas_script.sh │ ├── mk_separate_expression_files.py │ ├── mk_wgcna_module_table.py │ ├── predict_svm_behav_rnaseq.py │ ├── predict_svm_behav_wgcna.py │ ├── regress_rin.py │ └── regress_rin_pca.py ├── rsfmri │ ├── Makefile │ ├── README.md │ ├── __init__.py │ ├── aseg_fields.txt │ ├── bct_analyses.m │ ├── circos_selftracking.py │ ├── collapse_module_data.py │ ├── collapse_quic_pcor_data.py │ ├── connectome_similarity_timeseries.py │ ├── extract_datafiles.m │ ├── extract_module_assignments.py │ ├── extract_module_summary.py │ ├── get_corrdata.py │ ├── get_fed_fasted_corr.py │ ├── get_parcel_info.py │ ├── l2_icov.R │ ├── mk_connectome_figures.py │ ├── mk_full_network_graph.py │ ├── mk_mean_corrdata.py │ ├── mk_parcellation_boundaries.py │ ├── mk_participation_index_giftis.py │ ├── mk_renumbered_parcel_file.py │ ├── mk_sorted_adjmatrices.py │ ├── predict_svm_behav_fullcorr.py │ ├── predict_svm_behav_wincorr.py │ ├── quic_density.R │ ├── reorder_adjmtx_by_network.py │ ├── reorder_all_adjmtx_for_netviz.py │ ├── rsfmri_combine_data.py │ ├── rsfmri_get_netstats.py │ ├── rsfmri_get_subcortical_data.py │ ├── run_all_infomap.py │ ├── run_all_quic.py │ ├── statespace.py │ └── subcodes.txt ├── scripts │ ├── bct_analyses.m │ ├── metabolomic_analysis.py │ ├── rnaseq_analysis.py │ ├── rsfmri_analysis.py │ ├── run_everything.py │ └── timeseries_analysis.py ├── surface │ └── setup_workbench_specfile.py ├── taskbehavior │ ├── copy_breathhold_events.py │ ├── mkfiles_task001.py │ ├── mkfiles_task002.py │ ├── mkfiles_task003.py │ ├── mkfiles_task004.py │ └── mkfiles_task005.py ├── taskfmri │ ├── __init__.py │ ├── analyze_task_corr.py │ ├── combine_task_data.py │ ├── contrast_annotation.txt │ ├── encoding_model.py │ ├── get_task_connectome.py │ ├── get_task_contrast_names.py │ ├── map_feats_to_surface.py │ ├── mk_l2_task_connectome.R │ ├── selectivity.py │ └── surface_stats.py ├── tests │ ├── __init__.py │ └── check_results.py ├── timeseries │ ├── Make_Timeseries_Heatmaps.Rmd │ ├── Make_combined_timeseries_table.Rmd │ ├── Make_timeseries_plots.Rmd │ ├── Mediation_analysis.Rmd │ ├── README.md │ ├── __init__.py │ ├── add_timeseries_links.py │ ├── data_utilities.R │ ├── est_bivariate_arima_model.R │ ├── load_myconnectome_data.R │ ├── load_myconnectome_data.py │ ├── make_expression_heatmaps.R │ ├── make_illness_immport_heatmap.R │ ├── make_modcorr_vs_wgcna_summary_figures.py │ ├── mk_behavcorr_fdr_adjmtx.py │ ├── mk_bwcorr_expression_figure.R │ ├── mk_bwcorr_wgcna_matrix.py │ ├── mk_graph_fullmetab_behav.py │ ├── mk_graph_metab_behav.py │ ├── mk_modularity_graph.py │ ├── mk_phenomewide_graph.py │ ├── summarize_tu_th_adjmtx.Rmd │ ├── timeseries_analyses.Rmd │ ├── timeseries_helpers.R │ └── timeseries_power_simulation.Rmd └── 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