From d8e37ba45c585004dd17261b5692f2993460cab9 Mon Sep 17 00:00:00 2001 From: poldrack Date: Sun, 2 Feb 2020 09:47:35 -0800 Subject: [PATCH 1/2] add README [skip ci] --- ImageAnalyses/README_outputs.txt | 154 +++++++++++++++++++++++++++++++ 1 file changed, 154 insertions(+) create mode 100644 ImageAnalyses/README_outputs.txt diff --git a/ImageAnalyses/README_outputs.txt b/ImageAnalyses/README_outputs.txt new file mode 100644 index 0000000..098f627 --- /dev/null +++ b/ImageAnalyses/README_outputs.txt @@ -0,0 +1,154 @@ +Outputs from automated analysis code for NARPS project +See https://github.com/poldrack/narps for more details + +Legend for files contained in this directory: + + +./image_diagnostics_zstat: image diagnostics for resampled statistical images (one file per team) + +./image_diagnostics_orig: image diagnostics for original (submitted) statistical images (one file per team) + +./output: outputs from analyses + +./output/npboot_output.RData: stored samples from nonparametric bootstrap analysis + +./output/overlap_binarized_thresh: images showing proportion of teams with activation at each voxel (separate image for each hypothesis) + +./output/ALE: outputs from coordinate-based meta-analysis, containing 1 - FDR-corrected p-value (separate image for each hypothesis) + +./output/cluster_maps: average unthresholded statistical maps for clusters of teams (separate maps for each hypothesis/cluster) + +./output/consensus_analysis: outputs from image-based meta-analysis, containing 1 - FDR-corrected p-value (separate image for each hypothesis) + +./output/correlation_unthresh: correlation data for unthresholded maps +./output/correlation_unthresh/spearman_unthresh_hyp[1-9].csv: correlation matrix for unthresholded maps between teams for each hypothesis +./output/correlation_unthresh/unthresh_cluster_membership_spearman.json: stored cluster membership +./output/correlation_unthresh/mean_unthresh_correlation_by_cluster.csv: mean correlation between teams within each cluster + +./output/unthresh_concat_zstat/hypo[1-9]_voxelmap.nii.gz: maps showing proportion of teams with data at each voxel + +./cached/narps_prepare_maps.pkl: cached data structure for NARPS analysis + +./logs/AnalyzeMaps-plot_distance_from_mean.txt: results from analysis of distance from mean pattern + +./logs/AnalyzeMaps-mk_correlation_maps_unthresh.txt: results from analysis of number of nonzero voxels (unthresh zstat) and median correlation between teams + +./logs/narps.txt: main log file for analysis + +./logs/ThresholdSimulation.log: results from simulation using consistent thresholding + +./logs/AnalyzeMaps-analyze_clusters.txt: results from cluster-specific analyses of unthresholded maps + +./logs/AnalyzeMaps-get_thresh_similarity.txt: results from analysis of percent agreement and Jaccard similarity across thresholded maps + +./logs/image_diagnostics.log: log from image processing + +./logs/ConsensusAnalysis.txt: results from image-based meta-analysis, including tau statistics + +./logs/AnalyzeMaps-mk_overlap_maps.txt: results from analysis of maximum voxel overlap + +./logs/zstat_diagnostics.log: log from processing of zstat maps + +./figures: analysis outputs and figures (note: for many of these figures there are both PDF and PNG versions present) + +./figures/hyp[1-9]_combined_clusters.png: combined heatmap and cluster slices (separately for each hypothesis) + +./figures/hyp[1-9]_pctagree_map_thresh.pdf: heatmaps for percent agreement + +./figures/ModelingSummaryTable.tsv: summary of results from mixed effects logistic regression and nonparametric bootstrap analyses +./figures/OddsRatios.tsv + +./figures/hyp[1-9]_ALE_z.png: Z statistic maps for coordinate-based meta-analysis +./figures/hyp[1-9]_ALE_p.png: uncorrected p-value maps for coordinate-based meta-analysis +./figures/hyp[1-9]_ALE_fdr_oneminusp.png: FDR corrected p-value maps for coordinate-based meta-analysis +./figures/hyp[1-9]_ALE_fdr_thresh_0.05.png: thresholded FDR corrected p-value maps for coordinate-based meta-analysis +./figures/hyp[1-9]_ALE_ale.png: Activation likelihood estimation maps for coordinate-based meta-analysis +./figures/ALE_map.png + +./figures/hyp[1-9]_spearman_map_unthresh.pdf: heatmap for spearman correlation of unthresholded maps between teams + +./figures/range_map.png: maps of range in Z stats for all hypotheses + +./figures/cluster_correlation.pdf: correlation map between all hypotheses/clusters + +./figures/overlap_map.png: maps of overlap in thresholded maps for all hypotheses + +./figures/hyp[1-9]_cluster_means.png: thresholded mean activation map for each cluster, separately for each hypothesis + +./figures/tau_histograms.pdf: histograms of tau statistic across voxels for all hypotheses + +./figures/tau_maps.pdf: tau maps for all hypotheses + +./figures/ConfidenceDataWide.csv: confidence data for each team (used in generating final table) + +./figures/median_corr_sorted.pdf: sorted median correlation for each team + +./figures/std_map.png: maps of standard deviation across z statistics for all hypotheses + +./figures/Table1.tsv: Summary of team reports (decision, confidence, similarity) + +./figures/TomEtAl_correlation.pdf: correlation of each hypothesis/cluster with maps from original Tom et al. study + +./figures/SuppFigure1.png: original version of figure showing all teams with modeling choices + +./figures/ThresholdSimulation: results from simulations using consistent thresholding +./figures/ThresholdSimulation/simulation_results.csv: summary of overall results +./figures/ThresholdSimulation/ventralstriatum_mask.nii.gz: mask for ventral striatum +./figures/ThresholdSimulation/vmpfc_mask.nii.gz: mask for vmpfc +./figures/ThresholdSimulation/amygdala_mask.nii.gz: mask for amygdala +./figures/ThresholdSimulation/decision_vs_activation.png: plot of relative decision likelihood for original vs. re-thresholded data + +./figures/MethodsTableMetadataMerged.csv: analysis metadata, using in creating final table + +./figures/DecisionAnalysis.html: results from logistic regression analyses and bootstrap + +./figures/NARPS_mean_correlation.pdf: correlation for each hypothesis/cluster with overall activation map from original NARPS analysis + +./figures/DecisionDataWide.csv: decision data (used to generate final table) + +./figures/consensus_map.pdf: maps from image-based meta-analysis + +./figures/correlation_unthresh +./figures/correlation_unthresh/spearman_unthresh_hyp[1-9]_cluster[1-3].png: histograms of correlations for each hypothesis/cluster +./figures/correlation_unthresh/spearman_unthresh_hyp[1-9]_mean.png: histograms of correlations for each hypothesis overall + +./PredictionMarkets: results from prediction market analyses +./PredictionMarkets/Figures/SuppTable_HoldingStats.tsv: Analyses of holdings +./PredictionMarkets/Figures/Active_vs_All_traders.pdf: Figure showing analysis of all traders vs. active traders +./PredictionMarkets/Figures/SuppTable_MarketDetails.tsv: Details regarding markets +./PredictionMarkets/Figures/SuppTable_MarketResults.tsv: Comparison of team vs. non-team market results +./PredictionMarkets/Figures/SuppTable_PanelRegressions.tsv: results from regression models on market results +./PredictionMarkets/Figures/PMbeliefs_Figure3.pdf: figure showing final market price vs. fundamental value +./PredictionMarkets/Figures/PM_Analyses.html: Results from Prediction market analyses +./PredictionMarkets/Figures/PM_Figures.html: Output from figure creation notebook +./PredictionMarkets/Figures/Timeseries.pdf: Price timeseries for each market + +./PredictionMarkets/Combined: Data files used in Prediction Market analyses +./PredictionMarkets/Combined/position.RData +./PredictionMarkets/Combined/asset.RData +./PredictionMarkets/Combined/portfolio.RData +./PredictionMarkets/Combined/transaction.RData +./PredictionMarkets/Combined/teamresults.RData + +./PredictionMarkets/Processed: Intermediate data files used in Prediction Market analyses +./PredictionMarkets/Processed/Fundamentals.RData +./PredictionMarkets/Processed/Prices.RData +./PredictionMarkets/Processed/BalancedPanel.RData +./PredictionMarkets/Processed/Transactions.RData +./PredictionMarkets/Processed/TeamResults.RData +./PredictionMarkets/Processed/Holdings.RData + +./metadata: various metadata outputs +./metadata/cluster_corr_TomEtAl.csv: correlation between each hypothesis/cluster and Tom et al. original maps +./metadata/cluster_metadata_df.csv: cluster membership by team/hypothesis +./metadata/thresh_voxel_statistics.csv: statistics on thresholded maps for each hypothesis +./metadata/smoothness_est.csv: smoothness estimates per hypothesis/team +./metadata/all_metadata.csv: full metadata output +./metadata/rectified_images_list.txt: list of teams/hypotheses that required direction-flipping +./metadata/cluster_corr_NARPS_mean.csv: correlation of each hypothesis/cluster with NARPS overall task activation maps +./metadata/pctagree_hyp[1-9].csv: percent agreement data across teams +./metadata/image_metadata_df.csv: number of NA and nonzero voxels for each team +./metadata/narps_metadata_all_teams.csv: original metadata for all teams +./metadata/median_pattern_corr.csv: median correlation for each team with mean map across teams +./metadata/thresh_voxel_data.csv: metadata for each team's thresholded maps +./metadata/R_package_info.txt: listing of all R package/versions used in analysis From dfc7f5649a30cde8cef9d77a82846fe6e1756e5c Mon Sep 17 00:00:00 2001 From: poldrack Date: Sun, 2 Feb 2020 09:50:44 -0800 Subject: [PATCH 2/2] add README to artifact file --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index b228210..295b038 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -62,6 +62,6 @@ jobs: - run: name: create results tarball command: | - cd /tmp/data; tar zcvf results.tgz ./output/npboot_output.RData ./cached ./figures ./logs ./metadata ./image_diagnostics* ./output/unthresh_concat_zstat/hypo*_voxelmap.nii.gz ./output/overlap_binarized_thresh/hypo*.nii.gz ./output/consensus_analysis/hypo*_1-fdr.nii.gz ./output/ALE/hypo*_fdr_oneminusp.nii.gz ./output/cluster_maps ./output/correlation_unthresh ./PredictionMarkets + cp /root/project/ImageAnalyses/README_outputs.txt /tmp/data; cd /tmp/data; tar zcvf results.tgz ./output/npboot_output.RData ./cached ./figures ./logs ./metadata ./image_diagnostics* ./output/unthresh_concat_zstat/hypo*_voxelmap.nii.gz ./output/overlap_binarized_thresh/hypo*.nii.gz ./output/consensus_analysis/hypo*_1-fdr.nii.gz ./output/ALE/hypo*_fdr_oneminusp.nii.gz ./output/cluster_maps ./output/correlation_unthresh ./PredictionMarkets ./README_outputs.txt - store_artifacts: path: /tmp/data/results.tgz