NEMO ERP Analysis Toolkit ERP Metric Extraction An Overview

NEMO Information Processing Pipeline

NEMO Information Processing Pipeline Metric Extraction Component

NEMO Information Processing Pipeline ERP Pattern Extraction, Identification and Labeling  Obtain ERP data sets with compatible functional constraints – NEMO consortium data  Decompose / segment ERP data into discrete spatio-temporal patterns – ERP Pattern Decomposition / ERP Pattern Segmentation  Mark-up patterns with their spatial, temporal & functional characteristics – ERP Metric Extraction  Meta-Analysis  Extracted ERP pattern labeling  Extracted ERP pattern clustering  Protocol incorporates and integrates:  ERP pattern extraction  ERP metric extraction/RDF generation  NEMO Data Base (NEMO Portal / NEMO FTP Server)  NEMO Knowledge Base (NEMO Ontology/Query Engine)

ERP Metric Extraction Tool MATLAB and Directory Configuration  Get Latest Toolkit Version (NEMO Wiki : Screencasts : Versions ) – Update your local (working) copy of the NEMO Sourceforge Repository  Configure MATLAB (NEMO Wiki : Screencasts : NEMO ERP Analysis Toolkit I) – MATLAB R2010a / R2010b, Optimization and Statistics Toolboxes – Add to the MATLAB path, with subfolders:  NEMO_ERP_Dataset_Import / NEMO_ERP_Dataset_Information  NEMO_ERP_Metric_Extraction / NEMO_ERP_Pattern_Decomposition / NEMO_ERP_Pattern_Segmentation  Configure Experiment Folder (NEMO Wiki : Screencasts : NEMO ERP Analysis Toolkit I & II) – Create an experiment-specific parent folder containing Data, Metric Extraction, Pattern Decomposition and Pattern Segmentation script subfolders – Copy the metric extraction, decomposition and segmentation script templates from your NEMO Sourceforge Repository working copy to their respective script subfolders – Add the experiment-specific parent folder, with its subfolders, to the MATLAB path

 File_Name  Electrode_Montage_ID  Cell_Index  Factor_Index  ERP_Onset_Latency  ERP_Offset_Latency  ERP_Baseline_Latency ERP Metric Extraction Tool Metascript Configuration – Step 1 of 6: Data Parameters

 File_Name – Name of an EGI segmented simple binary file, as a single-quoted string  Example: ‘SimErpData_tPCA_GAV.raw’  At present, Metric Extraction only accepts factor files from the Pattern Decomposition tool  Electrode_Montage_ID – Name of an EGI/Biosemi electrode montage file, as a single-quoted string  Valid montage strings: ‘GSN-128’, ‘GSN-256’, ‘HCGSN-128’, ‘HCGSN-256’, ‘Biosemi-64+5exg’, ‘Biosemi-64-sansNZ_LPA_RPA’  The NEMO ERP Analysis Toolkit will require EEGLAB channel location file (.ced) format for all proprietary, user-specified, montages  Cell_Index – Indices of cells / conditions to import, as a MATLAB vector  Indices correspond to the ordering of cells in the data file  See Metric_obj.Dataset.Metadata.SrcFileInfo.Cellcode for the ordered list of conditions  Factor_Index – Indices of PCA factors to import, as a MATLAB vector  Indices correspond to the ordering of factors in the data file ERP Metric Extraction Tool Metascript Configuration – Step 1 of 6: Data Parameters

 ERP_Onset_Latency – Time, in milliseconds, of the first ERP sample point to import, as a MATLAB scalar  0 ms = stimulus onset  Positive values specify post-stimulus time points, negative values pre-stimulus time points  All latencies must be in integer multiples of the sampling interval (for example, +’ve / -’ve multiples of Hz)  ERP_Offset_Latency – Time, in milliseconds, of the last ERP sample point to import, as a MATLAB scalar  0 ms = stimulus onset  Positive values specify post-stimulus time points, and must be greater than the ERP_Onset_Latency  ERP_Offset_Latency must not exceed the final data sample point (for example, a 1000 ms ERP with a 200 ms baseline: maximum 800 ms ERP_Offset_Latency)  ERP_Baseline_Latency – Time, in negative milliseconds, of the pre-stimulus ERP sample points to exclude from import, as a MATLAB scalar  ERP_Baseline_Latency = 0  no baseline  To import pre-stimulus sample points, specify ERP_Baseline_Latency < ERP_Onset_Latency < 0  All latencies must be within the data range (for example, a 1000 ms ERP with a 200 ms baseline: ERP_Baseline_Latency = -200 ms, ERP_Onset_Latency = 0 ms and ERP_Offset_Latency = 800 ms imports the 800 ms post-stimulus interval, including stimulus onset) ERP Metric Extraction Tool Metascript Configuration – Step 1 of 6: Data Parameters

ERP Metric Extraction Tool Metascript Configuration – Step 2 of 6: Experiment Parameters (Required)  Lab_ID  Experiment_ID  Session_ID  Subject_Group_ID  Subject_ID  Experiment_Info

ERP Metric Extraction Tool Metascript Configuration – Step 2 of 6: Experiment Parameters (Required)  Lab_ID – Laboratory identification label, as a single-quoted string  Example: ‘My Simulated Lab’  Experiment_ID – Experiment identification label, as a single-quoted string  Example: ‘My Simulated Experiment’  Session_ID – Session identification label, as a single-quoted string  Example: ‘My Simulated Session’  Subject_Group_ID – Subject group identification label, as a single-quoted string  Example: ‘My Simulated Subject Group’  Subject_ID – Subject identification label, as a single-quoted string  Example: ‘My Simulated Subject # 1’  Experiment_Info – Experiment note, as a single-quoted string  Example: ‘tPCA with Infomax rotation’

ERP Metric Extraction Tool Metascript Configuration – Step 3 of 6: Experiment Parameters (Optional)  Event_Type_Label  Stimulus_Type_Label  Stimulus_Modality_Label  Cell_Label_Descriptor

ERP Metric Extraction Tool Metascript Configuration – Step 3 of 6: Experiment Parameters (Optional)  Event_Type_Label – MATLAB cell array of cell/condition event type labels  One label per cell/condition, as a single-quoted string  Example: {‘SimEventType1’, ‘SimEventType2’, ‘SimEventType3’}  Stimulus_Type_Label – MATLAB cell array of cell/condition stimulus type labels  One label per cell/condition, as a single-quoted string  Example: {‘SimStimulusType1’, ‘SimStimulusType2’, ‘SimStimulusType3’}  Stimulus_Modality_Label – MATLAB cell array of cell/condition stimulus modality labels  One label per cell/condition, as a single-quoted string  Example: {‘SimStimulusModality1’, ‘SimStimulusModality2’, ‘SimStimulusModality3’}  Cell_Label_Descriptor – MATLAB cell array of cell/condition description labels  One label per cell/condition, as a single-quoted string  Optional Labels: E-prime assigned cell codes imported from input data file  Example: {‘SimConditionDescription1’, ‘SimConditionDescription2’, ‘SimConditionDescription3’}

ERP Metric Extraction Tool Metascript Configuration – Step 4 of 6: NemoErpMetricExtraction Parameters  ERP_Component_Label  ERP_Component_Analysis_ Method_Label  ERP_Component_Label – ERP individual component identification label, as a single-quoted string  Example: ‘PcaFactor#’ or ‘MicrostateSegment#’  ERP_Component_Analysis_Method_Label – ERP component-generation-procedure identification label, as a single-quoted string  Example: ‘tPCA with Infomax rotation’ or ‘Microstate segmentation via Centroid Dissimilarity’

ERP Metric Extraction Tool Metascript Configuration – Step 5 of 6: Class Instantiation Instantiate EGI reader class object Initialize object parameters Import metadata Import signal (ERP) data Instantiate Metric Extraction class object Initialize object parameters

ERP Metric Extraction Tool Metascript Configuration – Step 6 of 6: Class Invocation Call RDF method: Generate RDF-formatted metric info Call CSV method: Generate CSV-formatted metric info Call XLS method: Generate XLS-formatted metric info

 Metric Extraction output folder contents – CSV files, one per condition – RDF files, one per condition – NemoErpMetricExraction object in MATLAB (.mat) format ERP Metric Extraction Tool Folder Output for SimErpData_tPCA_GAV.raw Input data fileTime stamp

 Comma Separated Value (CSV) format output file – Column 1: Factor Label – Column 2: Metric Label – Column 3: Metric Value (microvolts | milliseconds) ERP Metric Extraction Tool Example Output for SimErpData_tPCA_GAV.raw …

 Resource Description Format (RDF) format output file – RDF N-Triple syntax – Subject, Predicate (Relation), Object triple – Example: Subject, has property, object property ERP Metric Extraction Tool Example Output for SimErpData_tPCA_GAV.raw

ERP Metric Extraction Tool Viewing Metric Extraction Class Properties in MATLAB  MATLAB Workspace view NemoErpMetricExtraction object EgiRawIO object Double click to open…

ERP Metric Extraction Tool Viewing Metric Extraction Class Properties in MATLAB  MATLAB Workspace view Keep on double clicking …