Code to look for evoked potentials in variable spacing stimulation data as well as fit analytic models to the volume conducted signals

This repository contains code to analyze human intracranial datasets from the stimulation spacing and stimulation geometry projects.

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To analyze evoked potentials:

An example workflow is shown for Subject ID 010dcb. The relevant code is under StimulationVoltageAnalysis/look_for_eps.

running ep_search_iterate.m as setup will create the data files for 010dcb, which can then be fed into analyze_010dcb.m which illustrates how once the data has been extracted into a chunked form, the peak to peak voltages can be calculated. Plots are also made showing the stimulation artifact in ep_search_iterate.m, as well as the evoked potentials in analyze_010dcb.m*. This requires the data generated by ep_search_iterate to be placed in a single folder.

The functions which extract the peak to peak voltages of the EPs are in the analysisFunctions folder, while functions helpful for plotting are under helperFunctions

Scripts which function on single files are available with ep_search_gui_select.m, which requires various parameters to be set in code, but this enables rapid loading of converted data files for further analysis.

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To analyze the volume conducted signals:

To fit the analytic models from 8 subjects as discussed in David Caldwell's thesis, the following master scripts are useful: calculate_spherical_patient.m in ElectrodeModeling/manuscript/spherical_model as well as calculate_spherical_patient_3ada8b.m in ElectrodeModeling/manuscript/spherical_model

To extract the volume conducted data.

The folders ECoG_subjs and DBS_subjs under manuscript/extraction_analysis_pipeline/recorded_waveforms_analysis/individual_subject_scripts highlights example scripts for previous subject on how to extract their data for volume conduction analysis.

The key function is voltage_extract_avg

To extract the voltage monitor data

The folder manuscript/extraction_analysis_pipeline/Analyze_Stim_Curves has scripts and functions to analyze the applied stimulation voltage waveform.

To analyze saline validation measurements

The folder StimulationVoltageAnalysis/salineAnalysis contains scripts and functions to process TDT saline stimulation data sets.

To extract the volume conduction datasets

A folder with legacy code for extracting data epochs is under StimulationVoltageAnalysis/resistivity_extraction

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A link to a large amount of the compiled human ECoG and DBS data is below

https://drive.google.com/open?id=1j\_J7ncKy4aAgdwGUmLxid6NIPJ8\_Eytz

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David J Caldwell, BSD-3 License