Work Description

Title: Supporting data and scripts for the paper "Interictal high frequency background activity as a biomarker of epileptogenic tissue" Open Access Deposited

h
Attribute Value
Methodology
  • Intracranial EEG data was acquired at 4,096 Hz from patients with epilepsy as part of their standard clinical care. Consent was provided for the data to be deidentified and analyzed as part of an Institutional Review Board approved study. Quantitative features of the frequency, interictal background were computed. Full details in the accompanying manuscript.
Description
  • This data repository includes the quantitative features of high frequency, intracranial EEG along with all necessary scripts to reproduce the figures of the accompanying manuscript.
Creator
Depositor
  • sgliske@umich.edu
Contact information
Discipline
Funding agency
  • National Institutes of Health (NIH)
Keyword
Date coverage
  • 2013-01-01 to 2021-04-01
Citations to related material
  • (under review)
Resource type
Last modified
  • 11/18/2022
Published
  • 06/21/2021
Language
DOI
  • https://doi.org/10.7302/hnvs-f543
License
To Cite this Work:
Gliske, S. V., Stacey, W. C. (2021). Supporting data and scripts for the paper "Interictal high frequency background activity as a biomarker of epileptogenic tissue" [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/hnvs-f543

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Files (Count: 2; Size: 2.56 GB)

Thumbnailthumbnail-column Title Original Upload Last Modified File Size Access Actions
README.md 2021-06-15 2021-06-15 3.67 KB Open Access
hfa.zip 2021-06-16 2021-06-18 2.56 GB Open Access

high-frequency-activity-paper

Derived data and Matlab (Natick, MA) scripts to support the following publication: [Reference to be inserted after acceptance of the manuscript.]

Scripts are licensed under NC-BY 4.0.

Derived data is licensed for educational use only, with no warrenty implied. Requests must be made with the corresponding author for any other use of the data, including additional research.

Parameter key

The data files names, and several of the scripts, use a parameter key in the form of

'width-<www>.mask-<x><y>.nBands-<z>'.

  • The width values refer to the width of the epoch. Data was
    computed with values of <www> being 120, 300, or 600 (in units
    of seconds).

  • The mask parameter <x> specifies whether HFOs were rejected and
    the mask parameter <y> specifies whether artifacts were
    redacated: 1 == redacted, 0 == not redacted.

  • The number of bands parameter <z> specifies whether to use the
    data from the 2 or 3 band option. See text of the manuscript for
    the specific frequency bands used.

  • The parameter key for the main results is 'width-300.mask-11.nBands-2'

Instructions

  1. Copy the files into a new directory
  2. Open matlab
  3. Run full_protocol(paramKey) with paramKey being a string as described above.

Scripts

Main functions

Filename Description
full_protocol.m Main entry point to the code. This scripts calls all needed functions to reproduce the analysis, results, and plots of the paper
inferenceAnalysis.m Main function to perform the inference (Internal Association) analysis (See Section 2.3 of Stovall et al., 2020).
predictionAnalysis.m Main function to perform the prediction analysis (Section 2.4 of Stovall et al., 2020).

Plotting functions

Filename Description
plotRawData.m Raw data plot (Fig. 1)
plotFeatureExample.m Example features (Fig. 2)
plotInferenceResults.m Inference results (Fig. 3)
plotScorePerchannel.m pHFA Score per channel (Fig. 4)
plotPredictionResults.m Prediction results (Fig. 5)

Auxillery functions

Filename Description
adjustFeatures.m Auxillery function to adjust features based on the median value overall channels for a given epoch
computeAsym.m Auxillery function to compute asymmetries
computeDurations.m Auxillery function to compute durations per subject
getNumStars.m Auxillery function to determine the number of stars (enumerated of significance) for a given p-value
makePanels.m Auxillery function to make mutliple panels for the complex figures
median_with_CI.m Auxillery function to compute the median and its confidence interval
table_2.m Auxillery function to gather data for Table 2
transformFeatures.m Auxillery function to apply transformations (log or atan) to the feature values

Derived (input) data

Filename Description
data-input/hfo_rates.mat HFO rates for comparison
data-input/raw-data.mat Short sample of raw data (for Fig. 1)
data-input/UMHS-00*.hfa.mat Features of each epoch per channel and related metadata.
data-input/subjectTable.csv Comma seperated file of the surgery outcome for each subject
data-input/TLEinfo.mat Information about which electrodes were located in the temporal lobe

Other files

Filename Description
Fig-3-table.csv Table of values to support Figure 3 (regenerated by plotInferenceResults.m).

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