Help for package LeadSense

Title:

Medtronic Brain Sense Local Field Potencial Analysis

Version:

0.0.2.0

Description:

Extracts and creates an analysis pipeline for the JSON data files from Brain Sense sessions using Medtronic's Deep Brain Stimulation surgery electrode implants.

License:

MIT + file LICENSE

Encoding:

UTF-8

RoxygenNote:

7.3.2

Imports:

dplyr, ggplot2, ggpubr, seewave, tidyr, reshape2, signal

Suggests:

testthat (≥ 3.0.0)

Config/testthat/edition:

Depends:

R (≥ 3.5)

LazyData:

true

NeedsCompilation:

Packaged:

2025-04-21 17:58:46 UTC; paulo

Author:

Paulo Bastos [aut, cre], Raquel Barbosa [aut]

Maintainer:

Paulo Bastos <pauloandrediasbastos01@gmail.com>

Repository:

CRAN

Date/Publication:

2025-04-21 18:10:08 UTC

Plot BrainSense Spectrograms and Return Data (with Optional Band Filtering)

Description

This function generates spectrograms for Medtronic BrainSense time-domain signals across one or more data passes. Optionally, the user can select specific passes to plot, filter by frequency band, save the plots, and extract the underlying spectrogram data.

Usage

brain_sense_spectrogram(
  dataset = NULL,
  wl = 512,
  ovlp = 75,
  collevels = seq(-80, 0, by = 0.2),
  save_as = NULL,
  output_dir = getwd(),
  passes = NULL,
  band = NULL
)

Arguments

dataset

A JSON-like object (e.g., parsed with jsonlite::fromJSON()) containing Medtronic BrainSense data. If NULL, attempts to load the default dataset from the LeadSense package.

wl

Integer. Window length for FFT. Default is 512.

ovlp

Numeric. Overlap percentage between successive windows. Default is 75.

collevels

Numeric. A sequence of color levels for the spectrogram image (in dB). Default is seq(-80, 0, by = 0.2).

save_as

Character. File format to save plots ("png", "pdf", or "jpeg"). If NULL (default), plots are not saved.

output_dir

Character. Path to the directory where plots will be saved. Default is current working directory.

passes

Integer vector. Indices of passes to plot (e.g., c(1,3)). Default is NULL, which plots all available passes.

band

Character. One of "Delta", "Theta", "Alpha", "Beta", "Gamma". If provided, filters signal to this frequency band before generating the spectrogram.

Details

WARNING: This function may be computationally intensive and take significant time to execute. Please wait until all plots are rendered.

Value

A list of data frames (invisible). Each data frame corresponds to one spectrogram and contains:

time: Time in seconds
frequency: Frequency in Hz
magnitude: Spectral power in dB
channel: Channel label
pass: Pass index (i)

Examples

brain_sense_spectrogram(dataset, passes = c(2), band = "Beta")

JSON list sample session file

Description

JSON list sample session file

Usage

dataset

Format

A Large list obtained using jsonlite::JSON("myJSON_sessionFile.json")

AbnormalEnd: AbnormalEnd name
FullyReadForSession: FullyReadForSession
FeatureInformationCode: FeatureInformationCode
SessionDate: SessionDate
SessionEndDate: SessionEndDate
ProgrammerTimezone: ProgrammerTimezone
ProgrammerUtcOffset: ProgrammerUtcOffset
ProgrammerLocale: ProgrammerLocale
ProgrammerVersion: ProgrammerVersion
PatientInformation: PatientInformation
DeviceInformation: DeviceInformation
BatteryInformation: BatteryInformation
GroupUsagePercentage: GroupUsagePercentage
LeadConfiguration: LeadConfiguration
Stimulation: Stimulation
Groups: Groups
BatteryReminder: BatteryReminder
MostRecentInSessionSignalCheck: MostRecentInSessionSignalCheck
Impedance: Impedance
GroupHistory: GroupHistory
SenseChannelTests: SenseChannelTests
CalibrationTests: CalibrationTests
LfpMontageTimeDomain: LfpMontageTimeDomain
BrainSenseTimeDomain: BrainSenseTimeDomain
BrainSenseLfp: BrainSenseLfp
LFPMontage: LFPMontage
DiagnosticData: DiagnosticData

Source

In-house created

Examples

data(dataset)  # Lazy loading (!)

Extract and summarize Impedance data if available

Description

This function extracts impedance data from a JSON-like dataset and computes summary statistics.

Usage

impedance_summary(dataset = NULL)

Arguments

dataset

A JSON object/list loaded into the work environment. If NULL, attempts to load the default dataset from the LeadSense package.

Value

A list containing:

combined_impedance_df - The full impedance dataset (if available).
impedance_summary - Summary of mean impedance values by Hemisphere and Type.

If no valid impedance data is found, a message is printed instead.

Examples

impedance_results <- impedance_summary(dataset)
print(impedance_results$impedance_summary)
print(impedance_results$combined_impedance_df)

Extract and summarize LFP data

Description

This function extracts and summarizes LFP (Local Field Potential) data from a JSON-like dataset.

Usage

lfp_data(dataset = NULL)

Arguments

dataset

A JSON object/list loaded into the work environment. If NULL, attempts to load the default dataset from the LeadSense package.

Value

A structured LFP dataset including:

Power in each frequency band
LFP Frequency vs Magnitude for each electrode
Time-domain signals for all sequences in the LFP montage

Examples

lfp_dataset <- lfp_data(dataset)
print(lfp_dataset$band_power_results)
print(lfp_dataset$structured_lfp_dataset)

Extract basic session summary information in long format

Description

Extract basic session summary information in long format

Usage

summary_long(dataset = NULL)

Arguments

dataset

A JSON object/list loaded into the work environment

Value

Long format table with summary session information

Examples

summary_long()