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‎code/plugins/reformat_plugin.py

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@@ -17,6 +17,7 @@ def reformat_wiki_pages(filepath, filename, parent, output_file, wiki_input_dir=
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layout: default
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parent: {parent}
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grand_parent: Plugins
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render_with_liquid: false
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'''.format(filename=filename, parent=parent)
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print(f"Reformatting {filename} of {parent}...")
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append_text += '''
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title: {title}
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long_title: {title}
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render_with_liquid: false
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'''.format(title=title)
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append_text += 'nav_order: {order}\n'.format(order=order+1)
@@ -86,7 +86,7 @@ def reformat_plugin_dir(plugin_input_dir, plugin_name, formatted_name, order, li
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shutil.copytree(os.path.join(plugin_input_dir, 'images'), os.path.join(plugin_output_dir, 'images'), dirs_exist_ok=True)
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# copy all .jpg and .png files from input to output dir
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for file in os.listdir(plugin_input_dir):
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if file.endswith('.jpg') or file.endswith('.png'):
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if file.endswith(('.png', '.jpg', '.gif')):
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shutil.copyfile(os.path.join(plugin_input_dir, file), os.path.join(plugin_output_dir, file))
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# if plugin is 'imat', copy the Docs directory recursively to the output directory
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layout: default
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title: {plugin_name}
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long_title: {plugin_name}
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parent: Plugins'''.format(plugin_name=formatted_name)
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parent: Plugins
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render_with_liquid: false'''.format(plugin_name=formatted_name)
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if plugin_type == 'wiki':
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append_text += '\nhas_children: true'
@@ -110,14 +111,14 @@ def reformat_plugin_dir(plugin_input_dir, plugin_name, formatted_name, order, li
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shutil.copytree(os.path.join(wiki_plugin_input_dir, 'images'), os.path.join(plugin_output_dir, 'images'), dirs_exist_ok=True)
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# copy all .jpg and .png files from wiki input to output dir
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for file in os.listdir(wiki_plugin_input_dir):
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if file.endswith('.jpg') or file.endswith('.png'):
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if file.endswith('.jpg') or file.endswith(('.png', '.jpg', '.gif')):
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shutil.copyfile(os.path.join(wiki_plugin_input_dir, file), os.path.join(plugin_output_dir, file))
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for root, dirs, files in os.walk(wiki_plugin_input_dir):
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for file in files:
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if file.endswith('.md') and not file.startswith('index') and not file.startswith('Home'):
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reformat_wiki_pages(os.path.join(wiki_plugin_input_dir, file), file.strip('.md'), formatted_name, os.path.join(plugin_output_dir, file), wiki_plugin_input_dir)
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reformat_wiki_pages(os.path.join(wiki_plugin_input_dir, file), file.replace('.md', ''), formatted_name, os.path.join(plugin_output_dir, file), wiki_plugin_input_dir)
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with open(index_file) as f:

‎plugins/ARfitStudio/index.md

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title: ARfitStudio
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long_title: ARfitStudio
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parent: Plugins
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nav_order: 18
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render_with_liquid: false
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nav_order: 20
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---
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To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/ARfitStudio).
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‎plugins/BVA-io/index.md

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---
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layout: default
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title: BVA-io
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long_title: BVA-io
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parent: Plugins
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render_with_liquid: false
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nav_order: 28
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---
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To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/bva-io).
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# BVA-io for Brain Vision Analyzer format
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This repository is a plugin for EEGLAB to import/export
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Brain Vision Analyzer EEG data files.
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# Version history
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v1.73 - Writing data now in MULTIPLEXED format as a new option; show warning when VMRK file is missing
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v1.72 - Avoid crashing when event file is absent
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v1.71 - Allow to import .ahdr files
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v1.7 - Better handling of VMRK and EEG file non-consistant witht the header VHDR file; allow empty marker info section; allow importing truncated binary file

‎plugins/BrainBeats/brainbeats_logo.png

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‎plugins/BrainBeats/brainbeats_logo2.png

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‎plugins/BrainBeats/index.md

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---
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layout: default
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title: BrainBeats
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long_title: BrainBeats
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parent: Plugins
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render_with_liquid: false
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nav_order: 9
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---
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To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/amisepa/BrainBeats).
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<!-- <p align="center"> -->
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# BrainBeats
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<!-- </p> -->
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<p align="center" width="100%">
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<img width="30%" src="https://github.com/amisepa/BrainBeats/blob/main/brainbeats_logo2.png">
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</p>
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The BrainBeats toolbox, implemented as an EEGLAB plugin, allows joint processing and analysis of EEG and cardiovascular signals (ECG and PPG) for brain-heart interplay research. Both the general user interface (GUI) and command line are supported (see tutorial). BrainBeats currently supports: 1) Heartbeat-evoked potentials (HEP) and oscillations (HEO); 2) Extraction of EEG and HRV features; 3) Extraction of heart artifacts from EEG signals; 4) brain-heart coherence.
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## THREE METHODS AVAILABLE
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<p align="center" width="100%">
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<img width="50%" src="https://github.com/amisepa/BrainBeats/blob/main/figures/diagram.png">
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</p>
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1) Process EEG data for heartbeat-evoked potentials (HEP) analysis using ECG or PPG signals. Steps include signal processing of EEG and cardiovascular signals, inserting R-peak markers into the EEG data, segmentation around the R-peaks with optimal window length, time-frequency decomposition.
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<p align="center">
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Example of HEP at the subject level, obtained from simultaneous EEG-ECG signals
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</p>
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<p align="center" width="100%">
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<img width="50%" src="https://github.com/amisepa/BrainBeats/blob/main/figures/fig11.png">
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</p>
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<p align="center">
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Example of HEP at the subject level, obtained from simultaneous EEG-PPG signals
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</p>
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<p align="center" width="100%">
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<img width="50%" src="https://github.com/amisepa/BrainBeats/blob/main/figures/fig17.png">
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</p>
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2) Extract EEG and HRV features from continuous data in the time, frequency, and nonlinear domains.
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- HRV time domain: SDNN, RMSSD, pNN50.
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- HRV frequency domain: VLF-power, ULF-power, LF-power, HF-power, LF:HF ratio, Total power.
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- HRV nonlinear domain: Poincare, fuzzy entropy, fractal dimension, PRSA.
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- EEG frequency domain: average band power (delta, theta, alpha, beta, gamma), individual alpha frequency (IAF), alpha asymmetry.
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- EEG nonlinear domain: fuzzy entropy, fractal dimension
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<p align="center">
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Example of power spectral density (PSD) estimated from HRV and EEG data
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</p>
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<p align="center" width="100%">
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<img width="50%" src="https://github.com/amisepa/BrainBeats/blob/main/figures/fig21.png">
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</p>
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<p align="center">
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Example of EEG features extracted from sample dataset
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</p>
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<p align="center" width="100%">
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<img width="50%" src="https://github.com/amisepa/BrainBeats/blob/main/figures/fig22.png">
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</p>
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3) Remove heart components from EEG signals using ICA and ICLabel.
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<p align="center">
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Example of extraction of cardiovascular components from EEG signals
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</p>
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<p align="center" width="100%">
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<img width="50%" src="https://github.com/amisepa/BrainBeats/blob/main/figures/fig27.png">
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</p>
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4) Compute brain-heart coherence (beta version, please test and give feedback)
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<p align="center">
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Example of several brain-heart coherence measures computed with BrainBeats from simultaneous EEG and ECG signals
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</p>
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<p align="center" width="100%">
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<img width="50%" src="https://github.com/amisepa/BrainBeats/blob/main/figures/coherence_allfreqs.png">
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</p>
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<p align="center">
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Scalp topography showing scalp regions coherent with ECG signal for each frequency band
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</p>
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<p align="center" width="100%">
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<img width="50%" src="https://github.com/amisepa/BrainBeats/blob/main/figures/coherence_topo.png">
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</p>
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## Requirements
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- MATLAB installed (https://www.mathworks.com/downloads)
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- EEGLAB installed (https://github.com/sccn/eeglab)
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- Some data containing EEG and cardiovascular signals (ECG or PPG) within the same file (i.e. recorded simultaneously).
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Or use the tutorial dataset provided in this repository located in the "sample_data" folder.
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## Step-by-step tutorial
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See our publication for a step-by-step tutorial using the sample dataset: https://www.jove.com/t/65829/brainbeats-as-an-open-source-eeglab-plugin-to-jointly-analyze-eeg
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Full-text preprint: https://www.biorxiv.org/content/10.1101/2023.06.01.543272v3.full
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## Version history
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v1.5 (5/2/2024) - METHOD 4 (brain-heart coherence) added
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v1.4 (4/1/2024) - publication JoVE (methods 1, 2, 3)

‎plugins/EEG-BIDS/EEG‐BIDS-docs.md

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---
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layout: default
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title: EEG-BIDS
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long_title: EEG-BIDS
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parent: EEG-BIDS
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grand_parent: Plugins
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render_with_liquid: false
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title: EEG‐BIDS-docs
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long_title: EEG‐BIDS-docs
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---
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# Documentation and tutorial videos
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‎plugins/EEG-BIDS/index.md

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title: EEG-BIDS
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long_title: EEG-BIDS
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parent: Plugins
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render_with_liquid: false
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has_children: true
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nav_order: 2
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nav_order: 26
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---
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To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/EEG-BIDS).
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‎plugins/ICLabel/index.md

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title: ICLabel
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long_title: ICLabel
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parent: Plugins
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render_with_liquid: false
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nav_order: 0
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---
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To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/ICLabel).

‎plugins/MFF-matlab-io/1.-Plugin-install.md

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---
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layout: default
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parent: MFF-matlab-io
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grand_parent: Plugins
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render_with_liquid: false
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title: 1.-Plugin-install
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long_title: 1.-Plugin-install
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---
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Select EEGLAB menu item **File > Import data > Using EEGLAB functions and plugins > From EGI/Phillips .mff file** as shown below.
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![](EEGLAB_install2.png)
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If the MFFmatlabio plugin has not be installed, EEGLAB will prompt you to install it (see also [plugin installation](Plugin-installation)). After this, MFFmatlabio will prompt an interface to select an MFF ressource as shown below.
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![](mff_import.png)

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