Connectivity Measures
Different methods to quantify functional connectivity between brain regions:
Phase-Based Measures
Phase Locking Value (PLV)
Measures the consistency of phase relationships between two signals across time or trials.
Range: 0 (no coupling) to 1 (perfect coupling)
Corrected Imaginary PLV (ciPLV)
Removes zero-lag interactions to eliminate volume conduction artifacts, focusing on true neural connectivity.
Amplitude-Based Measures
Coherence
Measures the linear relationship between two signals in the frequency domain, combining both phase and amplitude information.
Envelope Correlation
Correlation between the amplitude envelopes of band-limited signals, indicating synchronized fluctuations in power.
Orthogonalized Envelope Correlation (OAEC)
Removes zero-lag correlations from envelope correlation to reduce spurious connectivity from volume conduction.
Event-Based Measures
Spike Co-occurrence
Measures how often epileptic spikes occur simultaneously between electrode pairs within a time window.
Gamma/Ripple Co-occurrence
Quantifies the temporal relationship between high-frequency oscillations (gamma bursts, ripples) across electrode sites.
Nodal Measures
Metrics that characterize individual nodes (electrodes) in the brain network:
Strength
Sum of all connection weights for a given node. Indicates the total connectivity of a brain region.
Clustering Coefficient
Measures the tendency of neighboring nodes to be connected to each other, indicating local network cohesion.
Eigenvector Centrality
Measures a node's influence based on the connectivity of its neighbors. Nodes connected to highly connected nodes have higher centrality.
Epileptogenicity Index
Quantifies the propensity of a brain region to generate epileptic activity, based on spectral analysis during seizure onset.
Event Rates
Spike Rate: Frequency of interictal epileptic discharges
Gamma Burst Rate: Frequency of high-frequency oscillations
Ripple Rate: Frequency of ripple events (80-250 Hz)
EEG Topography Visualization
Explore the relationship between brain sources and scalp EEG voltage distributions. This interactive tool demonstrates how dipole sources within the brain create voltage patterns on the scalp surface.
Visualization Elements
Display Components
- EEG Electrodes: Represented as yellow spheres positioned on the scalp
- Voltage Map: Color-coded surface representing electrical potential distribution
- Red colors indicate positive voltage values
- Blue colors indicate negative voltage values
- Brain Source: A dipole source positioned within the brain volume that generates the voltage distribution
Interactive Controls
Brain Source Slider
Navigate through different source locations within the brain. Click on the slider and use arrow keys for precise navigation through predefined brain source positions.
XRay Slider
Adjust the transparency of the head model to visualize internal structures and the relationship between brain sources and scalp electrodes.
Min/Max Threshold Sliders
Control the voltage range displayed on the topography map. Adjust minimum and maximum thresholds to focus on specific voltage ranges or enhance contrast.
Gamma Slider
Modify the color map contrast to enhance visualization of voltage gradients. Higher gamma values increase contrast, making subtle differences more visible.
Normalized Leadfield Checkbox
Toggle between normalized and unnormalized leadfield matrices. Normalization accounts for differences in electrode sensitivity and source depth.
Source Orientation Controls
The dipole source has a specific orientation that affects the resulting voltage distribution. You can control this orientation using the following options:
X, Y, Z Radio Buttons
Select a primary axis orientation for the dipole source. Each axis represents a different anatomical direction in the brain coordinate system.
Custom Orientation
Enable custom orientation mode to define arbitrary dipole directions using azimuth and elevation angles.
Azimuth Slider
When custom orientation is selected, adjust the azimuth angle (rotation around the vertical axis) of the dipole source.
Elevation Slider
When custom orientation is selected, adjust the elevation angle (tilt from horizontal plane) of the dipole source.
Ictal Connectivity Analysis
Navigation Overview
Navigate the connectivity changes during an epileptic seizure using the integrated traces and MRI visualization. The interface provides real-time exploration of network dynamics throughout the ictal period.
Interactive Controls
- Hover on the traces to view the name of the iEEG channel.
- Click once on a channel to display it on the MRI view.
- Click again on the same channel to show only its neighbourhood connections.
- Click a third time to reset the view to default.
Visualization Elements
Electrode Display
- SEEG electrodes: Displayed in yellow on the MRI
- Bipolar electrodes: Colored according to the maximum of the current time window, matching the connectivity map colors
Visualization Controls
Edge Size Slider
Adjust the thickness of connection edges displayed on the MRI to enhance or reduce visual prominence of network connections.
Node Size Slider
Change the size of electrode markers on the graph to improve visibility or reduce clutter in the visualization.
Edge Percentage Slider
Display only a specified percentage of edges on the MRI, filtering by connection strength to focus on the most significant pathways.
Network Time Point Slider
Navigate through different time windows (indicated by the dotted rectangle on traces) to observe how the network evolves during the seizure.
Interictal Functional Connectivity
Navigation Overview
Use the matrix and MRI view together to explore functional connectivity patterns during interictal periods. The interactions below explain how to explore regions (nodes) and adjust the visualization.
Interactive Controls
- Hover over the matrix to highlight the corresponding region (node) on the y-axis.
- Click once on a region to display it on the MRI view.
- Click again on the same region to show only that region's neighbourhood connections.
- Click a third time to reset the view to default.
Structural Connectome Visualization
Navigation Overview
Navigate the structural connectivity using the integrated matrix and 3D network visualization. The interface provides comprehensive exploration of anatomical connections and network topology.
Interactive Controls
- Hover over the traces to view the name of the ROI.
- Click once on a ROI to display it on the MRI view.
- Click again on the same ROI to show only that ROI's neighbourhood connections.
- Click a third time to reset the view to default.
Visualization Elements
MRI Display
- SEEG electrodes: Displayed in yellow on the MRI
- Bipolar electrodes: Colored according to the maximum of the current time window, matching the connectivity map colors
- Network edges: Represent structural connections between electrodes
Visualization Controls
Edge Size Slider
Adjust the thickness of connection edges displayed on the MRI to enhance or reduce visual prominence of structural connections.
Node Size Slider
Change the size of electrode markers on the graph to improve visibility or reduce clutter in the 3D visualization.
Edge Percentage Slider
Display only a specified percentage of edges on the MRI, filtering by connection strength to focus on the most significant pathways.
Network Time Point Slider
Navigate through different time windows (indicated by the dotted rectangle on traces) to observe how the network evolves.
Point spread function for several inverse solution methods
Explore the relationship between brain sources and the point spread function that is inherent to each source localization method.
Visualization Elements
Display Components
- Sources: A dipole source within the brain volume, represented as white circles in the MRI slices
- PSF map: Color-coded surface representing the point spread function
Interactive Controls
Brain Source Slider
Navigate through different source locations within the brain. Click on the slider and use arrow keys for precise navigation through predefined brain source positions.
Min/Max Threshold Sliders
Control the voltage range displayed on the topography map. Adjust minimum and maximum thresholds to focus on specific voltage ranges or enhance contrast.
Gamma Slider
Modify the color map contrast to enhance visualization of voltage gradients. Higher gamma values increase contrast, making subtle differences more visible.
Impact of Regularization Parameter on Inverse Solutions
Explore how the regularization parameter (lambda) affects the localization of interictal epileptiform discharges (IEDs) across different inverse solution methods. This interactive tool demonstrates the trade-off between spatial resolution and noise sensitivity in source reconstruction.
Overview
The regularization parameter controls the balance between fitting the data and constraining the solution.
Available Inverse Solution Methods
eLORETA
Exact Low Resolution Electromagnetic Tomography - provides zero localization error for point sources under ideal conditions. Produces distributed source solutions with depth normalization.
LCMV
Linearly Constrained Minimum Variance beamformer - adaptive spatial filter that minimizes output variance while maintaining unit gain in the direction of interest. Particularly effective for localizing oscillatory sources.
Dipole Fit
Equivalent Current Dipole fitting - parametric approach that models sources as point dipoles. Provides precise localization when the number and orientation of sources are correctly specified. Note: Lambda parameter does not apply to dipole fitting.
Visualization Elements
Display Components
- EEG Trace: Time series showing the interictal epileptiform discharge with a red vertical line indicating the selected time point for source localization
- 2D Voltage Map: Topographic representation of the scalp voltage distribution at the selected time point, providing a sensor-level view of the data
- 3D Brain Visualization: Multi-planar MRI views (axial, coronal, sagittal) with overlaid source reconstruction showing the estimated location and extent of brain activity
- Source Activity Map: Color-coded overlay on the anatomical MRI indicating source strength:
- Warmer colors (red/yellow) indicate stronger estimated source activity
- Color intensity reflects the amplitude of reconstructed sources
- Dipole Arrows (Dipole Fit only): Arrow visualization showing the position and orientation of the fitted equivalent current dipole
Interactive Controls
Time Point Slider
Navigate through five key time points during the IED evolution. The selected time point is marked by a red line on the EEG trace and determines which source distribution is displayed.
Lambda Slider
Adjust the regularization parameter across five logarithmically-spaced values (0.00001, 0.001, 0.01, 0.05, 0.1). Lower values produce more focal solutions; higher values produce smoother, more distributed solutions. This control is disabled when Dipole Fit is selected.
Min/Max Threshold Sliders
Control the range of source amplitudes displayed in the 3D visualization. Adjust minimum and maximum thresholds to focus on specific amplitude ranges or enhance contrast between strong and weak sources.
Percentage Thresholding
Alternative thresholding mode that displays only the top percentage of source values (20%, 10%, 5%, or 1%). Enable the checkbox to activate, then select the desired percentage. This helps identify the most active brain regions while filtering out weaker activity.
Adaptive Color Scale
When enabled, the color scale adjusts independently for each time point based on the maximum amplitude at that moment. When disabled, a global color scale is used across all time points, allowing direct amplitude comparison between different time points.
Reset Button
Restore all visualization settings to their default values, including view orientation, threshold values, and color scale settings.
Method Selection
Use the "Inverse solutions" dropdown menu to switch between different source reconstruction algorithms. Each method has distinct characteristics:
Visualization Options
View Menu
Select different anatomical views (Axial, Sagittal, Coronal, Render, or combined multi-planar layouts). Toggle colorbar display, radiological convention, and rendering clip plane.
PSF Color Menu
Choose from various color maps for the source visualization including Hot (default), Viridis, Plasma, Inferno, and others. Different color maps may enhance visualization of different spatial patterns.
Interactive ROI Network Visualization
Explore the structural connectome of the brain through an interactive 3D visualization of the Lausanne parcellation. This tool allows you to investigate white matter connections between brain regions and analyze network properties using diffusion tractography data.
Overview
The Interactive ROI Network displays structural connectivity derived from diffusion MRI tractography. Regions of interest (ROIs) are represented as nodes, and white matter fiber connections between them are shown as edges. The visualization combines anatomical MRI views with network visualization to provide comprehensive insight into brain structure.
Visualization Elements
Display Components
- ROI Nodes: Brain regions represented as spheres, color-coded according to nodal metrics
- Node size can be adjusted with the Node Size slider
- Node color intensity reflects the selected metric value
- Connection Edges: White matter fiber tracts between regions, visualized as lines
- Edge thickness reflects connection strength (fiber count or log fiber count)
- Edge color indicates connection strength using the selected colormap
- MRI Background: T1-weighted MRI in MNI152 standard space provides anatomical context
- Hemisphere Separation: ROIs are organized by hemisphere (Right and Left) in the selection panels
Region Selection and Interaction
The interface provides two modes for exploring the network: viewing individual nodes or examining node neighbourhoods.
Selection Modes
Node Mode
Default mode. Clicking on a region name centers the crosshair on that ROI's location in the brain. All network connections remain visible.
Node Neighbourhood Mode
When activated, clicking on a region shows only the connections to and from that specific node, highlighting its local connectivity pattern. The selected node appears in green, while connected neighbours are shown in purple.
Interactive Navigation
- Select a mode using the radio buttons: node (default) or node neighbourhood
- Click on an ROI button in either the Right hemisphere or Left hemisphere panel to navigate to that region
- In neighbourhood mode: The selected ROI is highlighted in green, connected ROIs in purple, and unconnected regions appear grayed out
- Click the same ROI again to deselect and return to the full network view
Network File Options
Choose from multiple network configurations that combine different edge weights and nodal metrics:
Fiber Count & Strength
Edge: Raw fiber count
Node: Node strength (sum of connections)
Log Fiber Count & Strength
Edge: Logarithm of fiber count (reduces dominance of very strong connections)
Node: Node strength
Fiber Count & Clustering Coeff
Edge: Raw fiber count
Node: Clustering coefficient (local network cohesion)
Log Fiber Count & Clustering Coeff
Edge: Log fiber count
Node: Clustering coefficient
Fiber Count & Nodal Efficiency
Edge: Raw fiber count
Node: Nodal efficiency (how efficiently a node communicates with the network)
Log Fiber Count & Nodal Efficiency
Edge: Log fiber count
Node: Nodal efficiency
Visualization Controls
Edge Size Slider
Adjust the thickness of fiber tract connections. Increase to make connections more visible; decrease to reduce visual clutter in densely connected regions.
Edge Threshold Slider
Filter edges based on connection strength. Values range from 0-99%. Only connections above the threshold percentage are displayed, allowing you to focus on the strongest pathways.
Node Size Slider
Adjust the size of ROI spheres in the visualization. Larger nodes are easier to identify; smaller nodes reduce overlap in the 3D view.
Node Threshold Slider
Filter nodes based on their metric values. Values range from 0-99%. Only nodes with values above the threshold are displayed, highlighting regions with high network importance.
Reset Button
Restore all visualization settings to default values, including view orientation, threshold values, and color scales.
Color Schemes
Customize the appearance of edges and nodes independently using different color maps:
Edge Color Menu
Plasma
Default colormap with perceptually uniform gradients from purple through red to yellow
Viridis
Perceptually uniform colormap from dark purple through teal to yellow
Inferno
Dark colormap progressing from black through red to bright yellow
Random
Each edge assigned a random color, useful for distinguishing individual connections
Node Color Menu
Same color options as edge colors (Plasma, Viridis, Inferno, Random), applied independently to node coloring.
View Options
Anatomical Views
Axial: Horizontal slices (top-down view)
Sagittal: Side view slices
Coronal: Front-to-back slices
Render: 3D surface rendering only
Multi-Planar Views
A+C+S: Combined axial, coronal, and sagittal slices
A+C+S+R: All slices plus 3D rendering (default view)
Display Options
Colorbar: Toggle color scale legend
Radiological: Switch between radiological and neurological conventions
Render Clip Plane: Enable/disable clipping plane in 3D render
Interpretation Guide
Understanding the Network
- Strong edges: Indicate robust white matter connections, typically corresponding to major fiber bundles like the corpus callosum, arcuate fasciculus, or corticospinal tract
- High-degree nodes: Regions with many connections, often serving as network hubs (e.g., precuneus, posterior cingulate, thalamus)
- High clustering coefficient: Indicates regions with tightly interconnected neighbours, suggesting local processing modules
- High nodal efficiency: Regions that enable efficient information transfer across the network, often corresponding to integration hubs
- Hemisphere differences: Compare left and right hemisphere connectivity patterns by examining the separate region lists