The Virtual Brain Project

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Simulator

This page shows a configurable multicolumn interface that combines TheVirtualBrain simulation, analysis and visualization capabilities.

../../_images/simulator.jpg

Preview for Simulator Area

Simulation History

We call History the most left column on the Simulator page. Along with the History title, you can observe two buttons on the top bar of this column.

The star_icon button allows you to initialize a new simulation, using the default Simulator parameters. This default initialization is already happening, if you just landed on this page for the first time. The button can be useful in case you started configuring a complex simulation and you lost track of the changes, to return to the safe defaults.

The upload_icon button allows you to upload a JSON file. This file can be exported from a previously configured and run simulation (on the same or different TVB installation, as long as versions are compatible). Details on how to export such a JSON file can be found just bellow, when we explain the pencil_icon icon.

As main content in this left column, a history of all simulations is kept and can be accessed at any time.

Each simulation execution has a color label that represents its current status:

  • pale blue: simulation is running,
  • green: simulation is finished,
  • gray: simulation has been canceled by the user,
  • red: an error occurred during the simulation.

Each simulation can be renamed, copied, exported or deleted by clicking on pencil_icon icon, next to its name.

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Simulation editing menu

To rename a simulation, click the pencil_icon icon first, then edit the text in the input field, and do not forget to press save_icon icon when you are done writing.

Note

You cannot rename a Simulation while it is running, but instead you could cancel it (e.g. if you see it eats too many of your machine resources, or you simply changed your mind about this run).

../../_images/simulator_history_running.jpg

Copy simulation means loading in memory the same configuration, as used for that particular simulation. It will be your job to optionally change something in the configuration and, when done, press the play_icon icon, to actually run this copy of the simulation.

Export JSON is a new feature which allows you to create a text file, which stores the current simulation parameters. This text file will be downloaded from your browser window, and can be reused later. You could use it on the same TVB installation, or on a totally different TVB server, in several manners:

  • from web GUI, using the upload_icon button, on this page (top of column History)
  • in the python console of TVB, for better debugging capabilities. Examples for this later case can be found in the set of examples for COMMAND and LIBRARY profiles.

Caution

Please notice that deleting a simulation will remove the parameters configuration, and also delete all resulting data that had been produced in relation to that simulation.

Configure a Simulation


A simulation is configured from the middle column.

On the top of this column there is:
  • a field to enter the new simulation name,
  • the Launch button on the top right to start the simulation, and
  • the Configure Interface button to select which of the simulation components are visible.
  • links to pages that allow detailed configuration
    • region model configuration
    • region noise configuration
    • surface level configuration (available for surface simulations)

../../_images/simulator_configuration_buttons.jpg

In this column you can change all the configurable parameters of a simulation:

  • Long Range Connectivity
  • Long Range Coupling Function
  • Conduction Speed
  • Cortical Surface
  • Stimulus
  • Local Dynamics Model
    • State Variable Range
    • State Variables to be recorded
    • Initial Conditions
  • Integration Scheme
    • Integration Step Size
  • Monitors
  • Simulation Length

You can find more detailed information by clicking on the interrogationicon icon next to each element.

Note

You can filter DataTypes (like Long Range Connectivity) from UI

../../_images/simulator_filter_datatypes.jpg
  • Click on Add Filter button bellow a DataType
  • select the attribute to be filtered, the operator to apply and the value in this filter
  • click Apply Filters to have the results filtered in the selector component right above the filters
  • this ca also be used in the context of Parameter Space Exploration of TheVirtualBrain

The Phase plane page

It is used to explore and define parameter configurations. It is accessible from the top menu:

../../_images/simulator_phase_plane_link.jpg

This page allows you to observe how the dynamics of the physical model change as a function of its parameters.

On the left column you select the model you want to explore and set it’s parameters.

The selected model will generally have a n-dimensional phase space. The right column shows a 2-dimensional axis cut of this space. Gradients are shown and nullclines if they exist. To control this cut use the Axes and State variables regions in the left column. There you can select what state variables should be shown and their ranges. Also you can set values for the variables that are not shown.

If you click in the phase plane a state trajectory will be computed. The integration method for this trajectory is configured on the left column. To make trajectories longer increase the integration step. This will not influence the simulation. For stochastic integrators decreasing the dispersion usually makes sense. Below the phase graph you will see the signals for all state variables. These signals belong to the latest trajectory.

Finally to save a parameter configuration give it a name and click Save new parameter configuration. This saved configuration can be used in Region-based simulations

../../_images/simulator_phase_plane_interactive.jpg

The phase plane.

Note

TVB performs region-based and surface-based simulations

You can access specific configuration pages for both types of simulation.

Region-based simulations

The Set up region Model button leads you to the region model page. Here you can associate model parameter configurations to connectivity nodes.

../../_images/simulator_region_model.jpg

Region model configuration.

The Configure noise button leads to the region noise page. Here you can associate noise dispersions to connectivity nodes. Select some nodes using any of the selection components or the 3d view. Choose dispersions for all state variables then place those values in the selected nodes.

../../_images/simulator_region_noise.jpg

Region noise configuration.

Surface-based simulations

If you are launching a surface-based simulation, then it is possible to add more complexity by spatially varying the model parameters.

In order to do that, click on Set up surface model. A new configuration page will be loaded.

../../_images/simulator_spatialized_parameters.jpg

Preview for surface model configuration.

Tip

Parameter Space Exploration

It is possible to launch parallel simulations to systematically explore the parameter space of the local dynamics model. In the current TVB version, up to 2 parameters can be inspected at the same time.

../../_images/simulator_pse_configuration.jpg

The results will be presented in a discrete two dimensional graph. Each point represents the results of a simulation for an unique combination of parameters. The disk size corresponds to Global Variance and the color scale corresponds to Variance of the Variance of nodes.

Display Simulation Results

On the right column you will find an area where you can configure displays to exhibit your simulation results.

Hint

Maximize this column by clicking on the zoom icon located in the top right corner.

There are 4 tabs:

  • three View tabs you can set up by selecting:

    • TVB time-series Visualizers that directly plot the resulting time-series or
    • TVB-Visualizers associated with a TVB-Analyzer. In this case, simulation results undergo two steps: they are first analyzed and those secondary results are shown in a corresponding visualizer.
  • one Results tab containing the current simulation data structure tree. You can inspect each element through this tree in the same way as in Projects –> Data Structure. A full list of visualizers and analyzers is available from the component overlay menu.

Tip

Once your results are available, by clicking on launch_full_viz you will be redirected to a new page where only the currently selected visualizer is presented. In this new page, you can click on brainicon in the top right corner to access a new menu which will allow you to:

  • Save a snapshot of the current figure.
  • Relaunch the visualizer using a different entity, if available. For instance, a different time-series.
../../_images/visualizer_save_figure.jpg

Preview for Full Visualizer mode.

All the snapshots you save can be managed in Projects –> Image Archive page.

orphan:

Simple Visualizers

Brain Activity Visualizer

A 3D scene of the brain activity.

Mouse interaction:

You can change the view by pressing a mouse button and dragging it.

  • the left button rotates the brain around the center of the screen.
  • the right button translates the brain.
  • the middle button and the scroll wheel zoom towards the center of the screen.

Pressing the shift key and the left button has the same effect as the right button.

Pressing the control key will rotate or translate in the model space; while without control key pressed, the rotation happens in the space of the navigator (with center in (0,0,0) ).

The SPACE key will show a top view. The CURSOR Keys will show axis aligned views.

For region level time series the brain is represented by a coarse granularity - each region is represented with only one color. For surface level time series each vertex has an individual measure.

The color coding is determined by the current color scheme. A legend of it is on the right side of the brain view. You can change this color scheme and other viewer parameters from the brain menu in the upper right corner.

From the visualizer toolbar you can pause and resume the activity movie. For region level time series there is a selection component in the toolbar. Use it to show activity only for the selected regions.

../../_images/visualizer_brain.jpg

Preview for Brain Activity Visualizer at the region level

Time Series Visualizer (svg/d3)

In the center area you click and drag to zoom, click once to reset zoom and use the scroll wheel to scroll signals.

The horizontal bottom part is the temporal context. Here the solid line marks the mean across channels, in time. The shaded area marks standard deviation across channels, in time. You Click and drag to select a subset of signals. The selection can be changed again by dragging it. Click outside selection box to cancel and reset view. You can resize the view by dragging blue box in the bottom right corner.

The vertical left part is the signal context. Here solid lines show each signal. Selection works like in the temporal context.

In the brain menu there is a slider you use to change the signal scaling.

../../_images/visualizer_timeseries_svgd3.jpg

Preview for Time-Series Visualizer (svg/d3)

Animated Time Series Visualizer

../../_images/visualizer_timeseries_animated.jpg

Preview for Animated Time Series Visualizer

This is an alternative for the Time Series Visualizer (svg/d3). It is used to display signal lines in 2D.

The label “animated” comes from the red line which will pass the entire signal step by step, at a configurable speed. In single mode, this red-line might not be very useful, but it makes more sense when the same 2D display gets reused in the Dual Visualizers (combined with the 3D display on a surface) where the red-line shows the current step displayed in the 3D movie on the left.

Select zoom area with your mouse (you may do that several times to zoom in further). From the toolbar you can pause resume the activity and zoom out.

This viewer can display multiple time series. On the right side of the toolbar there will be a selection component for each signal source. These selection components determine what signals are shown in the viewer. To select additional time series use the brain menu in the upper left corner. From that menu you can change viewer settings. The page size determines how much data should appear at once in the viewer. The spacing determines the space between the horizontal axis of each signal. Setting it to 0 will plot all signals in the same coordinate system. A side effect of this setting is that as you decrease this axis separation the amplitude of signals is scaled up.

../../_images/visualizer_timeseries_channel_selection.jpg

Selecting the “channels” to be displayed (available in several viewers of TVB).

Dual Brain Activity Visualizer

This visualizer combines the brain activity movie shown in a 3D display on the left, with the explicit channels recording lines on the right. Movie start/stop, speed control, color schema change, channel selection are some of the features available in this visualizer.

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Brain activity wit EEG recordings.

../../_images/visualizer_dual_seeg_and_regions.jpg

Brain activity with sEEG recordings (on the left instance) and region level activity (on the right).

Volume Visualizer

This family of viewers display volumetric data, usually in an anatomical space. If the data has a time component then on the right side it will display timelines for selected voxels. FMri data is an example of this. A structural mri volume may be used as a background.

../../_images/visualizer_tsv.jpg

TimeSeries Volume with selections

Volumetric fragment

There are 3 navigation and viewing quadrants on the left and one main “focus quadrant” (left-central). It is possible to navigate in space using the slide controls on the top-left toolbar or by clicking on the 3 navigation quadrants on the most left part of the screen. So clicking in the 3 left squares will change the X, Y, Z of the planes slicing through the currently displayed volume (as the sliders on top are doing), while clicking in the main (central) square will select the clicked point for display of details on the right.

The crosses designate the selected voxel. It’s value is shown at the bottom of the focus quadrant. A white bar on the color legend also indicates this value.

The playback function is activated by clicking the play button on the top bar, and it will then change the display with time (left and right areas); The time series data is buffered from the server according to the currently section of view.

A different color map can be selected by clicked the Brain call-out in the top-right side of the screen. You might want to use the trim middle values feature with this viewer. It renders values around the mean transparent in the view. Also to be found un the Brain call-out.

Time Series Line Fragments

This is the right part of the TimeSeries Volume visualizer and is composed of three main parts:

Global Time Series Graph

All selected lines are shown here (top area), with the same scaling. Some transparency is applied to the lines and only one line is highlighted at a time. Highlighting can be done be passing the mouse over the line on the global graph or by clicking the selected line in the sortable graphs bellow. Vertical scaling is done based only on the selected values and not on the complete data set. A red vertical line shows the current time point (correlated with the movie in TimeSeries Volume section). A blue line follows the mouse showing the value of the highlighted line at each point.

Time slice selection (focus):

This function can be used to display only a portion of the data, zooming on it bellow. Try dragging in this region. The grey selection box can be moved and resized. If the focused data looks flat, increase the selected window length. The selection will automatically set itself around the current time point with a default extent during playback.

Sortable Graphs:

Every selected time series from the volume is shown on a separate line and labeled based on its coordinates from the 3D space. Adding lines in this section can be done by clicking in the left area on the main quadrant.

Important notice: While these time lines share the temporal axis they do not share the vertical one. The signal amplitudes are dynamically scaled so as to make the signal features visible. Amplitudes are not comparable among two of these signals.

The lines are colored following the selected feature in “Color Lines by” at the top of the screen. They are then sorted automatically by one of the selected methods or manually, by dragging and dropping each line in the desired position, as seen on the picture bellow. Lines can be removed by dragging them to the top “trash bin area” that appear every time a line is selected to be dragged.

../../_images/visualizer_tsv_fragment.jpg

TimeSeries Fragment

Connectivity Measure Visualizer

This visualizer can be used for displaying various Brain Connectivity Measures, related to a given Connectivity.

On the X axis, we will see the Connectivity nodes listed, and for each of them, we see the computed measure on the Y axis.

../../_images/visualizer_histogram.jpg

Connectivity Measure Visualizer.

Topographic Visualizer

This visualizer can be used for displaying various Brain Connectivity Measures, related to a given Connectivity. Its input is same as for the previous visualizer (Connectivity Measure Visualizer), but the display is completely different. Instead of a discrete view, this time, we can have a continous display (with gradients).

../../_images/visualizer_topographic.jpg

Preview for Topographic Visualizer

Surface Visualizer

This visualizer can be used for displaying various Brain Surfaces. It is a static view, mainly for visual inspecting imported surfaces in TVB. Optionally it can display associated RegionMapping entities for a given surface. Navigate the 3D scene like in the Brain Activity Visualizer.

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Surface Visualizer.

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Cortical Surface Visualizer with Region Mapping applied.

Sensor Visualizer

This visualizer can be used for displaying EEG, MEEG, and internal sensors . It is a static view, intended for visual inspecting imported sensors in TVB. Optionally it can display the sensors on a EEG cap surface.

To show sensors displaying on a Cap, check the call-out on the top-right corner.

When displaying the EEG sensors on a EEG Cap surface, we are automatically computing a “parcellation”. Currently this parcellation has no anatomical meaning, it is only based on distance (a vertex gets coloured as the closest sensor).

Navigate the 3D scene like in the Brain Activity Visualizer.

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EEG and MEG Sensors.

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Internal Sensors.

Local Connectivity Visualizer

Once a Local Connectivity DataTypes (which in fact is a huge sparse matrix of max size surface vertices x surface vertices, shaped after the cut-off) gets computed, one can view the correlation of a given vertex compared to all its neighbours, by launching this viewer. The Local Connectivity viewer can be launched from the DataType overlay (after clicking on a Local Connectivity datatype, and then selecting TAB Visualizers), or from Connectivity (bottom page menu), Local Connectivity option on top of the page, then select an existing LocalConnectivity and finally click “View” from the right side menu.

../../_images/local_connectivity_viewer.jpg

Inspect local connectivity on surface.

In order to see actual correlations, one should pick (by mouse click) a vertex on the 3D cortical surface once it loads in the canvas. The colors displayed nearby, show connected vertices with the selected point.

Annotations Visualizer

This viewer shows ontology annotations linked with TVB connectivity regions. It is composed of two main display areas:
  • 3D left-side canvas with TVB regions. These regions are color coded, based on the connectivity region index (similar to Surface Visualizer when a Region Mapping entity is selected). From the most top-right corner menu, you can change the color scheme used to draw these regions coloring.
  • 2D tree display of ontology annotations. A tooltip will appear if you go with the mouse over various nodes, and will show you details imported from the ontology.
The two areas (left and right) are linked, both ways:
  • You can pick a vertex in 3D and have the corresponding tree node highlighted on the right-side, or backwards:
  • Click on the tree, and have the corresponding region(s) highlighted in 3D.
../../_images/visualizer_annotations.jpg

Pick a vertex in 3D and have the corresponding tree node selected on the right.

Hints:
  • There is an checkbox on the top-right menu to draw region boundaries in the 3D canvas
  • When you click on an ontology node on the right, a message text will appear on the top area of the page, telling you how many TVB regions are linked to this ontology term
../../_images/visualizer_annotations_back.jpg

Select a tree node on the right, and have the linked regions highlighted in 3D.

Group Display

Discrete PSE Visualizer

Discrete Parameter Space Exploration (PSE) View, will show up information on multiple simulation results at once.

In TVB is possible to launch multiple simulations by varying up to 2 input parameters (displayed on the X and Y axis of the current viewer). Each simulation result has afterwards “metrics” computed on the total output. Each metric is a single number. Two metrics are emphasized in this viewer in the node shapes and node colors.

When moving with your mouse cursor over a graph node, you will see a few details about that particular simulation result. When clicking a node, an overlay window will open, which gives you full access to view or further analyze that particular Simulation result.

../../_images/visualizer_pse_discreet.jpg

Preview for Discrete PSE Visualizer, when varying two input parameters of the simulator

A newly incorporated feature is the option to pan the canvas in/out or left/right/up/down. To pan you may click and drag on top of one of the axes, and to zoom in double click or out shift + double click. This will allow for inspection of very large batch simulations section by section. The same mouse over, and clicking rules apply from above.

../../_images/visualizer_pse_discreet_panning.jpg

Panning the Graph

../../_images/visualizer_pse_discreet_filter.jpg

Filter support

The next new tool is the filter button. This allows users to specify threshold values for either the color or size metric and render results transparent if they are below that value. This tool has the option to invert the threshold rule which makes the results above that threshold transparent instead. Also, the user has the choice to make their filter more specific by adding further criteria rows that relate to the one which came before it through selected logical operators (AND OR). It is worth noting that in order to perform filtering that require grouping of the logical operations ([foo and bar] or baz) as different from (foo and [bar or baz]) sequential filters must be applied: one filter execution then the other.

../../_images/visualizer_pse_discreet_explore.jpg

Explore Tool, with Region Selected

(The Explore button is currently disabled because this functionality is not fully implemented)

The last tool to be described in the PSE Discrete Viewer is the Explore tool. This tool is meant to give users the option to select regions of the Parameter Space to be filled in with new results. Currently only the front end of this tool is complete, so upon clicking the explore button the mouse cursor becomes a cross hair, and sections of the graph can be selected. Upon creation of this selection, grid lines are placed to demonstrate where new results would be added given the user’s chosen step values. To adjust these values simply drag the sliders in the drop down menu for the explore tool, and the grid lines will adjust until they suit the user.

../../_images/visualizer_pse_sparse.jpg

Sparse results

Isocline PSE Visualizer

Continuous Parameter Space Exploration View, will show the effect of varying Simulator parameters in a continuous form.

When running a range of Simulations in TVB, it is possible to do it by varying up to 2 input parameters (displayed on the X and Y axis of current viewer). This visualizer supports ranges with 2 dimensions only, it does not support ranges with only one dimension. Also both varying dimensions need to be numeric parameters (no DataType ranges are supported for display in this visualizer).

../../_images/simulator_pse_iso.jpg

Preview for Continuous PSE Visualizer, when varying two numeric input parameters of the simulator

Controls for scaling or zooming the graph are available in this viewer. When you click on the coloured area, an overlay window will open, containing possibility to view or further analyze the simulation result closest to the point where you clicked.

Analyzers + Visualizers

Covariance Visualizer

Displays the covariance matrix. The matrix size is number of nodes x number of nodes

../../_images/visualizer_covariance.jpg

Preview for Covariance Visualizer

Cross Coherence Visualizer

Displays the cross-coherence matrix. Axes represent brain nodes. The matrix size is number of nodes x number of nodes.

../../_images/visualizer_cross_coherence.jpg

Preview for Cross Coherence Visualizer

Complex Coherence Visualizer

Displays the complex-cross-coherence matrix. Axes represent brain nodes. The matrix is a complex ndarray that contains the number of nodes x number of nodes cross spectrum for every frequency frequency and for every segment The thick line represents the Mean and the colored area the SD of CohSpec

This visualizer is very similar with the previous one (Cross Coherence Visualizer).

../../_images/visualizer_complex_coherence.jpg

Preview for Complex Coherence Visualizer

Cross Correlation Visualizer

Displays the cross-correlation matrix. Similar to the previous three visualizers.

Pearson Coefficients Visualizer

Displays the Pearson cross correlation coefficients matrix. As the correlation matrix is symmetric, only half is actually displayed.

../../_images/visualizer_pearson_correlation.jpg

Preview for Pearson Cross Correlation Visualizer

Fourier Spectrum Visualizer

Plots the power spectrum of all nodes in a time-series.

From the top bar, you can choose the scale (logarithmic or linear) and when the resulted Timeseries has multiple modes and State variables, choose which one to display. After you change a selection in this top bar, the viewer will automatically refresh.

../../_images/visualizer_fft.jpg

Preview for Fourier Spectrum Visualizer

Principal Component Visualizer

On the left, the ring plot displays the fraction of the variance that is explained by each component.

On the right, the first ten components are plotted against the brain nodes (variables).

../../_images/visualizer_pca.jpg

Preview for Principal Components Analysis Visualizer

Independent Component Visualizer

ICA takes time-points as observations and nodes as variables.

As for PCA the TimeSeries datatype must be longer (more time-points) than the number of nodes. Mostly a problem for TimeSeriesSurface datatypes, which, if sampled at 1024Hz, would need to be greater than 16 seconds long.

../../_images/visualizer_ica.jpg

Preview for Independent Components Analysis Visualizer

Wavelet Spectrogram Visualizer

2D representation that shows how the signals wavelet spectral coefficients (frequency) vary with time.

../../_images/visualizer_wavelet.jpg

Preview for Wavelet Visualizer

Matrix Visualizer

This is a 2D representation of a generic matrix-like result.

In case the current Datatype has more than 2 dimensions, the ND array will be cut, with a default slice. The user can also input the slice manually.

../../_images/visualizer_matrix.jpg

Preview for Matrix Visualizer

Connectivity Edge Bundle Visualizer

Shows structural connectivity coming in and out of a brain region by highlighting paths to other regions.

../../_images/visualizer_connectivity_edge_bundle.jpg

Preview for Connectivity Edge Bundle Visualizer

Pearson Edge Bundle Visualizer

Shows functional connectivity coming in and out of a brain region by highlighting paths to other regions.

../../_images/visualizer_pearson_edge_bundle.jpg

Preview for Pearson Edge Bundle Visualizer