Tutorial 17: Visual exploration
Authors: Francois Tadel, Elizabeth Bock, Sylvain Baillet
This tutorial explores the options Brainstorm offers to represent graphically and explore interactively the evoked responses we computed in the previous tutorial. It shows how to produce spatial maps of the sensors, temporal averages, save screen captures and movies.
Contents
2D/3D topography
The sensor values at one time instant can be represented on a surface. Each amplitude value gets associated with a color using a colormap (described in the next tutorial). We call this type of representation "sensor topography", it shows the spatial distribution of the magnetic fields (or electric potentials).
Show the MEG signals for the standard average in Run#01 (double-click on the file). This gives us a direct feedback of the current time instant and allows to jump quickly at a different time.
Right-click on the same file > MEG > select the menus: 3D sensor cap, 2D sensor cap, 2D disc.
3D sensor cap: Represents the real 3D positions of the sensors.
2D sensor cap: The sensors are projected on a 2D plane. Realistic distribution of the sensors.
2D disc: The sensors are projected on a sphere, then displayed as flat disc. Sometimes distorted...
In each of these views, you can add markers to indicate the sensors and their labels.
Right-click on the figure > Channels > Display sensors/labels (or Ctrl+E).You can change the number of contour lines: Right-click > Contour lines > 0-20.
- In the 3D view, you can notice a hole in the right-occipital area. It corresponds to a damaged sensor in the MEG system we used for collecting this dataset.
For EEG/sEEG/ECoG recordings, there is an additional representation mode available:
"3D Electrode". This will be detailed in the advanced tutorials corresponding to these modalities.
Magnetic interpolation
Some of the views re-interpolate by default the fields that are recorded by the MEG sensors to get smoother displays. A simple inverse problem and forward problem are solved to reconstruct the magnetic fields on a high-resolution surface of virtual magnetometers (function channel_extrapm.m).
On Elekta-Neuromag systems, this interpolation has the effect of converting the topographies of the planar gradiometers into topographies of magnetometers, which deeply affects the display.
The menu "No magnetic interpolation" offers the same views, but without using this reconstruction of the magnetic field. A spatial interpolation of the values between the sensors is performed instead.
2D Layout
The menu 2D Layout allows to represent in the same figure the spatial information (the values for each channel is represented where the sensor is actually located) and the temporal information (instead of just one single value, we represent the signal around the current time).
The light gray lines represent the zero amplitude (horizontal) and the current time (vertical lines).
Only a part of the full time window is displayed for each channel, before and after the current time. The length of this time window can be modified either with the mouse shortcut Ctrl+mouse wheel, or with the 2D Layout options, in the figure popup menu. The amplitude of the signal can be controlled with the shortcut Shift+mouse wheel.
Time selection
Click somewhere on the white part of the time series figure, hold the mouse button, and drag your mouse left or right: A transparent blue rectangle appears to represent the time selection. If you right-click on the figure, new options become available in the popup menu:
Set current time: Move the time cursor where the right-click occurred. The shortcut Shift+Click can be useful when trying to move in time on dense displays in columns view.
Set selection manually: Type the beginning and end of the selected window (in milliseconds).
Average time: Average over the selected time window and save it as a new file in the database.
Note that the best way to do this is to run the process "Average > Average time".Export to database: Extract the recordings and save them in a new file in database.
If some sensors are selected, only their values are extracted, all the others are set to zero.
Note that the best way to do this is to run the process "Extract > Extract time".Export to file: Same, but in a user-defined file (not in the database).
Export to Matlab: Same, but export the selection as a variable in the current Matlab workspace.
Snapshots
Using Brainstorm, you will quickly feel like saving the beautiful images you produce. Your operating system already provides some nice tools for doing this. Many other options are available in the "Snapshot" menu, available when you right-click on any Brainstorm figure.
Operating system
Windows/Linux: Press the PrintScreen key on your keyboard and paste the copied screen in your favorite image or text editor. The combination Alt+PrintScreen only copies the figure that is currently selected.
MacOS: Many more options available, Google for the best ones (see example).
Snapshot menu
The options available in the Snapshot menu depend on the type of data represented. Examples:
Save as image: Save the figure (without the title bar and borders) in a file. Many formats available.
Open as image: Capture the figure and open it in as an image. This can be useful if you want to compare visually the selected figure with another one that you cannot display at the same time (because they have different time or frequency definitions)
Open as figure: Similar, but copies the figure as a new Matlab figure with some interactivity.
Contact sheet and movies: See next section.
Export to database: Save the recordings in the figure as a new entry in database.
If there are selected channels, only their values will be saved, the others being set to zero.Export to file: Extract the time series displayed in this figure (or only the selected sensors), and save them in a file. Several exchange file formats available for exporting to another program.
Export to Matlab: Same thing, but exports the structure in a variable of the Matlab workspace.
Save as SSP projector: Create an SSP projector that removes the current topography.
Save surface: Save the surface in a file, with the current modifiers applied (smooth, resect).
Movie studio
Movie (horizontal/vertical): Rotate spatially the 3D scene.
Movie (time): Selected figure: Create .avi movies to show the evolution of the selected figure.
The dimensions of the movie depend on the actual size of the figure on the screen.
Resize the figure to the appropriate dimensions for the movie before using this menu.- Zoom in/out (mouse wheel) and move the image (middle click+move) to give enough space to the time stamp that is added at the bottom-left of the rendered movie.
- Don't do anything else while rendering: the captured figure must be visible all the time.
Movie (time): All figures: Instead of capturing one figure only, it captures them all. Arrange your figures the way you want and create a movie of all your workspace at once.
Contact sheets
A contact sheet is a large image representing many time frames of the same figure.
- Same recommendations as for movies: if you don't want the final image to be too big, reduce the size of the figure, zoom in, move, hide the colorbar. Keep the figure visible during the capture.
At the end, the image is displayed in an image viewer with which you can zoom (menu or wheel), move (click+move) and save the image (File > Save as).
Example for the standard average, run#01:
Edit the figures
All the figures can be edited with the Figure popup menu:
If you select both "Matlab controls" and "Plot edit toolbar", you will get all the tools available in the Matlab environment to explore the data and edit the figure. Select the button "Edit plot" to edit the graphic properties of an object (eg. select a signal, then right-click on it to edit its properties) or unselect it to get back to the regular Brainstorm figure interactivity.
Mouse shortcuts
Scroll
Mouse wheel: Zoom in / zoom out
Shift + mouse wheel: Change the amplitude gain of the channels
Control + mouse wheel: Change the length of the displayed time window (2D Layout)
Control + mouse wheel: Vertical zoom (time series)
Click
Left click + move: Rotate (3D) or select (time)
Middle click + move: Move in zoomed figure (ie. panning)
Left click + right click + move: Move in zoomed figure (ie. panning)
Shift + left click: Force setting the current time, ignoring if a line was clicked (time series)
Right click + move: Select sensors (2D topography)
Right click: Popup menu
Click on something
Click on a line: Select a sensor
Shift + click on a line: Select a sensor and unselect all the others (2D topography)
Click on the colorbar + move: Change contrast (up/down) and brightness (left/right)
Keyboard shortcuts
Here is a memo of all the keyboard shortcuts for time series and topography figures. If you don't remember them, you can find most of them in the figure popup menus.
Arrows: Left, right, PageUp, PageDown: Move in time
Delete: Mark selected sensors as bad
Shift + Delete: Mark non-selected sensors as bad (=keeps ony the selected sensors)
Enter: View time series for the selected sensors
Escape: Unselect all the selected sensors
Shift + Escape: Set all the bad sensors as good (=brings back all the channels in the display)
Ctrl + A: Show axis on 3D figures (X,Y,Z)
Ctrl + B: Set trial as bad
Ctrl + D: Dock/undock figure in Matlab's figures list
Ctrl + E: Show sensors markers and labels (E=Electrode) or add an event marker (E=Event)
Ctrl + F: Copy figure, removes all the callbacks and detach from Brainstorm figure management
Ctrl + I: Save figure as image
Ctrl + J: Open figure as an image
Ctrl + R: Open Time series view (R=Recordings)
Ctrl + S: Open Sources view (R=Sources)
Ctrl + T: Open 2D sensor cap view (T=Topography)
Shift + letter: Change selected montage.
F1, F2, F3: with or without Shift, calls the database navigator (F1=subject, F2=condition, F3=file)
=: Apply view to all figures
*: Apply montage to all figures
Notes for Mac users:
PageDown = Fn + DOWN
PageUp = Fn + UP
Delete = Fn + Delete
F1 = Fn + F1
Mouse wheel = Two finger up/down on the MacBook pad
Graphic bugs
If you observe any graphic problem with these displays, there might be an issue with the OpenGL drivers.
Change the OpenGL rendering properties: Menu File > Set preferences.
- Update the drivers for your graphics card.
- Use a newer version of Matlab or the compiled version of Brainstorm.