Turbo-BrainVoyager v3.2

Keyboard and Mouse Functions

Keyboard and mouse functions can be used to quickly access important features of Turbo-BrainVoyager. Short cuts are described below allowing to quickly switch between available views on the data. Then options are described available within each specific brain view. Finally general options are presented, which are valid for all views. Finally options for Time Course Windows are described.

Switching Brain Views

F key. Switches to the Multi-Slice View of the data. The same function is also provided with the Multi-Slice View item in the View menu and with the Multi-Slice View icon located below the Brain Window. The Multi-Slice View shows the (incrementally) calculated contrast maps on original slices in a multi-slice arrangement allowing to inspect the whole data at once. As default, the EPI images from the first measured volume are shown in the multi-slice arrangement but the EPI images may be replaced by higher-resolution inplane (T1 or T2) images from a scan prior to functional measurements (see "I" button below). It is possible to zoom into a single slice by clicking in a slice while holding down the SHIFT key (Single-Slice View, see below).
V key. Switches to the Volume View of the data. The same function is also provided with the Volume View item in the View menu and with the Volume View icon located below the Brain Window. The Volume View shows (incrementally) computed statistical maps in three subwindows in 3D mode. The three subwindows show a sagittal, coronal and axial plane of the data, which is interpolated to a 1mm x 1mm x 1mm data set from the original data. This view uses only data from the original slice positions without any translation or rotation transformation. As default, the EPI images from the first measured volume are used to build the orthographic 3D view but the EPI images may be replaced by higher-resolution inplane (T1 or T2) images from a scan prior to functional measurements (see "I" button below).
A key. Switches to the Anatomical Volume View. The same function is also provided with the Anatomical Volume View item in the View menu and with the Anatomical Volume View icon located below the Brain Window. This option is only available if an intra-session, ACPC or Talairach transformed 3D data set is loaded. As opposed to the standard Volume View, the statistical data is projected on a full high-resolution 3D data set in this visualization. The projection uses a spatial transformation matrix and eventually a Talairach transformation step. Specifications in the TBV settings file determine whether the anatomical 3D data resides in intra-session, AC-PC or Talairach space and requires appropriate transformation files.
S key. Switches to the Surface View. The same function is also provided with the Surface View item in the View menu and with the Left Hemisphere and Right Hemisphere Surface View icons located below the Brain Window. This option is only available if meshes are loaded, which must be prepared in BrainVoyager QX. The meshes are typically representations of the left and right cortical sheet. This option furthermore requires that a 3D data set is also loaded residing in the same space as the cortex meshes. The statistical data is projected on the cortex meshes by using the same transformation pipeline as used for the inplane, AC-PC or Talairach anatomical 3D data set used in the Anatomical Volume View.

Options in Multi-Slice View

Dragging rectangle with left mouse button. Drag a rectangle on a slice to obtain the average time course of pixels within the region. The time course is shown in one of the Time Course Windows. Time courses can also be shown in the Time Courses Container. If no time course is visible yet, the data will be shown in the top most Time Course window. New drag operations will replace the data in the current ROI window with the average time course of the newly selected voxels. If a rectangle is dragged while the SHIFT key is down, the time course of the selected voxels is shown in a new Time Course window. Note that the mapping between a rectangle and the corresponding Time Course window is established by the color of the drawn ROI rectangle (and/or voxel highlight color), which is also shown in the lower corner of the Time Course window. If multiple Time Course windows show data, you can make one of them the current ROI window by clicking with the left mouse button in its window. As default, the averaged time course of the significant (color-coded) pixels within the dragged rectangle are selected. If no significant pixels are inside the rectangle, the time courses of all pixels in the rectangle are chosen. Slices above and below the current slice can be included for ROI selection by using a MultiSliceROI value larger than 1.
I key. Switches between scanned functional (EPI) images (in first-volume-of-current-run mode) and images from a scan with higher-resolution T1 or T2 inplane images. The same function is also provided in the View menu with the Overlay On Inplanes and Overlay On First Func Volume items.
C key. Switches between displaying first functional (EPI) volume or current functional volume. The same function is also provided in the View menu with the Overlay On Current Func Volume and Overlay on First Func Volume items. The current display mode is shown in the Log pane.
B key. Switches between display of the current volume before or after spatial preprocessing (e.g. motion correction, spatial smoothing if turned on). This key toggle has an effect only when the option to show the current functional volume is turned on (see item above). The current display mode is shown in the Log pane.
ALT-Click. Click at any position within a slice while holding down the ALT key to switch to Single-Slice View showing an enlarged view of the selected slice within the area of the view window. In order to leave Single-Slice View switching back to Multi-Slice View, SHIFT-Click the zoomed slice.
CTRL-R. Toggles the visualization of ROIs between rectangle mode, highlighted voxel mode and combined mode (see also corresponding items in View menu).

Options in Single-Slice View

CMD/CTRL-Click. Click a pixel on the enlarged slice view while holding down the CTRL (on Windows and Linux) or CMD (on Mac) key to include or exclude the respective voxel from the current ROI.
PgUp/PgDwn or CursorKey-Left/CursorKey-Right. Use these buttons to switch slices in zoomed single-slice mode.
Dragging rectangle with left mouse button. Although this view is often used to select individual voxels, you may also drag a rectangle on a slice to obtain the average time course of pixels within the region in the same way as in Multi-Slice View.
I key. Switches between scanned EPI images (first volume of current run) and images from a scan with higher-resolution T1 or T2 inplane images. The same function is also provided in the View menu with the Overlay On Inplanes and Overlay On First EPIs items.
ALT-Click. Click at any position within the slice while holding down the ALT key to switch back to Multi-Slice View.
CTRL-R. Toggles the visualization of ROIs between rectangle mode and marked voxel mode (see also corresponding items in View menu).

Options in Volume View

Mouse navigation. Click in any of the three orthographic sub-view windows (sagittal, coronal and axial) windows. Navigate to any region by moving the mouse left/right and up/down while holding down the left mouse button.
CursorKey navigation. Navigate stepwise through slices of the Volume View moving left/right with the LEFT and RIGHT cursor keys, and up/down with the UP and DOWN cursor keys. To move forward/backward, use the UP and DOWN cursor keys while holding down the SHIFT button.
CTRL-Click. Click on a voxel in any of the three sub-views with the left mouse button while holding down the CTRL key to select a region-of-interest (ROI). If a significant (color-coded) voxel is hit, a functional cluster with only significant pixels will be selected. If a non-significant voxel is hit, all voxels within a 3D cube around the voxel will be included in the ROI. The averaged time course of the voxels within the ROI will be shown in the current Time Course Window. To put the data of a selected ROI in a new Time Course Window, hold down both the CTRL and SHIFT key.
I key. Switches between scanned EPI images (first volume of current run) and images from a scan with higher-resolution T1 or T2 inplane images. The same function is also provided in the View menu with the Overlay On Inplanes and Overlay On First EPIs items.

Options in Anatomical Volume View

Mouse navigation. Click in any of the three orthographic sub-view (sagittal, coronal and axial) windows. Navigate to any region by moving the mouse left/right and up/down while holding down the left mouse button.
CursorKey navigation. Navigate stepwise through slices of the Volume View moving left/right with the LEFT and RIGHT cursor keys, and up/down with the UP and DOWN cursor keys. To move forward/backward, use the UP and DOWN cursor keys while holding down the SHIFT button.
CTRL-Click. Click on a voxel in any of the three sub-views with the left mouse button while holding down the CTRL key to select a region-of-interest (ROI). If a significant (color-coded) voxel is hit, a functional cluster with only significant pixels will be selected. If a non-significant voxel is hit, all voxels within a 3D cube around the voxel will be included in the ROI. Note that functional ROI selection does not operate in the space of the Anatomical Volume View (e.g. Talairach space), but in the space of the original slice data. The coordinates of the selected voxel in intra-session, AC-PC or Talairach space are transformed back into the original space of the current functional measurement and the selection of voxels is performed in that space according to the rules described earlier. After having expanded the selection in the data's native space, the coordinates of the marked voxels are forward transformed to be visualized adequately in the space of the Anatomical Volume View. The averaged time course of the voxels within the ROI will be shown in the current Time Course window. To put the data of a selected ROI in a new Time Course Window, hold down both the CTRL and SHIFT key.

Options in Surface View

Mouse navigation. Move the mouse left/right and up/down to rotate the viewpoint around the mesh(es). Hold down the left mouse button and move the mouse up and down and left and right to perform translations of the viewpoint. Hold down both the SHIFT and CTRL keys and move the mouse up and down in order to move the viewpoint closer or further away (zooming).
CursorKey navigation. Rotations of the viewpoint can be performed also in small steps by clicking the left/right and up/down cursor keys.
CTRL-Click. Click on a mesh while holding down the CTRL key to select a region-of-interest (ROI). If a significant (color-coded) vertex is hit, a functional cluster with only significant vertices will be selected. If a non-significant vertex is hit, a region around the vertex will be included in the ROI. Note that functional ROI selection does not operate on the surface, but in the space of the original slice data. The coordinates of the vertex are transformed back into the space of the current functional measurement and the selection of voxels is performed in that space according to the rules described earlier. After having expanded the selection in the data's native space, the coordinates of the marked voxels are forward transformed to be visualized on the mesh. The averaged time course of the voxels within the ROI will be shown in the current Time Course Window. To open a new time course window, hold down both the CTRL and the SHIFT key.

Statistical options

P key. Toggles between significance color coding and multi-map color coding in the View window. The same function is also provided with two entries in the Analysis menu, namely Colors Code Significance and Colors Code Contrasts. If colors code significance, a red-to-yellow range of colors is used for gr contrasts, and a typical blue-to-green range of colors for lt contrasts. Since the same color range is used for all contrasts, it is not recognizable which contrast is shown at a particular voxel. In colors code contrasts mode, each significant voxel is visualized with the color of the contrast with the highest t-value.
CTRL-CursorKey-Up. Increases the statistical t threshold by a value of "0.2". The same function can be also performed using the Threshold spin box.
CTRL-CursorKey-Down. Decreases the statistical t threshold by a value of "0.2". The same function can be also performed using the Threshold spin box. The value can not be set lower than t = 1.0. The current value of the threshold is shown in the Information Window and in the Threshold spin box.

Time Course Windows

Mouse Selection. Clicking within a Time Course Window makes the respective window the current one. When selecting a region-of-interest in one of the Brain Views, the time course data is shown in the current Time Course Window replacing the data previously shown. When holding down the ALT key when selecting a ROI, the data of the new region is shown in a new Time Course Window. The number of time course windows corresponds directly to the number of simultaneously visualized ROIs. The data of the current Time Course Window is also used to calculate event-related averages, which are shown in the Volume and Anatomical Volume Views. If you have selected one of these views, you can thus inspect event-related averages for all currently available ROIs by clicking within the respective Time Course Window.
T key (toggle). Show / hide the Time Courses Container.
D key (toggle). Turns on (default) and off display of detrended ROI time courses that are visible in the main window and the Time Courses Container. This option is only available in case that linear trend removal has been enabled as a confound predictor in the design matrix. This feature can also be turned on and off using the Display detrended ROI Time Courses option in the View menu.
CTRL-B key combination (toggle). Shows/hides the beta bar plot on the right side of a Time Course Window. The bars of the beta plot are estimates of the beta values of the respective main conditions of the protocol. The color of the bars matches those defined for the corresponding condition in the protocol.
CTRL-N key combination. Expands the horizontal space for the beta bar plot. Use this option if the bars are drawn to closely to each other or if you want to see the condition names below the plot without interference with names of other conditions. This option does not work in separate Time Course Windows detached from the main window, which can be freely resized.
CTRL-M key combination. Shrinks the horizontal space available for the beta bar plot. Use if you want to use more space in the window for drawing the ROI time course. This option does not work for the Time Courses Container detached from the main window, which can be freely resized.

Miscellaneous

R key. The speed of real-time data processing depends normally on how fast the data arrives from the scanner. With the R key, the ForceTRDelay option can be turned on, which forces TBV to wait the time specified in the TR value in the TBV Settings File before progressing with reading the next data point (volume). This option can be, for example, be used when rerunning the real-time analysis to slow down the program, otherwise it will work as fast as possible since all data is available. The option might also be helpful in a real situation because it can be used to avoid that the program "peeks" into not fully written data files, which seem to slow down processing in some situations. The key can be pressed again to stop the ForceTRDelay mode. In this case, the program will wait until the time N*TR has elapsed with N reflecting the current data point.