The glass brain view is intended to provide a visualization for statistical group analysis results but can also be used for individual data. In the glass brain view, the functional clusters of a statistical map are represented and visualized as shaded polygon meshes in a transparently rendered Talairach brain. The glass brain view integrates a number of tools described in other chapters. After launching the glass brain view tool, the following steps are performed:
For each contigours functional cluster a VOI is created and reconstructed as a polygon mesh (for details, see section "VOI segmentation and surface reconstruction options" in chapter "Region-Of-Interest Analysis Tool"). The created VOIs are saved in the file "clusters.voi" within the current working directory. The surface representation of the clusters is saved in the file "Clusters.srf". Additionally, the files "Clusters_tal.txt" and "Clusters_tcs.txt" are saved. The file "Clusters_tal.txt" contains information about the cluster size (number of voxels) and location (Talairach coordinates of the center of gravity). The file "Clusters_tcs.txt" contains the time courses of the clusters from the currently linked VTC file.
The surface "GlassBrain.srf" is loaded from the BrainVoyager folder. This polygon mesh represents the "glass brain" and has been created from the outer contours of the Talairach brain. The glass brain is rendered transparently to allow viewing the functional clusters created in step 1.
The file TalairachBrain.vmr (see "Talairach brain atlas") is loaded from the BrainVoyager folder as the secondary VMR data set. If the glass brain is cut, slices from the Talairach brain are shown because the secondary VMR is set as the current VMR. It is possible to toggle between the Talairach brain and the initially loaded (primary) VMR data set using the F8 key. This allows to see the statistical map either with respect to the Talairach brain or with respect to the brain of an individual subject or an averaged brain.
A surface representation of the reduced Talairach grid is shown. This grid can be turned on or off within the 3D Axes Options dialog, which can be invoked using the Meshes -> Rendering options -> Axes and Tal grid... menu item.
In the following example, we visualize the statistical map from of a two-subject analysis using the glass brain tool. The only prerequisite to use the glass brain view is the availability of a VMR data set and a VMP data structure. Load the file "BS_TAL.vmr" from the "BrainVoyager\Samples\ClockTask" folder. Since our sample data does not contain the VMR data set of the second subject, we will visualize the "group" map on top of the brain of subject BS. If we would have all subject's VMR's (in Talairach space), we could average the brains using the buttons in the Average 3D data sets field of the Talairach tab of the 3D Volume Tools dialog. Now enter the Overlay GLM Contrasts and Contribution Maps dialog by clicking the Analysis -> Overlay General Linear Model... menu item. Using the local File menu, open the file "ClockTaskTwoSubjects.glm". Click the Fill contrast button to "plus-select" all six listed predictors. Click the OK button to overlay the GLM. Enter the Overlay Statistical Maps dialog clicking the Analysis -> Overlay maps... menu item. Change the min: value in the Confidence range field to "30" and the Size: value in the Cluster field to "200". These optional changes reduce the size and number of activated clusters by using more strict statistical criteria. Click the OK button to accept these settings. You will now see a screen similar to the snapshot shown below.
To run the glass brain tool, click the Analysis -> Glass brain view of VMP clusters menu item (see red rectangle). The program is now executing the steps listed above, which may take several seconds or minutes depending on the number and size of functional clusters. You can observe how the program adds one cluster after the other in the surface module window. When the glass brain tool has been finished creating the VOIs, you will finally see an output similar to the following one:
Initally, a left lateral view of the glass brain is shown. You can use the Viewpoint Settings dialog to quickly inspect other standard views. To invoke this dialog, click the "V" button or the Meshes -> Viewpoint settings... menu item. Then click through the icons on the left side to obtain other standard views. The next snapshot shows, for example, a top view.
You can also change the values in the Translation and Rotation field or use the mouse and keyboard to change the viewpoint. You can also change the viewing projection from orthographic (default) to perspective by clicking the "P" button. The following snapshot shows a perspective back view of the glass brain. For this view, the colors of the surface VOIs have been changed (for details, see section "VOI segmentation and surface reconstruction options" in chapter "Region-Of-Interest Analysis Tool"). Now the same color is used for presumed homologue areas in the left and right hemisphere. The snapshot also shows a slice of the Talairach brain. Slicing is enabled, as usual, by clicking the TRA cut icon and subsequent slice plane adjustments.
