BODB Talairach Applet

The Research Imaging Center of The University of Texas Health Science Center at San Antonio has given us permission to use the brain templates and database of regional Talairach coordinates from their Talairach Daemon. We now describe the Talairach Applet (TA) that we provide in BODB. It has been improved by incorporating features from an earlier, but only partially implemented, effort of the USC Brain Project, NeuARt (the NeuroAnatomical Registration viewer). There are two versions of the Talairach applet: two-dimensional and three-dimensional. The default version is two-dimensional, but this can be changed in the User Profile. When clicking on the Talairach link in the main toolbar, the default applet is loaded.

Two-Dimensional Talairach Applet

The Two-Dimensional Talairach Applet provides 3D brain information via 2D brain images in 3 views: axial, coronal and saggital.

The two-dimensional version of the Talairach applet.

The two-dimensional version of the Talairach applet.

Navigation

The two basic navigation actions that can be performed are changing the slice and changing the view. The current slice can be changed by three methods: dragging the red slider to the right of the slice image, clicking anywhere in the image navigator, or selecting a slice from the dropdown list to the right of the image navigator. The view can be changed by selecting one of Axial, Coronal or Saggital from the topmost dropdown list to the right of the image navigator.

The two-dimensional version of the Talairach applet in coronal view mode.

The two-dimensional version of the Talairach applet in coronal view mode.

The two-dimensional version of the Talairach applet in saggital view mode.

The two-dimensional version of the Talairach applet in saggital view mode.

Viewing Coordinates

Selected coordinates are displayed in the slice image if they fall within the bounds of the current slice, and the image navigator. The blue and green sliders control the thickness of the slice by increasing or decreasing the lower and upper bounds on coordinates to display in the current slice image.

Typically, brain imaging coordinates are given along with a measure of their statistical significance (usually scores for a t or z test). When these values are entered with coordinates, the significance threshold for the Talairach Daemon can be set such that only coordinates with a statistical significance above that threshold will be shown. The current significance threshold is shown below the image navigator. The significance metric used to determine significance can be selected by checking either “t Score” or “z Score”. All coordinates that do not have a value for the selected metric will be displayed regardless of the threshold value. The threshold value can be adjusted by clicking and dragging the black slide bar (the maximum threshold is the highest significance level in the current set of selected coordinates, given the chosen significance metric).

In addition, a user can select not to see some coordinates or change the color or shape by clicking the button, “Display Properties”. A new window will pop up where the user can click at a checkbox to set or unset visibility, click at the color box to select a new color, or click on the shape dropdown to change the shape of the coordinate. Under each SED coordinate list there are links to check or clear the visibility, change the color, or change the shape of every coordinate in the SED all at once. After a change is made, hit “Save” to save the changes.

The display properties window of the two-dimensional version of the Talairach applet.

The display properties window of the two-dimensional version of the Talairach applet.

Search Functions

There are 2 search functions on the applet: search for coordinates (A) and search for regions (B). The user can click at any location on the slice (2D image) in the left-hand window of the applet and then click the “Search coordinate(s)” button to see what brain regions it is in, shown hierarchically. A red cross on the image and an exact coordinate value (x,y,z) will appear after each click and can be erased by clicking the “Clear all coordinate(s)” button. On the other hand, the user can input some brain region names and click the “Search region(s)” button to see where they are on 2D images. Each area is displayed distinctively by different color blobs in all three views. The color blobs also appear on the image navigator in order to help the user see the brain regions clearly. The size and minimum/maximum values of x, y, z coordinates of brain regions are also given in the search results box. The color of each blob can be changed in the window shown after clicking “Display Properties”. Color blobs can be removed from the image by clicking on the button “Clear region(s).”

The two-dimensional version of the Talairach applet when using the search regions option.

The two-dimensional version of the Talairach applet when using the search regions option.

Export Functions

The current slice image (including selected coordinates and regions) can be saved in a variety of image formats by clicking on the “Save Slice” button. A full report including an image of each slice in each view can be generated by clicking on the “Generate Report” button. If the “Print Region labels” checkbox is selected the images will contain a key describing the color and name of each selected brain region.

Three-Dimensional Talairach Applet

The Three-Dimensional Talairach Applet allows the user to view selected coordinates, brain regions, and a slice in each view (Axial, Coronal, Saggital) in three-dimensional space. This applet requires Java3D to be installed on the user’s system.

The three-dimensional version of the Talairach applet.

The three-dimensional version of the Talairach applet.

Navigation

The brain can be navigated by changing the current 3D view as well as changing the slice in each view. The 3D view can be rotated by left-clicking and dragging, panned by right-clicking and dragging, or zoomed by using the mouse scroll wheel. The “Reset” button will return the 3D view to the default initial position. The slice in each view can be changed by dragging the appropriate slider at the bottom of the applet. This will move the slice plane as well as change the slice image.

The three-dimensional version of the Talairach applet after rotating the view and zooming in.

The three-dimensional version of the Talairach applet after rotating the view and zooming in.

Viewing Coordinates

Selected coordinates are displayed in the 3D view as colored three-dimensional shapes. Moving the mouse over a coordinate shape will popup a tooltip displaying the coordinate and hierarchical brain regions it is part of. The user can select not to see some coordinates or change the color or shape by clicking the button, “Display Properties”. A new window will pop up where the user can click at a checkbox to set or unset visibility, click at the color box to select a new color, or click on the shape dropdown to change the shape of the coordinate. Under each SED coordinate list there are links to check or clear the visibility, change the color, or change the shape of every coordinate in the SED all at once. After a change is made, hit “Save” to save the changes.

The display properties window of the three-dimensional version of the Talairach applet.

The display properties window of the three-dimensional version of the Talairach applet.

Search Functions

The user can input some brain region names and click the “Search” button to see where they are in 3D space. Each area is displayed distinctively by semi-transparent colored blobs. The size and minimum/maximum values of x, y, z coordinates of brain regions are also given in the search results box. Moving the mouse over a blob will popup a tooltip displaying the region name. The color and transparency of each blob can be changed in the window shown after clicking “Display Properties”. Color blobs can be removed from the image by clicking on the button “Clear region(s).”

The three-dimensional version of the Talairach applet when using the search regions function.

The three-dimensional version of the Talairach applet when using the search regions function.

Export Function

The current 3D view (including selected coordinates and regions) can be saved in a variety of image formats by clicking on the “Save Snapshot” button.