Please launch BrainVoyager and open an inhomogeneity-corrected 3D dataset in native space, e.g. sub-01_ses-04_T1w_IIHC.vmr from the Getting Started Guide dataset.
The Talairach transformation can be started in the “Talairach” tab of the “3D Volume Tools” dialog. Switch to the “Talairach” tab of the “3D Volume Tools” and switch from “Automatic” to “Manual” AC-PC transformation. Click the “Find AC Point…” button.
The “3D Volume Tools” dialog will be replaced by the “Find AC Point” dialog. You can directly move the cross by clicking the spin controls of the “Find AC Point” dialog. The most convenient, but still precise navigation method is using the cursor keys, try the left, right, up and down cursor key, as well as SHIFT-UP and SHIFT-DOWN.
Now click the “OK” button in the “Find AC Point” dialog. The dialog will be replaced by the “3D Volume Tools” dialog and appropriate translation parameters (in the x, y, and z direction) will be specified for the AC-PC transformation. The display now also changes into a 2 x 3 arrangement. The upper row shows the original data set, while the lower row shows the data set after the application of the specified transformation.
Note: You can inspect the defined translation parameters in the “Coregistration” tab of the “3D Volume Tools” dialog. The values in the “Translation” field reflect the shifts (x = 0.0, y = 14.0, z = 16.0) necessary to move the original center of the 3D data set to the AC point, which will become the new center of the transformed data set. If desired, you can fine-adjust the translation values further.
After having specified the AC point, the “Find AC Point” button is disabled and the “Find AC-PC Plane...” button is enabled in the “Talairach” tab of the “3D Volume Tools” dialog. The next task is to rotate the data set in the coregistration window (lower row) in such a way, that we also see the posterior commisure in the axial slice. To find the posterior commisure, click the “Find AC-PC Plane...” button. The “Find AC-PC Plane” dialog will appear on the right side of the “VMR” window.
Use the “x” spin control in the “Rotation” field to rotate the dataset in the lower row until the view shows the posterior commissure. The rotation is executed around the position of the green cross. Since the cross is located at the anterior commissure, it will remain visible in the coregistration window, despite the rotation. The green cross can be used to adjust two additional angles, if necessary. Change the “y” and “z” angle to rotate the dataset in the coregistration window, so that the green cross separates the left and right hemisphere of the brain.
Tip: It might be helpful to temporarily hide the green and white cross. Deselect the “Show cross” item in the “3D Coords” tab. More conveniently, you can also press the “A” key to display or hide the green / white cross.
Now click the “OK” button in the “Find AC-PC Plane” dialog.
Info: The “Find AC Point” and “Find AC-PC Plane” dialogs provide a convenient way to specify the AC-PC transformation values. You can also do the same steps directly in the “Coregistration” tab. After you have placed the green cross on the AC, click the “Set Translation” button to fixate this point. If you click in the dataset afterwards, you can get back to the AC by clicking the “Center” button. Then adjust the rotation parameters by using the spin controls in the “Rotation” field on the “Coregistration” tab.
Click on the “Talairach landmarks” list box in the “Specification and visualization of Talairach landmarks” field. In the opened list box, you will see some landmarks and a spin control. You can use the spin control to navigate to a desired landmark. The first landmark is “AC”, which does not need to be specified again. Select the “PC” landmark. This point is easy to find in the data set, because it must be in the same axial plane as “AC”. Note that BrainVoyager automatically jumps to a location in the vicinity of the PC. Press repeatedly SHIFT-DOWN to move the white cross from the AC point to the PC.
Click the “Set point” button to define the “PC” point as the current location of the white cross.
Select the “AP” landmark. Click the “Set point” button to define the “AP” point as the current location of the white cross.
Tip: Although instructive, it is not necessary to set the AP point precisely in all dimensions. The only critical dimension is the y-axis or anterior-posterior axis. The z-coordinate (superior-inferior dimension) and the x-coordinate (left-right dimension) are irrelevant. This holds true also for all remaining points - only one dimension is critical.
Select the “PP” landmark. Click the “Set point” button to define the “PP” point as the current location of the white cross.
Note: You can easily verify and adjust the location specified for any landmark. To do this, select a landmark in the landmarks list, for example “AP”. The white cross will immediately jump to the respective coordinates. If you adjust the location of the landmark, do not forget to click the “Set point” button to accept the new coordinates.
Select the “SP” landmark. Click the “Set point” button to define the “SP” point as the current location of the white cross.
Select the “IP” landmark. Click the “Set point” button to define the “IP” point as the current location of the white cross.
Select the “RP” landmark. Please note that in BrainVoyager, MRI images are displayed in radiological convention. This means that LEFT is RIGHT and RIGHT is LEFT! Therefore, you need to locate “RP” on the left side of the image. In radiological convention, BrainVoyager shows an “R” symbol on the left side of the “COR” and “TRA” view to remind you of the convention. After having located “RP” on the left side, click the “Set point” button.
Select the “LP” landmark on the right side of the cerebrum (see remarks above). After having located “LP”, click the “Set point” button.
Note: The specified landmarks are now used to change the size of the brain in such a way that it fits into the size of the standard Talairach brain. This fitting procedure is done differently for 12 sub-volumes, which are defined by the 8 landmarks. After a few seconds, the resulting new 3D volume has been computed and saved to disk. In addition, it is also automatically shown in a new window.
Remark: Please note that you might have defined slightly different landmarks for the Talairach transformation compared to the automatic definition of the landmarks. Therefore, you might notice some small, but negligible differences in the Talairach coordinates of significant voxels.