Automatic Talairach Transformation

• 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”.

  

   

• Select the “Visualize intermediate results” checkbox and click on “Auto-ACPC-TAL”. This will initialize the automatic Talairach transformation. The “Visualize intermediate results” option gives you the opportunity to review all steps performed during the transformation process in the so called “Image Reporter”; a new window that is opened by BrainVoyager. Figures below, labeled with Image Reporter, were copied from this additional review window.

  

   

• BrainVoyager automatically performs the following steps: It identifies the mid-sagittal plane (MSP) and uses this information to detect, segment and rotate the corpus callosum (CC), which is, in turn, removed to identify the fornix. The location information of the fornix is used to detect the anterior commissure (AC), which is the landmark that defines the origin of the Talairach coordinate system and will become the new center of the transformed data set. The figures below illustrate these steps.

  

• After the AC and PC are specified, the 3D data set is translated and rotated into the AC-PC plane. This is indicated by a progress window, as shown below
   

  

• After a few seconds, the transformation procedure is completed, and the resulting new 3D volume has been computed and saved to disk as sub-01_ses-04_T1w_IIHC _aACPC.vmr. In addition, it is shown automatically in a new window. The “aACPC” in the new file name indicates that the transformation was applied automatically and that the brain is in the AC-PC plane. This can be seen clearly in the “TRA” view, which shows both the AC and PC point (see figure below).

  

   

• In the second automatic step of Talairach transformation, the 3D data set has to be transformed from ACPC space into Talairach space by specifying eight landmarks within the AC-PC transformed data set: AC, PC, AP (the most anterior point of the cerebrum), PP (the most posterior point), SP (the superior point), IP (the inferior point), RP (the most right point) and LP (the most left point). In order to identify those points, BrainVoyager cleans the background of the data set and removes non-brain tissue. Afterwards the image is binarized so that the background intensity is 0 (black) and the brain tissue has an intensity value close to 225 (white).

  

• In a last step, BrainVoyager uses this binarized version of the original data set to detect the smallest and biggest coordinate for each axis of the coordinate system with an intensity value above 0, which corresponds to the following 6 landmarks:

  RP - smallest coordinate on x axis	LP - biggest coordinate on x axis
  AP - smallest coordinate on y axis	PP - biggest coordinate on y axis
  SP - smallest coordinate on z axis	IP - biggest coordinate on z axis

   

• All Talairach landmarks have now been specified. This information is used by BrainVoyager to change and fit the size of the brain to the size of the standard Talairach brain. This fitting procedure is done separately 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 (see figure below). The name of the new file is “sub-01_ses-04_T1w_IIHC_aTAL.vmr” and indicates that the data set is in Talairach space and that the automatic transformation procedure was used.

  

   

• The center of the new Talairach data set is still the AC point and the brain is still located in the AC-PC plane. The cerebrum’s size is, however, adjusted to fit into Talairach space. This can be easily tested by showing the Talairach grid over the new data set. The grid is shown by default when the transformation process is finished. In the “Talairach tab” of the “3D Volume Tools” dialog, you can choose whether you want to see the full or the partial grid, or no grid at all. Switch to the “Talairach tab” of the “3D Volume Tools” dialog. Check the “Display full grid” item in the “Specification and visualization of Talairach landmarks” field.

  

• Another option to verify that the cerebrum’s size is correctly adjusted to Talairach space is to review the location of the landmarks. To do this, select a landmark in the drop-down list of the “Specification and visualization of Talairach landmarks” field, for example “LP”. The white cross will immediately jump to the respective coordinates.

  

• After Talairach transformation, the “3D Coords” tab of the "3D Volume Tools" also shows Talairach coordinates in addition to the system coordinates. You can test this by switching to the “3D Coords” tab and by clicking on any point in the data set.

  

In total 7 new files are saved to disk during Talairach transformation:

Remark: For details about the sub-steps performed during automatic Talairach transformation, please consult the User’s Guide.