Applied Neurobiological Imaging

Hemisphere Masking in BrainSuite

This Protocol will show you how to Hemisphere Mask a Skull Stripped Brain using BrainSuite.
You will need two things.

1. A skull stripped brain(*img/*hdr) format.
2. A mask of your skull stripped brain.
   1. (To learn how to skull strip and to make a mask visit our Protocols page.)
      
   2. Open Brainsuite and load your Skull Stripped Brain(SS brain) as your volume.
      
   3. Load your mask as your Label
      
   4. This Protocol will Mask the Left Side First.
      Click Tools and then select Painter Tool. The Label Painter should pop up.
      
   5. Change the Label ID to 1. This will change the color of the Active Label to green.
      Click the box next to Edit Labels. A purple dot should appear on your screen indicating the Label Brush.
      
   6. The first thing we need to do is to cut our brain in half. Click on yz for the Sagital View and Click on the Solid Black box indicating a single slice view.
      Move your slice view to the slice which best represents the interhemispheric fissure.
      
   7. To erase part of our label hold down Ctrl and right click. Erase all traces of the label from this slice.
      Note: You can increase the size of your brush by changing the Brush Size under the Label Painter options.
      
   8. Move to the right one slice by using the arrow keys. Change the Label ID of the Label Painter to 0. This will change your Active Label to Black.
      
   9. Make sure your brush is within the confines of your label and click Fill 3D on the Label Painter options.
      This will erase all of your label on the right side.
      
   10. The next step is to clean up the medial border. Click the xz view at the top of the screen. This will allow you to work in the coronal view where it is easy to see the medial border.
       Look at the screen shot on the left. The blue arrows show the types of areas that were cut out when we erased the Right Hemisphere.
       
   11. Move to the back of the brain to start drawing your label. Change the Label ID back to 1 so that the Active Label shows a green label.
       Hold down Ctrl and Left click to draw labels. Move through the brain by using the arrow keys.
       
   12. In order to save the label click on File -->Save -->Labels and enter the file name of your label.img
   13. You can either make your right hemisphere mask the same way or you can use a simple command on the Terminal.
       avwmaths is a program that will allow you to take our original whole mask and subtract the left hemisphere mask.
       
       avwmaths whole_mask_file -sub left_mask_file output_right_mask_file