Applied Neurobiological Imaging

Creating objects from masks

Written by Owen Phillips. Email Dr. Katherine Narr if you have any questions. For more information, see the protocols page.

This protocol will show you how to create an object from a mask using BrainSuite 2.45. You can then overlay this object on DTI data to make figures for ROI studies on diffusion measures, for example.

Part 1: Creating Objects from Masks

1. Load the *mask file you are interested in creating an object for your Volume.
   
   
2. Open the mask Tool and click Threshold MRI.
   This will create a green outline around your mask.
   
   
3. If your outline is too large you can reduce or enlarge it by clicking on the options. D[] D<> E[] E<>.
   
   
4. Leave the Mask Tool
5. Under Tools there is an option for Surface Generator. Click Tessellate. You can change the number of Iterations to change the smoothness of your object.
   
   
6. In GLView you can now look at the object you have created. In this case it is the Left frontal lobe.
   
   
7. Right click and take off the volume display. This will leave only the object.
   
   
8. You have now created your object. Right click and bring up Surface View Properties.
   Under Surfaces the object will be called (newsurface).
   You can now save the object as a *dfs.
   
   
9. Under Surface view Properties there are options for changing the look and color of your object.
   
   
10. Below you can see an example of the wireframe option with the color changed to red.
    
    
11. If you want to add more objects into the GL View and you have not created them you have to close Brainsuite and repeat steps 1-10. In the picture below I have created an object for the left cingulate gyrus and dragged in my *dfs left frontal hemisphere object.
    
    

Continue to PART 2: Adding Objects to *rgb data