Pre-op

Note

To install DBS Guide, visit the installation tutorial.

Two to three weeks prior to the surgery, the patient gets an MRI Scan along with several sequences. Among the sequences is a 3D Volumetric Stealth MRI. Using the Registration Widget, we can co-register the MRI scans with the 3D Volumetric Stealth MRI.

1. Load the patient’s directory.

   Click Browse to find your folder with the scans. Notice, we only select the folder and not the files inside the folder. This folder contains folders in the .nii.gz format which means each folder is a gzipped folder of NIFTI (Neuroinformatics Technology Initiative) files. NIFTI files are files of MRI scans.

   

   
   

   Note

   There are two folders now in your patient directory:

   scene

   Contains data/scans that will be edited by DBS Guide

   source

   Contains the original brain scans

2. Rename volumes [optional].

   If you would like to rename volumes you may do so.

   

   Note

   Frame Detection is going to be skipped because the CT frame scan is performed on the day of the surgery. Frame Detection will be explored in the next phase, intra-op.

3. Co-register the 3D Volumetric Stealth MRI with the other MRI scans.

   Using Registration, select the appropraite reference volume, which in our case is 3D Stealt. Leave CT Frame Volume as None because the frame CT has not been obtained yet. Choose the algorithm of your preference. Then Run Registration. Note, this may take a while (upto 10 minutes). If your computer freezes, just wait, the program is still running.

   

   Upon completion:

   

4. Confirm that the registration was a success.

   We want to make sure the the co-registered scan matches 3D Stealth. We will use the views on the right to do this. First link all the views so that they’re in sync as you zoom in and out.

   

   Next, we’ll need to set the background view to 3D Stealth and foreground view the co-registered scan.

   

   
   

   Note

   Any scan that ends with coreg has been coregistered.

   To confirm that coregistration is successful, use the slider to transition from background and foreground. As seen below, the scans have coregistered successfully.

   Note

   Quick controls for Slicer

   Slide image

   Hold Shift and drag

   Move through scan according to axis (e.g. Anterior to Posterior)

   Scroll up/down

   Increase size of image

   Hold right-click and drag

   

5. Plot the anatomical fiducials.

   There are four points that need to be marked.

   • Anterior Comissure (AC)
   • Posterior Comissure (PC)
   • Two midline points (Mid1 and Mid2)

   Select 3D Stealth as your fiducial volume.

   Note

   To adjust the the brightness of the window and level of volume of the scan, click on the window tool. Then drag your crusor across the scan until you reach the level of brightness desired. A helpful shortcut is to hold control (or command) and drag a square across the brain (exclude the skull). This will give you a good baseline.

   

   
   

   TIP

   Hold Control/Command and make a square across brain tissue

   

   Anterior Commissure

   The anterior commissure is the white matter tract connecting the two temporal lobes across the midline, and is placed in front of the columns of the fornix.

   

   
   

   Click Turn On Crosshairs. Hold shift while moving your crusor to position your crosshair on the anterior commissure. As long as you mark the AC fiducial on one view, the it’ll be marked on the other views as well.

   

   Now add the AC point to our list of Anatomical Fiducials.

   

   Repeat these steps for PC, Mid1, and Mid2.

   Posterior Commissure

   

   Mid1

   We can use the fourth ventricle.

   

   Mid2

   

   Note

   You may add more midlines (upto 5) if you would like to. Click Add Midline to add another one.

   Once done, click Confirm Fiducials. A new fiducial MCP (Mid Commissure Point) will be added automatically based on your AC and PC fiducials.

   

   
   

   6. Plan target trajectory.

      Using the Target Planning widget, we will plan the trajectory of the micoelectrodes.

      Note

      To center and zoom out of the scans, click on the square with four lines on the top left of each view’s menu bar.

      

      
      

      Click Turn On Crosshairs. Below this button are X, Y, and Z coordinates, relative to MCP. As you click on the scan the values update. If you have the planned coordinates from before, you can input them into these coordinates. In this example, the coordinates were already provided, so we input them into the appropriate boxes.

      

      
      

      Click Confirm Left Plan, and you will see an electrode plotted in 3D space.

      

      
      

      Left Plan is complete. We do not have any frame settings as the CT frame scan is taken on the day of surgery. Repeat these steps for Right Plan.

      

      
      

      

      
      

      View the scan on the 3D view with the electrodes:

      

      
      

      Target planning is now complete! To look down the electrode and ensure you’re not hitting any unwanted tissue, use the Probes Eye. After selecting the left or right planned lead as your Probe Eye Model, slide the Entry slider.

      

The preoperative phase of DBS Guide is complete! Moving onto the day of the surgery, visit Intraoperative Phase.