Review is checked and run, Lead-DBS brings up a window where you can visualize and modify the position of the electrodes.
This step should always be done in order to obtain a meaningful reconstruction. Moreover, this is probably the most difficult step in the standard processing pipeline of Lead-DBS, needs some anatomical insight and experience with interpretation of postoperative imaging. We recommend to watch our guided walkthrough example to better understand this crucial processing step of the pipeline.
The goal of this step is to adjust the localization of the electrode and contact templates within the artifact, in order to place it as accurately as possible.
In this window, the user is able to visualize the position of the electrode trajectory in the artifacts of the MR or CT images. Lead-DBS places within these artifacts the built-in templates for the electrodes, represented as straight lines that run along the artifacts. The contacts are represented as a set of circles on the electrode lead lines (4 or 8 circles, depending on the electrode model chosen).
The Manual Correction window is divided into the following sections:
Main view of the electrodes and contacts (center)
Transversal views of electrode contacts (right column)
In order to adjust the localization of the electrodes, two-dimensional planes are presented orthogonally to the lead trajectory. Changes are tracked within the main view and the transversal views. The main view presents the electrodes and contacts as a whole. The transversal views correspond to the position of the top and bottom contacts of each electrode. They are arranged in ascending order (top:
0, second from top
3, third from top
4, and bottom
A set of commands are available in the manual correction window in order to adjust the settings of the electrode trajectories. Some also have keyboard shortcuts for easier access.
The main view displays the different planes that are selected by clicking on the command button or by using the following keyboard shortcuts:
A: sets view from Anterior
P: sets view from Posterior
R: sets view from Right
L: sets view from Left
X: sets view from X direction
Y: sets view from Y direction
Brightness offset and contrast are adjusted using their command buttons or the following keyboard shortcurts:
C: decreases contrast
V: increases contrast
B: decreases offset
N: increases offset
If no contact is selected (scroll down to learn more on how to select a specific contact), the arrow keys will move the electrodes up or down (in the axial plane) as a whole within the artifact template in the following way:
Down arrow keys adjust the right electrode
Left arrow keys adjust the left electrode
Shift key together with the arrow keys will move the electrodes in even greater steps.
Although the electrode templates already provide a specific spacing between each contact, these can be brought together or separated by using the following commands:
+: increase spacing between contacts
-: decrease spacing between contacts
For easier adjustment, specific contacts can be selected and their changes checked in their respective transversal views. Contacts are selected by clicking the command button or by pressing the keyboard shortcut:
0: selects electrode 0 (right electrode)
3: selects electrode 3 (right electrode)
4: selects electrode 4 (left electrode)
7: selects electrode 7 (left electrode)
When a specific contact is selected, the arrow keys will adjust the position within the axial and coronal planes. Changes can be tracked in the main view and the transversal views.
Once the manual correction is finished, the work can be saved by clicking the check on the command buttons or by using the keyboard shortcut:
space bar: Finish manual corrections
Information will be saved as a Matlab file within the patient folder.
Sometimes, especially based on postoperative MRI, it is not straight forward to interpret where the electrode should be placed.
One piece of advise we can give is to – "just do a few". Really, reconstructing ~10-20 patients helps to shape the eye and you'll realize that you get better with each patient. In the first patient(s), you might not even know what to look for, but seeing more and more patient datasets will definitely help. Naturally, you should re-adjust your early work once you feel comfortable.
If you are still unsure, you can send us screenshots of just this manual reconstruction step and we can help judge whether leads are placed accurately.
If you have access to datasets with large electrodes (e.g. types 3387 or 3391 from Medtronic), start with these. These are usually much easier to reconstruct and their artifacts often reveal precise placement of each single electrode contact.
Finally, there are some specific hints that can often (not always) be seen that we will gather below:
Above figure shows two characteristic findings that may help in placing reconstruction fiducials correctly. First, the most dorsal contact often leads to a large signal loss artifact (blue dashed line) – the dorsal contact usually resides on the bottom of this artifact (green star). Below the most ventral contact (red star) one often sees two hyperintense artifacts, left and right to the trajectory (red dashed line). Please note that depending on how the trajectory cuts the acquired volumes, the hyperintense artifacts may render non-orthogonal to the electrode.