Once normalized volumes are found within the chosen patient folder, the images are ready to be used for pre-reconstruction of the electrode trajectories and for manual refinement (which is the actual electrode reconstruction step).
Below, the automatic pre-reconstruction is explained which needs to be followed up by the manual reconstruction step to yield meaningful results.
For the automatic pre-reconstruction step to take place, check the box
 Reconstruct, choose the preferred parameters for obtaining the images, and press
By default, Lead-DBS performs an automatic search of the artifacts caused by the electrode leads. This can be modified using the following parameters.
Entry point: set
STN, GPi, or ViM,
Manual. If set to Manual, you are prompted to select the starting point of the artifact for each side. The latter is important for troubleshooting but also if you try to reconstruct electrodes at uncommon DBS targets.
Axis: Several “preprocessing”-options can be selected to optimize the imaging data you want to use for the reconstruction here.
Mask window size: either set a concrete value (within the range of 5 to 20 might improve results) or set the value to “auto”. This option is only important for MR images, in CT imaging, a large mask size (e.g. 20) can be used but “auto” should work as well. If performing reconstructions based on MR images, please use a larger mask value if there is a lot of edema around the electrode and a smaller value if the images are rather noisy. Smaller values will prevent the algorithm to “lose track” but might stop to soon if the artifacts are rather large.
In most cases, using default parameters will find the trajectory.
Please note that this does NOT represent an adequate localization of DBS electrode placements yet and all automatic pre-reconstructions need to be manually refined to generate meaningful results.
If the pre-reconstruction step does not find the trajectory correctly or fails with an error, you can improve this process by choosing different options within the parameters
Mask window size (see above and below for more detail).
To perform a reconstruction as precise as possible, Lead-DBS uses different MR-acquisitions (if available) to pinpoint the artifacts caused by the electrodes. You can choose to reconstruct one or both hemispheres (
 RH checkboxes).
Several options are available to help in this process:
Entry point for electrodes presents following options:
- STN, GPi or ViM- Cg25- Manual
An automatic reconstruction will be performed if any of the first two options are chosen. The option
STN, GPi, or ViM targets electrodes that have been implanted in patients with movement disorders. The option
Cg25 targets those in patients with depression.
Manual will require you to pinpoint the entry points of the artifacts within the image slices. This option should in theory work with all DBS electrodes (wherever they might be implanted). Please select the right electrode when prompted the first time and the left one when prompted the second time. The red square shows the area, LEAD DBS would scan in the
STN, GPi or ViM mode and helps you to identify the right hemisphere in each step.
Axis determines the images and possible small preprocessing steps that Lead-DBS will use to locate the electrode. The following options should be preferred:
- Use transversal image only- Use transversal but smooth- Use average of coronal and transversal, smoothed
The default option is an automatic window size (enter “auto” into the field). This has proven to often give good results in the reconstruction.
However, numeric values (best results obtained with values between 5 to 15 or 20) can be entered to fix the size of the mask. A smaller mask will avoid nearby structures that could interfere in the reconstruction step. If the image shows large artifacts, e.g. due to local edema, a larger mask should be chosen (e.g. enter
15 instead of
auto). If the image is noisy, a smaller mask (e.g.
7) might be of better use.