Imaging setup

Imaging setup to use the Lead-OR platform


  1. 1.
    3D Slicer: 3D Slicer (v >= 5.2.2) together with the SlicerNetstim, SlicerOpenIGTLink and SlicerIGT extensions should be installed.
  2. 2.
    ORScene: An ORScene is a file that includes subject images, planning information and atlas-based segmentations ready to loaded into Slicer. It can be created from Lead-DBS and an example dataset is already included in the SlicerNetstim extension.

Loading sample ORScene

A sample ORScene is included to test the platform. To load it follow the next steps:
  1. 1.
    Open Slicer.
  2. 2.
    Switch to Sample Data module.
  3. 3.
    Scroll down and select STN Planning.
See the following screenshots as reference:
Step 2: Switch to Sample Data module.
Step 3: Select STN Planning ORScene.

Creating new ORScene

In order to create an ORScene follow the next steps:
  1. 1.
    Process a subject in Lead-DBS with the co-registration and normalization steps.
  2. 2.
    Place the surgical planning files under a leador subfolder within the subject folder.
  3. 3.
    Load the subject in Lead-DBS and select Tools > Lead-OR > Create ORScene. Note that the selected atlas will be put into the scene as well.
  4. 4.
    Drag and drop the ORScene.mrb file into Slicer.
See the following screenshots as reference.
Step 2: Lead-DBS subject processed and with Brainlab planning files in respective folder.
Step 3: Create ORScene from Lead-DBS.
Step 4: Output folder with file to load into Slicer.