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Junichi Tokuda edited this page Mar 28, 2019 · 4 revisions

Loading MR image and model of the patient

First, download the Slicer scene for ISMR19. This scene contains:

  • Scene description file (Scene-ISMR19.mrml)
  • MR image of the patient (MRI.nrrd)
  • 3D model of the patient (SkullDrilled1.stl)
  • 3D model of the links of the robot (*.stl except for SkullDrilled1.stl)
  • Transformation matrix for the links (*.h5)

Decompress the zip file. On a terminal on Linux/Mac, this can be done by:

$ unzip SlicerScene-ISMR19.zip
Archive:  SlicerScene-ISMR19.zip
  inflating: SlicerScene/MRI.nrrd    
  inflating: SlicerScene/Scene-ISMR19.mrml  
  inflating: SlicerScene/Scene-ISMR19.png  
  inflating: SlicerScene/SkullDrilled1_mm.stl  
  inflating: SlicerScene/base_mm.stl  
  inflating: SlicerScene/forearm_link.h5  
  inflating: SlicerScene/forearm_mm.stl  
  inflating: SlicerScene/needle.h5   
  inflating: SlicerScene/needle_holder.h5  
  inflating: SlicerScene/needle_holder_mm.stl  
  inflating: SlicerScene/shoulder_link.h5  
  inflating: SlicerScene/shoulder_mm.stl  
  inflating: SlicerScene/tool0.h5    
  inflating: SlicerScene/upper_arm_link.h5  
  inflating: SlicerScene/upperarm_mm.stl  
  inflating: SlicerScene/wrist1_mm.stl  
  inflating: SlicerScene/wrist2_mm.stl  
  inflating: SlicerScene/wrist3_mm.stl  
  inflating: SlicerScene/wrist_1_link.h5  
  inflating: SlicerScene/wrist_2_link.h5  
  inflating: SlicerScene/wrist_3_link.h5

Please note that the STL format does not contain the unit information. while the files should be loaded on 3D Slicer with the proper scale, they might not work on other environments.

Once all files are extracted, we load the scene from 3D Slicer as follows:

  • Open the "Add Data" dialog box ("File"->"Add Data").
  • Click "Choose File(s) to Add" button.
  • Choose "Scene-ISMR19.mrml" from the "Open" dialog box.
  • Click "Open". The file name should appear on the "Choose File(s) to Add" dialog box. After clicking "OK", the 3D Slicer starts loading the files into the scene.

If the files are loaded successfully, you should be able to see the MR images on the red/yellow/green viewers, and the models of the skull and the robot on the 3D viewer. The location of the skull with respect to the robot is not realistic, but it is because they are not registered (or calibrated) yet. We will register them later in the tutorial.

Planning Needle Placement

We plan a needle placement trajectory by defining 1) a target point and 2) an needle entry point on the skin.

First, we make the sections of the skull model visible on the 3-axis planes as follows:

  • Open the "Models" module ("Modules" menu -> "Models")
  • Choose "SkullDrilled1_mm from the list of the models.
  • In the "Slice Display" frame, check "Visible". Now you should see the sections of the skull model overlaid on the MR images.

To define the entry and target points:

  • Click the "create-and-place fiducial" button in the toolbar.
  • Click the center of the tumor as the target point. (Fiducial "F-1" should appear on the MR image)
  • Click the center of the hole on the skull as the entry point. (Fiducial "F-2" should appear on the MR image)
  • Open "Markups" module from the modules menu.
  • Pull down the List menu, and choose "Rename current MarkupsFiducials".
  • On the pop-up window, type in "Plan" (case-sensitive) as a new name, and click "OK".
  • Change the names of the points from "F-1" and "F-2" to "Target" and "Entry", by clicking the names (i.e. "F-1" and "F-2") and type in the new names. The names are case-sensitive as they will be transferred to ROS and used to identify the points.
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