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PatientDataSetup.md

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From DICOM series to HoloLens

MR Image Segmentation and Export

  1. Load Images in by creating a DICOM series and turning it into a volume.
  2. In Segment Editor, create a skin and ROI segment.
  3. Select the DICOM series's volume as the Master Volume.
  4. Add a new segment, called Skin.
  5. Threshold segment the majority of the scan, invert, keep largest island, median smoothing, invert; finally remove any excess areas manually.
  6. Add a new segment, called ROI.
  7. Manually segment or use level tracing and then manually clean the ROI (tumour / SDH, etc).
  8. Import the atlasMask (as LabelMap) and atlasImage into Slicer as volumes.
  9. Open Swiss Skull Stripper, select the DICOM series's volume as your input, create your output volume and mask as LabelMapVolumes, set the atlasMash and atlmasImage as the Atlas.
  10. Click apply and run the Skull Stripper.
  11. In Data, Convert Brain LabelMapVolume to Segmentation, then to a model. Then export ROI and Skin to models.
  12. In Surface Toolbox, decimate Skin, Brain and ROI to 0.6.
  13. Place a set of fiducial markers on tip of nose, and corners of each eye.
  14. Export models as OBJ and markers as CSV.

CT Image Segmentation and Export

TBD When we have CT images to confirm workflow.

Upload Patient Files to PatientManager File Browser

  1. Ensure file size of all exported models is under ~1MB so they can be loaded quickly by the PatientManager
  2. Create .xml as per the example template in SDH_Demo
  3. Create folder on desktop containing all exported models and .xml
  4. Access the HoloLens Device Portal on the desktop
  5. Go to File explorer then AppData/HoloQuickNav2/LocalState/PatientData and select the corresponding folder for the patient
    • Folders within PatientData are created by the script FileBrowser.cs
    • This script can be edited to create additional patient folders and the app can then be redeployed from Unity
    • In the future, these folders will be created automatically once the .xml is read from Slicer over the OpenIGTLink connection
  6. Upload all .obj files and the .xml file into the patient's folder on the Device Portal
  7. Load patient models for registration by selecting the patient's folder in the PatientManager scene in HoloQuickNav

Creating Scene for Patient Without PatientManager

Outdated - Use PatientManager setup for new patients

Setting up the Unity Scene

  1. Drag and drop the exported models and markers into HoloQuickNav > Models > Anatomy > (New Folder Name)
  2. In WorldAnchor > Model > Layers, delete previous models, replace with the exported models (Make sure to rename Skin model "Skin" if not already).
  3. Change the scale of all models to 0.001 in X Y and Z.
  4. In HoloQuickNav > Models > Anatomy > Materials, and place the materials for each model onto its respective model.
  5. In Controls > Home, drag and drop ROI and Brain into the Missing Objects of the Turn On Layers Script. Change the function for each of the objects as GameObject > SetActive(bool)
  6. In InputManager > QuickNavManager > LocationValues, drag and drop the exported markers into Location Values 'CSV Markers' field.

Build and Deploy

  1. In File > Build Settings, click Build and make sure that the build directory is UWP.
  2. Once the vs solution is built, open it and make sure that the build is in Release and on x86 architecture..
  3. Click Build > Deploy Solution.
  4. If the Hololens IP address changes, you can modify it in Project > HoloQuickNav2 Properties > Debug > Remote Machine.