Basics of Slicer 

Data

This module assumes you have already installed and set up Slicer. Slicer3D contains more than 100 modules for image segmentation, registration, and 3D visualization of medical imaging data. 

Most radiological imaging equipment produces images in DICOM file format. In this tutorial, we will explore the MR scan of the brain with a tumor. 

The data is sourced from the University of Pennsylvania from their Brain Tumor Segmentation (BraTS) Challenge 2020.

Load Data

• Click on Load Data in the Slicer 'Welcome module'

• Click on Choose File(s) to Add.

• Browse to the location of the Visualization directory and select the file MR-head.nrrd

• Click on OK to load the MR dataset into Slicer

Views

• The axial, sagittal and coronal views appear in the 2D viewers. 

• Click on the links icon(in each view) to link all three viewers, and on the eye icon to display the slices in the 3D Viewer.

• The three anatomical slices appear in the 3DViewer 

• Use the left mouse button to rotate the camera, and the right-mouse button to zoom in and out 

3D Volume Rendering 

• The Volume Rendering Module can be used to render the MR data into 3D models

• Click on the eye icon next to Volume to render the volume

• Set the preset to MR-Default. Different presets can be used to segment and highlight different density responses in the MR data, like bone, muscle, liquid, and voids.

• Click on Enable crop and eye icon next to display ROI(Region of Interest) to view different cross-sections of the model.

Saving a Scene

• Select File, Save from the main menu 

• The Save Scene and Unsaved Data lists all the elements of the Slicer Scene 

• Rename the scene myNewScene.mrml and click on OK

• Click on Enable crop and eye icon next to display ROI(Region of Interest) to view different cross-sections of the model.

Visualising other datasets:

Slicer VR 

• From the extension manager find and install slicerVR

• Connect Headset to paper space machine via virtual desktop app and connect to steam VR

• Open the virtual reality module, set the render definitions and controlled operations and click on the VR head set Icon to view the datasets in VR

• All operation performed on the desktop, reflect in VR and vice versa