Class ACTIVITY: 3D Slicer
By Shreya D'Souza
This is an adaptation of Slicer Tutorial #1 with the additional functionality of viewing on a HMD
Setting Up
Download 3D Slicer here (stable release 4.10.2, takes up 940MB of space): https://download.slicer.org/
Download one of the folders from BraTS Dataset > HGG > Any of the CBICA folders
Importing Data
Click on Load Data
Choose a directory to add, not a file. A directory allows you to see various scans of the same brain, as well as including a version that marks out the tumour
Make sure Volume is in the description and then press OK
Click Explore Loaded Data. This allows you to see all the imported scans. Clicking on the icon in column to the right of the names will show/hide scans.
Choose the scan that you think shows the brain the most clearly. Most of the time this is the t1 MRI.
The three panels on the bottom show different views of the brain. Use the sliders to look at different slices of the brain.
Linking MRI Scans
1. Click on the left button in the toolbar of each panel and then the eye to view the MRI scans in the 3D space. Pressing the link button will cause all to show up at once. Use the sliders to view different slices of the brain.
Segmenting Scans and Creating Models
The Tumour
Remove the MRI scans from the 3D space
Right-click the seg node (which represents the tumour) and select Convert labelmap to segmentation mode
Right-click the newly-created segmentation node which should have a sub-node with the newly-created segmentations, and select Export visible segments to models
This will create a 3D model of the tumour in the 3D space
The Brain Tissue
Right-click the selected scan from before and select Segment this. This will take you to the Segmentation module.
Press the Add button to insert a segment. Double-click on the colour to and name the segment and change the colour. Press select when completed.
Select Threshold from the effects menu. This will cause a slider to appear below.
The slider will be set to have no threshold. Move the two slides from the ends towards the middle until you think all the brain tissue is selected.
You can check this by looking at the three MRI panels on the right side of the screen. Use the sliders of the individual scans to look at different slices of the brain to ensure that the brain tissue is selected.
Press Apply.
Press Segmentations to see all the segments of the segmentation.
Go back to the node hierachy.
Click on the eyes next to the newly created segmentation so that it is not visible in the MRI scans.
Right-click the segmentation and select Export visible segments to models. This will create a 3D visualisation of the brain tissue.
Right click on Brain Tissue in the segmentation folder and select Edit properties.
Click on the opacity of 1.00 and move the slider so that the opacity is anywhere between 0.2 and 0.4. This will allow us to see the location of the tumour within the brain.
Viewing on a Head-Mounted Display
[This is only possible on a Windows computer (the SlicerVR extension is only available on Windows) so we will be migrating to the VC Lab to view a model on HTC Vives. Thank you Brandon for teaching me how to use the HTC Vives :)]
Download the SlicerVirtualReality Extension from the Extensions Manager. This will create a toolbar with an added icon of an HMD.
2. Ensure that the headset is correctly connected correctly using Steam
3. Click on the Button in 3D Slicer - this will cause the brain to show up. You can use the controllers to move the brain in the space and look at the tumour more closely.