Slicer Tutorial #1: Creating a model of a tumour

By Shreya D'Souza


The Cancer Imaging Archive

  • Archive of publicly available medical images

  • Data is downloaded as .tcia files: need to download NBIA Data Retriever to extract data files.

  • Several images from many different studies, not just of brains

BraTs Dataset (Suggested)

  • Need to request permission to access

  • (Luckily!) available on Google Drive here:

  • Glioblastoma is segmented into different colours:

    • Otherwise really hard to determine where the tumour is and to select the region for all the slices.


  1. Click on Load Data

  2. 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

  3. Make sure Volume is in the description and then press OK

  4. Click Explore Loaded Data. This allows you to see all the imported scans. Clicking on various ones will change the scan being seen.

  5. Choose the scan that you think shows the brain the most clearly. Most of the time this is the t1 MRI.

  6. The three panels on the bottom show different views of the brain. Use the sliders to look at different slices of the brain.

Importing Data .mov


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 parts of the brain.



The Tumour

  1. Remove the MRI scans from the 3D space

  2. Right-click the seg node (which represents the tumour) and select Convert labelmap to segmentation mode

  3. 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

  4. This will create a 3D model of the tumour in the 3D space

Segmentation -

The Brain Tissue

  1. Right-click the selected scan from before and select Segment this. This will take you to the Segmentation module.

  2. 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.

  3. Select Threshold from the effects menu. This will cause a slider to appear below.

  4. 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.

  5. Press Apply.

  6. Press Segmentations to see all the segments of the segmentation.

  7. Go back to the node hierachy.

  8. Click on the eyes next to the newly created segmentation so that it is not visible in the MRI scans.

  9. Right-click the segmentation and select Export visible segments to models. This will create a 3D visualisation of the brain tissue.

  10. Right click on Brain Tissue in the segmentation folder and select Edit properties.

  11. 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.

Segmentation - Brain