3D Slicer + MeshLab: Making a Brain MRI Mesh

Tutorial

By Sofia Vaca Narvaja, Spring 2025

This is a tutorial on how to create a 3D Mesh object from MRI DICOM data. This tutorial is part of the work I did for project one: comparing MRI visualizations in AR vs VR. Proposal. Activity. Results

Background Information

Softwares: 3D Slicer, MeshLab

Objective: Obtaining .obj file of brain model to use in Unity scene development.

Part 1: 3D Slicer

The goal is to use 3DSlicer to get a 3D object of the brain in .stl format built from an MRI scan.

Note: Look at the pictures as they indicate the menu item to click to get to the shown page.

Choose your data! Either upload your DICOM file (I didn’t have much luck working with NiFtl) or as I did, I chose from the pre-loaded data sets.

2. Add swissSkullStripper extension

https://github.com/lassoan/SlicerSwissSkullStripper

Now, we need to make sure we are stipping away the skull and other tissue that is not part of brain tissue, isolating the brain.

Open Swiss Skull Stripper, choose the input and outputs.

Skull stripper applied

We go to the segment editor

Choose threshold (I did it automatically using the moments algorithm)

Click Apply

Click show 3D and you’ll see the model

Pre Islands

(remove small islands, min. Size 2500 voxels)

Post islands

Go In with the scissors

Smoothing!

Pre (3mm kernel size)

Opening (removing extrusions)
Median (overall smoothing)

Smoothing post

Exporting as .stl file

Part 2: Meshlab

Now that we have the model of the brain, we need to prepare it to be used in a AR/VR environment.

The first step for that is to import the .stl file we just created into MeshLab by selecting "import mesh".

2. We want to make sure the file size + the polygon count (the number of triangles (or faces) that make up a 3D model) are what we want.

Reduce the polygon count to 250,000 to avoid lagging in AR/VR.

3. Scale

Next, we need to check that the scale of the model is appropriate to then be used in VR (considering Meta Quest 3 uses real-life scale)

I made my brain model a meter long, this ended up being quite big.

4. Lastly, we are ready to export our model in .obj format to then use in Unity development!

3D Slicer + MeshLab: Making a Brain MRI Mesh

Background Information

Part 1: 3D Slicer

Part 2: Meshlab

Other Resources and Tutorials in the Wiki:

External tutorials I referenced: