Rendering Three-dimensional images in 3D Slicer
Below area series of videos that teach you about the standard protocols we use to create skull models from raw CT data, export them as surface files, and to collect 3D coordinate data. It is critical that we all follow that same protocols so that our data is comparable in future analyses.
The following tutorial videos were created by Lilian Arnaoudoff, a Masters student in my lab. In them you will learn:
1) How to load data into 3D Slicer and to render a model.
2) How to crop that image down to the skull.
3) How to use thresholding to create the best image possible.
4) How to change the background to black.
5) How to export the model.
Coming soon: How to collect three-dimensional landmarks from your models.
LOADING TIFF STACKS
The CT data that we work with comes in two forms: DICOM and as TIFF stacks. DICOM (Digital Imaging and Communications in Medicine) is the international standard to transmit, store, retrieve, print, process, and display medical imaging information. DICOM files stores information about scanner settings and metadata entered about the specimen. TIFF stacks are the RAW data that comes off the machine and are the standard for comparative museum analyses. The data on resolution and the specimen in included in a separate text file and must be recorded separately.
The first step is learning how to load the TIFF stacks into 3D Slicer and to make a preliminary model.
CROPPING THE MODEL and CHANGING THE BACKGROUND
There are now a few small details that we need to adjust in the models. First, we want to change the background to black. Secondly, we want to crop the model so that we are only focused on the head/
THRESHOLDING
Thresholding is the process we use to remove the background noise and surrounding soft tissue from the skulls. There is an element of art in this. A little too much removed and we might lose small slips of bone. Don’t remove enough and there may be obstructions in front of the parts we care about. To the right you will see a guide to what we are looking for.
Also refer to the useful video below.
Filters provide the models with the desired appearance. They also, at times, make different features come to light that would otherwise be concealed. Watch this brief video to understand where to find the filers and how to apply them.
Almost there! You are nearly ready to take some images.
To the right are some examples of images of skulls and embryos that we take using 3D Slicer. Below is one last video to tutorial video that teaches you how to capture these images.
One of the most important lessons we have learned is that you want to take LOTS of images. Take right and left sides. Play with the angles. You never know how these images will be used in the future and it is far easier to take the images now, rather than reloading the files at a later time.
You will also need to export and STL file. Don’t forget about that. This is what we will use for landmarking and measurements.