The new segment editor in the 3D Slicer has features that the older Editor module lacks. One of this features is the awesome Scissors tool, which let’s you remove/retain any portion of the data by drawing an outline either in the slice views or in 3D.
Our goal in this tutorial will be to remove the foam and other support structures that usually show up in CT scans quickly (in about 2 minutes). We will use a dataset from the Terry Collection (TC 815) courtesy of Dr. Lynn Copes. For this tutorial I am using Slicer release r25914 (4.7.0-2017-04-10).
- Download the nifti file and drag it into Slicer.
- Go to the Segment Editor and create a new segment
- Use the threshold tool with 410 – 4096 range to segment bones. Note that this picks up a fair amount of the scanning platform, as well as the foam.
- If you want to visualize, you can click the create surface to see in 3D (takes a minute)
- Switch to scissors tool and in the axial plane (red slice view) make a tracing of the scanning platform. Your scissors settings should be ‘erase inside’. This will remove the scanning platform from the segment #1, and assign it to the background.
- Remaining foam particles can be easily dealt with using the Island tool. Just choose the option ‘Keep only the largest island‘.
- You should have the skull fully segmented from the scanning platform and free of foam particles.
Segment editor uses a different data structure than regular editor. If you want to save a new dataset without the platform and the foam, you need to:
- Convert the segments into a label map.
Right click on the Segment 1 and choose ‘convert visible segments to binary label map‘.For that, switch to Segmentations module, scroll down half to fine the tab Export/Import models and label maps. There you can specify to export the segmentation either as a label map or a surface model. Note that there is an option to directly export a surface model as well, if that’s what you prefer to work with.
- To remove the platform, use the “Mask Scalar Volume” module, specify TC815 as your input volume, the label map from the previous step as your mask volume, and create a new output volume.
Edit on 9/25: There is now an extension that adds masking functionality to Segment Editor. It is called “slicer segment editor extra effects” and can be installed through the Extension Manager using a nightly (it isn’t available for the latest stable 4.6). There is a video tutorial demonstrating the functionality.
You can use the scissors tool directly on the 3D view as well. Remember it is going to carve in (or carve out everything else depending your setting) into the screen plane, so orienting your specimen correctly is very important.