Sjoerd Kolk August 28, 2018

Designing a patient-specific device, performing an anatomical study, creating a virtual model for 3D printing, performing an FEA study. None of these applications would be possible without an accurate segmentation of the anatomy of interest from medical imaging data. Indeed, segmentation can rightfully be called the basis for all of these! Today I would like to point out some of the most important aspects to take into account for optimizing your segmentation process, in terms of accuracy as well as speed.

Materialise Mimics Innovation Suite Users
Materialise Mimics Innovation Suite 21
Materialise Mimics Innovation  Suite 21 Quick Tips - Image Import

1. Make sure the input data is of the highest possible quality

Choose the appropriate modality (usually CT or MRI) to obtain what you need to know from a scan. Stick to a consistent protocol to avoid variation. It is worth your while to invest some time in developing a high-quality imaging protocol together with the Radiology department and using sources from scientific literature. If you are working with multiple centers, make sure that the same protocol can be applied everywhere, for example fine tuning the protocol so that it works on machines from different manufacturers. Without the necessary slice thickness, slice increment or the right reconstruction algorithms, it will never be possible to reach a sufficient level of segmentation quality for surgeons’, patients’, or your own needs. Questions on how to find the perfect scanning protocol or image acquisition method? Don’t hesitate to get in touch with your Materialise representative!

Materialise Mimics Innovation  Suite 21 Quick Tips - Workflow

2. Organize your workflow

When it comes to segmentation quality, one of the largest sources of variation is the different approaches that team members take to a segmentation task. The Mimics Innovation Suite 21 offers several tools that can help you with this. ‘MyTab’ is a brand-new feature that allows you to create your own custom toolbar. So if you prefer to use your favorite tools in a certain order, or would like other team members to use them in that order as well, you can create your own custom workflow. If you want to increase speed and take even more variables out of your segmentation workflow, you could consider using the extensive automation options offered in the Scripting module. Practically all steps at the beginning (importing DICOM images, anonymizing, creating initial masks, …) and end (wrapping, smoothing, exporting to STL, …) can be automated, saving you precious time and increasing consistency as the script can be made in such a way that it always uses the same settings.

Materialise Mimics Innovation Suite 21 - MyTab

Materialise Mimics Innovation Suite 21 - MyTab

Materialise Mimics Innovation  Suite 21 Quick Tips - Latest Tools

3. Use the latest, most powerful tools

These are some of our favorite tools for segmenting bones from CT: Split Mask and Smart Fill. If you are dealing with scans with osteoarthritic patients, and Region Growing is not enough to separate the two bones, Split Mask is ideal for separating the two bones in a joint in just a few clicks. Then, if you want to obtain filled bone masks, use the brand new Smart Fill tool to fill up the bone much faster than with previous tools. Combined, these two tools can save you many minutes per scan. If you are working on 4D CT data of the heart, you will be happy to know that you can now import 4D CT scans into Mimics, and that you can easily copy-paste masks between phases to immediately obtain an initial segmentation of that next frame. Or, use the 4D CT Heart tool to segment all phases of the cardiac cycle in one go

Mimics Innovation Suite 21 - Filling Tool
Materialise Mimics Innovation  Suite 21 Quick Tips - Training

4. Get proper training

We cannot stress enough how much time you might be able to save on your project(s) with the proper training for the type of work that you do. The Mimics Innovation Suite is a toolbox that can sometimes be daunting to get started with (although the new user interface of Mimics 21 will certainly help!). Look here to find Mimics Innovation Courses near you, or order an on-site training to get customized training.

Materialise Mimics Innovation  Suite 21 Quick Tips - Stay in Touch

5. Stay tuned to news from us

On this blog, via email, and at events throughout the world. We release new versions of the Mimics Innovation Suite every year, and each release always contains improvements in segmentation. Furthermore, we also regularly offer customers the opportunity to try out new tools before they are officially released.


Good luck in your segmentation work!

And don’t forget to read all about and upgrade to the latest version of the Mimics Innovation Suite 23.