Please note the democratiz3D service was previously named "Imag3D"
In this tutorial you will learn how to quickly and easily make 3D printable bone models from medical CT scans using the free online service democratiz3D®. The method described here requires no prior knowledge of medical imaging or 3D printing software. Creation of your first model can be completed in as little as 10 minutes.
You can download the files used in this tutorial by clicking on this link. You must have a free Embodi3D member account to do so. If you don't have an account, registration is free and takes a minute. It is worth the time to register so you can follow along with the tutorial and use the democratiz3D service.
>> DOWNLOAD TUTORIAL FILES AND FOLLOW ALONG <<
Both video and written tutorials are included in this page.
Before we start you'll need to have a copy of a CT scan. If you are interested in 3D printing your own CT scan, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figures 1 and 2 show the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available.
Figure 1: The radiology department window at my hospital.
Figure 2: An example of what a DVD containing a CT scan looks like. This looks like a standard CD or DVD.
Step 1: Register for an Embodi3D account
If you haven't already done so, you'll need to register for an embodi3d account. Registration is free and only takes a minute. Once you are registered you'll receive a confirmatory email that verifies you are the owner of the registered email account. Click the link in the email to activate your account. The democratiz3D service will use this email account to send you notifications when your files are ready for download.
Step 2: Create an NRRD file with Slicer
If you haven't already done so, go to slicer.org and download Slicer for your operating system. Slicer is a free software program for medical imaging research. It also has the ability to save medical imaging scans in a variety of formats, which is what we will use it for in this tutorial.
Next, launch Slicer. Insert your CD or DVD containing the CT scan into your computer and open the CD with File Explorer or equivalent file browsing application for your operating system. You should find a folder that contains numerous DICOM files in it, as shown in Figure 3. Drag-and-drop the entire DICOM folder onto the Slicer welcome page, as shown in Figure 4. Click OK when asked to load the study into the DICOM database. Click Copy when asked if you want to copy the images into the local database directory.
Figure 3: A typical DICOM data set contains numerous individual DICOM files.
Figure 4: Dragging and dropping the DICOM folder onto the Slicer application. This will load the CT scan.
Once Slicer has finished loading the study, click the save icon in the upper left-hand corner as shown in Figure 5. One of the files in the list will be of type NRRD. make sure that this file is checked and all other files are unchecked. click on the directory button for the NRRD file and select an appropriate directory to save the file. then click Save, as shown in Figure 6.
Figure 5: The Save button
Figure 6: The Save File box
The NRRD file is much better for uploading then DICOM. Instead of having multiple files in a DICOM data set, the NRRD file encapsulates the entire study in a single file. Also, identifiable patient information is removed from the NRRD file. The file is thus anonymized. This is important when sending information over the Internet because we do not want identifiable patient information transmitted.
Step 3: Upload the NRRD file to Embodi3D
Now go to www.embodi3d.com, click on the democratiz3D navigation menu and select Launch App, as shown in Figure 7. Drag and drop your NRRD file where indicated. While NRRD file is uploading, fill in the "File Name" and "About This File" fields, as shown in Figure 8.
Figure 7: Launching the democratiz3D application
Figure 8: Uploading the NRRD file and entering basic information
Figure 9: Basic information fields about your uploaded NRRD file
Next, turn on democratiz3D Processing by selecting the slider under democratiz3D Processing. Make sure the operation CT NRRD to Bone STL is selected. Leave the default threshold of 150 in place. Choose an appropriate quality. Low quality produces small files quickly but the output resolution is low. Medium quality is good for most applications and produces a relatively good file that is not too large. High quality takes the longest to process and produces large output files. Bear in mind that if you upload a low quality NRRD file don't expect the high quality setting to produce a stellar bone model. Medium quality is good enough for most applications.
If you wish, you have the option to specify whether you want your output file to be Private or Shared. If you're not sure, click Private. You can always change the visibility of the file later. If you're happy with your settings, click Save & Submit Files. This is shown in Figure 10.
Figure 10: Entering the democratiz3D Processing parameters.
Step 4: Review Your Completed Bone Model
After about 10 to 20 minutes you should receive an email informing you that your file is ready for download. The actual processing time may vary depending on the size and complexity of the file and the load on the processing servers. Click on the link within the email. If you are already on the embodied site, you can access your file by going to your profile. Click your account in the upper right-hand corner and select Profile, as shown in Figure 11.
Figure 11: Finding your profile.
Your processed file will have the same name as the uploaded NRRD file, except it will end in "– processed". Renders of your new 3D model will be automatically generated within about 6 to 10 minutes. From your new model page you can click "Download this file" to download. If you wish to share your file with the community, you can toggle the privacy setting by clicking Privacy in the lower right-hand corner. You can edit your file or move it from one category to another under the File Actions button on the lower left. These are shown in Figure 12.
Figure 12: Downloading, sharing, and editing your new 3D printable model.
If you wish to sell your new file, you can change your selling settings under File Actions, Edit Details. Set the file type to be Paid, and specify a price. Please note that your file must be shared in order for other people to see it. This is shown in Figure 13. If you are going to sell your file, be sure you select General Paid File License from the License Type field, or specify your own customized license. For more information about selling files, click here.
Figure 13: Making your new file available for sale on the Embodi3D marketplace.
That's it! Now you can create your own 3D printable bone models in minutes for free and share or sell them with the click of a button.If you want to download the STL file created in this tutorial, you can download it here. Happy 3D printing!
Dear Community Members,
After many months of work, we are happy to announce the addition of a feature that will allow you to sell medical models you have designed on Embodi3D.com. While we always have encouraged our members to consider allowing their medical STL files to be downloaded for free, we understand that when a ton of time is invested in creating a valuable and high-quality model, it is reasonable to ask for something in return. Now Embodi3D members have two options: 1) You can share your medical models for free, or 2) you can charge for them. We hope these two options encourage more sharing and file uploads. The more models available, the more it helps the medical 3D printing community.
For more details on how to sell your medical masterpieces on Embodi3D, go to the selling page.
Thanks, and happy 3D printing!
In this tutorial we will learn how to use the free medical imaging conversion service on embodi3D.com to create detailed anatomic muscle and skin 3D printable models in STL file format from medical CT scans. Muscle models show the detailed musculature by subtracting away the skin and fat. Even when created from a scan of an obese person, the model looks like it comes from a bodybuilder, Figure 1A. Skin models show an exact replica of the skin surface. The finest details are captured, including wrinkles and veins underneath the skin. Hair however is not captured in a CT scan and thus the model does not have any hair, Figure 1B.
Figure 1A (left): A muscle 3D printable model. Figure 1B (right): A skin 3D printable model
These models can be used for a variety of purposes such as medical and scientific education and research. Additionally, the skin models can be used to re-create a person's likeness in 3D from a medical scan. If you have had a CT scan of the head, you can create a lifelike replica of your head. You can create replicas of your friends, family, or even pets if they have had a medical CT scan. Alternatively, if you have a loved one who passed away but had a CT scan prior to death, you can use the scan to re-create an exact replica of their face. Even scans that are years old can be used for this purpose. Some people may consider this to be a little creepy, so if you are considering doing this think carefully first.
Before proceeding please register for an embodi3D.com account if you haven't already. You will need an account to use the service.
It is highly recommended that you download the associated file pack for this tutorial so that you can follow along with the exact same files that are used in this tutorial.
>> DOWNLOAD THE FREE FILE PACK BY CLICKING HERE <<
If you are interested in learning how to use the free embodi3D.com service, see my prior tutorials on creating bone models, processing multiple models simultaneously, and sharing and selling your models on the embodi3D.com website.
If you are interested in converting your own CT scan or that of a friend or family member, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figure 2 shows the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available. If you have downloaded the file pack for this tutorial, example CT scans are included
Figure 2A, the Image Management (radiology) department at my hospital, where you can pick up a DVD of your CT scan as shown in Figure 2B (right). My hospital does this for free, but some may charge a trivial fee.
PART 1: Creating a Muscle STL model from NRRD File
Before we begin please bear in mind that this process only works for CT scan images. It will not work for MRI images. Before proceeding please check that the scan you wish to convert is a CT (CAT) scan!
Step 1: Convert Your CT scan to an Anonymized NRRD File with 3D Slicer
Open 3D Slicer. If you don't have the software program you can download it for free from slicer.org. Once Slicer has opened, take the folder from the download pack that is called STS_004. This folder contains anonymized DICOM images from a CT scan of the legs of a 24-year-old woman who had a muscle tumor. Drag and drop the entire folder onto the Slicer window, as shown in Figure 3. Slicer will ask you if you want to load the images into the DICOM database. Click OK. Slicer will also ask you if it should copy the images into the database, click Copy. Slicer will take about one minute to load the scanned.
Figure 3: Drag-and-drop the STS_004 DICOM folder from the file pack onto the Slicer window
Next, load the scan into the active wor king area in slicer. If the DICOM browser is not open, click on the Show DICOM browser button, as shown in Figure 4. Click on the STS_004 patient and series, and click the Load button, as shown in Figure 4. The leg CT scan will now load into the active seen within Slicer, as shown in Figure 5.
Figure 4: Open the DICOM browser and load the study into the active seen
Figure 5: The leg CT scan is shown in the active seen
Step 2: Trim the Scan so that only the Right Thigh is included.
Click on the Volume Rendering module from the Modules drop-down menu as shown in Figure 6. Turn on volume rendering by clicking on the eyeball button, as shown in Figure 7. Then, center the model in the 3D pane by clicking on the crosshairs button, Figure 7. If you don't have the same window layout as shown in Figure 7, you can correct this by clicking on the Four-Up window layout from the window layout drop-down menu, as shown in Figure 8.
Figure 6: Turn on the volume rendering module
Figure 7: Center the rendered volume.
Figure 8: Make sure you are in the Four-Up window layout
Next we are going to crop the volume so that we exclude everything other than the right knee and thigh. From the modules menu, select All Modules, Crop Volume, as shown in Figure 9. Turn on ROI visibility by clicking on the eyeball button, as shown in Figure 10. Then, move the region of interest box so that it only encapsulates the right thigh, as shown in Figure 10. You can adjust the size of the box by grabbing on the colored circular handles and moving the sides of the box as needed.
Figure 9: The Crop Volume module.
Figure 10: Turning on and adjusting the crop volume ROI (Region Of Interest)
Once the crop volume ROI is adjusted to the area that you want, perform the crop by clicking on the Crop button, Figure 11.
Figure 11: the Crop button.
The new, smaller volume that encompasses the right fight and knee has been assigned a cryptic name. The entire scan had a name of "2: CT IMAGES – RESEARCH," and the new thigh volume has a name "2: CT IMAGES-RESEARCH-subvolume-scale_1." That's a mouthful and I want to rename it to something more descriptive. I'm going to select the Volumes module, and then select the "2: CT IMAGES-RESEARCH-subvolume-scale_1" from the Active Volume drop-down menu. Then, from the same drop-down menu I'm going to select "Rename Current Volume". Type in whatever name you want. In this case I'm choosing "right thigh."
Figure 12: Renaming the newly cropped volume.
Step 3: Save the right thigh volume as an anonymized NRRD file.
Click on the Save button in the upper left-hand corner. The save window is then shown. All the checkboxes on the left except for the one that corresponds to the right by. Make sure the file format for this line says NRRD (.nrrd). Make sure you specify the proper directory you want the file to be saved as. When you are satisfied click on save. This is demonstrated in Figure 13. In the specified directory you should see a called right thigh.nrrd.
Figure 13: The save file options.
Step 4: Upload the NRRD file to embodi3D.com
Make sure you are logged into your embodi3D.com account. Click on Imag3D from the nav bar, Launch App. Then drag-and-drop your NRRD file onto the upload pain, as shown in Figure 14.
Figure 14: Uploading the NRRD file to embodi3D.com.
Figure 15: File processing options.
Step 5: Download your new STL file after processing is completed.
In about 5 to 15 minutes you should receive an email that says your file has finished processing and is ready to download. Follow the link in the email or access the new file via your profile on the embodi3D.com website. Your newly created STL file should have several rendered thumbnails associated with it on its download page. If you want to download the file click on the Download button, as shown in Figure 16.
Figure 16: the download page for your new muscle STL file
I opened the file in AutoDesk MeshMixer to have another look at it, and it looks terrific, as shown in Figure 17. This file is ready to 3D print!
Figure 17: The final 3D printable muscle model.
PART 2: Creating a Skin Model STL File Ready for 3D Printing
Creating a skin model is essentially identical to creating the muscle model, except instead of choosing the CT NRRD to Muscle STL on the embodi3D.com service, we choose CT NRRD to Skin STL.
Step 1: Load DICOM image set into Slicer
Launch Slicer. From the tutorial file pack drag and drop the MANIX folder onto the Slicer window to load this head and neck CT scan data set. This is shown in Figure 18.
Figure 18: Loading the head and neck CT scan into Slicer. It may take a minute or two to load. From the DICOM browser, click on the ANGIO CT series as shown in Figure 19.
Figure 19: Loading the ANGIO CT series from the MANIX data set
Step 2: Skip the trimming and crop volume operations
In this case we don't need to trim and crop a volume as we did with the muscle file above. We can skip Step 2.
Step 3: Save the CT scan in NRRD format.
Just as with the muscle file above, save the volume in NRRD format. Click on the save button, make sure that the checkbox for the nrrd file is selected and all other checkboxes are deselected. Specify the correct directory you want the file to be saved in, and click Save.
Step 4: Upload your NRRD file of the head to the embodi3D website.
Just as with the muscle file process as shown above, upload the head NRRD file to the embodi3D.com website. Enter in the required fields. In this case, however, under Operation choose the CT NRRD to Skin STL operation, as shown in Figure 20.
Figure 20: Selecting the CT NRRD to Skin STL file operation
Step 5: Download your new Skin STL file
After about 5 to 15 minutes, you should receive an email that says your file processing has been completed. Follow the link in the email or look for your file in the list the files you own in your profile. You should see that your skin STL file has been completed, with several rendered images, as shown in Figure 21. Go ahead and download your file. You can then check the quality of your file in Meshmixer as shown in Figure 22. In this instance everything looks great and the file is error free and ready for 3D printing.
Figure 21: The download page for your newly created 3D printable skin STL file.
Figure 22: Opening the file in Meshmixer for quality control checks. The file is error free and incredibly lifelike. It is ready for 3D printing.
Thank you very much! I hope you enjoyed this tutorial. If you use this service to create 3D printable models, please consider sharing your models with the embodi3D community. Here is a detailed tutorial that I wrote on exactly how to do this. This community is built on medical 3D makers helping each other. Please share the models that you create!
This tutorial is based on course I taught at the 2018 RSNA meeting in Chicago, Illinois. It is shared here free to the public. In this tutorial, we walk though how to convert a CT scan of the face into a 3D printable file, ready to be sent to a 3D printer. The patient had a gunshot wound to the face. We use only free or open-source software and services for this tutorial.
There are two parts to this tutorial:
Part 1: How to use free desktop software to create your model
Part 2: Use embodi3D's free democratiz3D service to automatically create your model
Key Takeaway from this Tutorial:
You can make high quality 3D printable models from medical imaging scans using FREE software and services, and it is surprisingly EASY.
A note on the FDA (for USA people):
There is a lot of confusion about whether expensive, FDA-approved software must be used for medically-related 3D printing in the United States. The FDA recently clarified its stance on the issue.* If you are not using these models for patient-care purposes, this does not concern you. If you have questions please see the FDA website.
If you are a DOCTOR, you can use whatever software you think is appropriate for your circumstances under your practice of medicine.
If you are a COMPANY, selling 3D printed models for diagnostic use, you need FDA-approved software.
If you are designing implants or surgical cutting guides, those are medical devices. Seek FDA feedback.
*Kiarashi, N. FDA Current Practices and Regulations, FDA/CDRH-RSNA SIG Meeting on 3D Printed Patient-
Specific Anatomic Models. Available at https://www.fda.gov/downloads/MedicalDevices/NewsEvents/WorkshopsConferences/UCM575723.pdf Accessed 11/1/2017.
Part 1: Using Desktop software 3D Slicer and Meshmixer
Step 1: Download the scan file and required software
To start, download the starting CT scan file at the link below. Also, install 3D Slicer (slicer.org) and Meshmixer (meshmixer.com).
Step 2: Open 3D Slicer
Open Slicer. Drag and drop the scan file gunshot to face.nrrd onto the slicer window. The scan should open in a 4 panel view as shown below in Figure 1.
Figure 1: The 4 up view.
If your view does not look like this, you can set the 4 up view to display by clicking Four-Up from the View menu, as shown in Figure 2
Figure 2: Choosing the four-up view
Step 3: Learning to control the interface
Slicer has basic interface controls. Try them out and become accustomed to how the interface works. Note how the patient has injuries from gunshot wound to the face.
Left mouse button – Window/Level
Right mouse button – Zoom
Scroll wheel – Scroll through stack
Middle mouse button -- Pan
Step 4: Blur the image
The CT scan was created using a bone reconstruction kernel. Basically this is an image-enhancement algorithm that makes edges more prominent, which makes detection of fractures easier to see by the human eye. While making fracture detection easier, this algorithm does unnaturally alter the image and makes it appear more "speckled"
Figure 3: Noisy, "speckled" appearance of the scan on close up view
To fix this issue, we will slightly blur the image. Select Gaussian Blur Image Filter as shown below in Figure 4
Figure 4: Choosing the Gaussian Blur Image Filter
Set up the Gaussian Blur parameters. Set Sigma = 1.0. Set the input volume to be Gunshot to face. Create a new output volume called "Gaussian volume" as shown in Figure 5.
Figure 5: Setting up the Gaussian parameters
When ready, click Apply, as shown in Figure 6. You will notice that the scan becomes slightly blurred.
Figure 6: Click Apply to start the Gaussian Blur Image filter.
Step 5: Create a 3D model using Grayscale Model Maker
Open the Grayscale Model Maker Module as shown below in Figure 7.
Figure 7: Opening the Grayscale Model Maker
Set up the Grayscale Model Maker parameters. Select the Gaussian volume as the input volume, as shown in Figure 8.
Figure 8: Choosing the input volume in Grayscale Model Maker
Next, set the output geometry to be a new model called "gunshot model." Set the other parameters: Threshold = 200, smooth 15, Decimate 0.5, Split normals unchecked as shown in Figure 9.
Figure 9: Grayscale Model maker parameters
When done, click Apply. A new model should be created and will be shown in the upper right hand panel, as shown in Figure 10.
Figure 10: The new model
Step 6: Save the model as an STL file
To start saving the model, click the save button in the upper left of the Slicer window as shown in Figure 11.
Figure 11: The save button
Be sure that only the 3D model, gunshot model.vtk is selected. Uncheck everything else, as shown in Figure 12.
Figure 12: The Save dialog. Check the vtk file
Make sure the format of the 3D model is STL as shown in Figure 13. Specify the folder to save into, as shown in Figure 14.
Figure 13: Specify the file type
Figure 14: Specify the folder to save into within the Save dialog.
Step 7: Open the file in Meshmixer for cleanup
Open Meshmixer. Drag and drop the newly created STL file on the meshmixer window. The file will open and the model will be displayed as in Figure 15.
Figure 15: open the STL file in Meshmixer
Get accustomed to the Meshmixer interface as shown in Figure 16. A 3 button mouse is very helpful.
Figure 16: Controlling the Meshmixer user interface
Choose the Select tool. In is the arrow button along the left of the window.
Figure 17: The select tool
Click on a portion of the model. The selected portion will turn orange, as shown in Figure 18.
Figure 18: Selected areas turn orange.
Expand the small selected area to all mesh connected to it. Use Select->Modify->Expand to Connected, or hit the E key. The entire model should turn orange. See Figure 19.
Figure 19: Expanding the selection to all connected mesh.
Next, Invert the selection so that only disconneced, unwanted mesh is selected. Do this with Select->Modify->Invert, or hit the I key as shown in Figure 20.
Figure 20: Inverting the selection
At this point, only the unwanted, disconnected mesh should be selected in orange. Delete the unwanted mesh using Select->Edit->Discard, or use the X or DELETE key as shown in Figure 21. At this point, only the desired mesh should remain.
Figure 21: Deleting unwanted mesh.
Step 8: Run the Inspector tool
The Inspector tool will automatically fix most errors in the model mesh. To open it, choose Analysis->Inspector as shown in Figure 22.
Figure 22: The Inspector tool
The Inspector will identify all of the errors in the mesh. To automatically correct these mesh errors, click Auto Repair All as shown in Figure 23.
Figure 23: Auto Repairing using Inspector
The Inspector will usually fix all or most errors. In this case however, there is a large hole at the edge of the model where the border of the scan zone was. The Inspector doesn't know how to close it. This is shown in Figure 24.
Figure 24: The inspect could not fix 1 mesh error
Step 9: Close the remaining hole with manual bridges
Using the select tool, select a zone of mesh near the open edge. The Select tool is opened with the arrow button along the left. Choose a brush size -- 40 is good -- as shown in Figure 25.
Figure 25: Choosing the select tool
The mesh should turn orange when selected, as shown in Figure 26.
Figure 26: Selected mesh turns orange.
Next, rotate the model and select a zone of mesh opposite the edge from the first selected zone, as shown in Figure 27.
Figure 27: Selecting mesh opposite the defect.
Once both edges are selected, create a bridge of mesh spanning the two selected areas using the Bridge operation: Select->Edit->Bridge, or CTRL-B, as shown in Figure 28.
Figure 28: The bridge tool
There should now be a bridge of orange mesh spanning the gap. Click Accept, as shown in Figure 29.
Figure 29: The new bridge. Be sure to click Accept.
Next, repeat the bridge on the opposite side of the skull. Be sure to deselect the previously selected mesh before working on the opposite side, as shown in Figure 30.
Figure 30: Creating a second bridge on the opposite side.
Step 10: Rerun the Inspector
Rerun the Inspector tool, as shown in Figure 31. Now with the bridges to "help" Meshmixer to know how to fill in the hole, it should succeed. If it fails, create more bridges and try again.
Figure 31: Rerun the Inspector tool
Next, export your file to STL.
Figure 32: Export to STL
Step 11: 3D print your file!
Your STL file is now ready to be sent to the 3D printer of your choice. Figure 33 shows the model after printing.
Figure 33: The final print
Part 2: Using the democratiz3D service on embodi3d.com
democratiz3D automatically converts scans to 3D printable models. It automates the mesh cleanup process and saves time. The service is free for general bone model creation.
Step 1: Register
Register for a free embodi3D account. The process takes only a minute. You need an account for your processed files to be saved to.
Step 2: Upload the NRRD source scan to democratiz3D.
From anywhere in the site, click democratiz3D-> Launch App
Figure 34: Launching the democratiz3D app.
Fill out basic information about your file. That information will be copied to your generated STL file, as shown in Figure 35.
Figure 35: Entering basic file information
Make sure democratiz3D processing is on. Choose an operation to convert your model. Set threshold to 200, as shown in Figure 36.
Figure 36: Operation, threshold, and quality parameters.
Click Submit! In 10 to 15 minutes your model should be done. You will receive an email notification. The completed model file will be saved under your account. Download the file and send it to your printer of choice!
Figure 37; The final democratiz3D file, ready for download.
That's it! I hope this tutorial was helpful to you. If you liked it, please rate it positively. If you want to learn more about democratiz3D, Meshmixer, or Slicer, please see our tutorials page. It has a lot of wonderful resources. Happy 3D printing!
I decided to give my Prusa MK3 printer a real challenge, so I cut my best skull model, I added some slots for neodymium magnets and I started to print the parts. I'm done with the half of them and I'll update my post when I'm done.
Here is another tutorial on hollowing meshes, specifically head meshes to obtain a face shell, but I use this method to hollow out bones as well.
Dr. Mike recently posted a great video tutorial on hollowing a head using Meshmixer: https://www.embodi3d.com/blogs/entry/359-how-to-create-a-hollow-shell-from-a-medical-stl-file-using-meshmixer/.
I tend to go back and forth between Meshmixer and Meshlab for different functions to prep a print, but I like to use Meshlab for hollowing because it's quick and you can easily control how much "external" surface is selected, which is especially handy for models that have highly complex internal structures.
Note that this workflow is also useful if you simply want a 3D model (for viewing/interacting in software, Sketchfab) of a smaller file size where you don't need the internal structures and/or you don't want to decimate the model to achieve a smaller file size.
Here are the steps to hollow a head model in Meshlab. I will post screeshots below which you can also find in the Gallery, https://www.embodi3d.com/gallery/album/73-hollowing-skin-model-with-meshlab/.
Import a model into Meshlab.
Go to Filters --> Color Creation and Processing --> Ambient Occlusion per Vertex.
When the new box opens, check the box to select "Use GPU Acceleration" and click "Apply." The default settings are fine for a first step.
Once you become comfortable with the workflow, you can play around with applying the light from different axes: "Lighting Direction" and "Directional Bias".
You will notice that your model is now colorized from light to dark, with "deeper" areas shaded darker.
On the main toolbar, select the "transparent wireframe" view.
You can now see the internal structures that are shaded completely black.
We can now use the shading values to select the areas we want to remove.
Go to Filters --> Selection --> Select Faces by Vertex Quality. The shading values are stored in the Vertex Quality field of your 3D model, with values from 0 (black) to 1 (white), so we can use these values to select the dark (internal or deep) areas we want to remove.
When the Selection box opens up, slide the "Min Quality" value all the way to 0 (to the left). Check the "Preview" box so that you can see which areas are selected in red.
Adjust the "Max Quality" slider left and right until you see that no external surfaces are selected in red. In the image below, you can see that the bottom edges of the eyelids are still red and some skin below the nostrils is also red. When you find a good value, click "Apply" and Close.
**Depending on the model, it may be difficult to adjust the Max slider to a value that doesn't include parts of the eyelids or nose, but I will explain in Step 6 how you can recover these features. Instead of deleting the selection in Step 5, skip to Step 6.
Once you are happy with your selection from Step 4, you can delete everything selected in red by clicking the button shown in the image below. You can see that the model is now hollow, although there may be some disconnected pieces which we will remove in multiple cleaning steps.
If you think you may have selected some external features in Step 4 that you don't want deleted, instead of deleting (Step 5), you can move the selected (red) areas to another layer. Sometimes with overhanging eyelids or very deeply set eyes, these areas might have the same shading values as some internal structures and can't be excluded from the red.
Go to Filters --> Mesh Layer --> Move selected faces to another layer (if your layer dialog is already open, you can right-click on the model name to access the Mesh Layer menu as well). The layer dialog will open up on the right and you will see the name of your original model as well as the new layer. Use the eye icons to toggle visibility.
The Meshlab selection tools can be used to select the areas from the red you want to keep, then move them to another layer. Right-clicking on a mesh name will open the Mesh Layer menu, from which you can "Flatten Visible Layers"--the layers you want to keep can be kept visible and merged into a new mesh.
This image shows the view from the bottom. The head is empty except for that big flat piece at the top of the head.
As an initial cleaning step to remove small pieces, go to Filters --> Cleaning and Repairing --> Remove Isolated pieces (wrt Diameter). The default size works well, but you can adjust it up to 40% or so to remove larger pieces. This is a deletion function, so the floating pieces will be removed and gone forever! Try to not to adjust the size too high--we'll remove large pieces in step 9.
Step 8 will usually not remove large pieces, especially if you're being cautious and only remove small pieces. To remove larger pieces, go to Filters --> Mesh Layer --> Split in Connected Components. The pieces will drop into separate layers in the layer dialog box on the right, and they will be named CC 0, CC 1, etc. You don't want to apply this filter until you've removed small pieces, or you might end up crashing the program because there are too many pieces separating out! As mentioned above, the Mesh Layer menu can also be accessed by right-clicking on the mesh name in the right-hand layer dialog box.
The largest layer is usually CC 0. Toggle visibility to figure out which layer is the one you want. Left-click on it to highlight it in yellow and then export using File --> Export Mesh as...
I prefer to fill holes (Inspector) and create internal walls (Extrude or Offset) in Meshmixer, so you can now import the hollowed model to Meshmixer to fix it up for printing if needed. You can also use the plane cut tool in Meshmixer to remove the flattened edge at the top of the skin model, or apply Ambient Occlusion again in only the z-direction (see Step 1--"Lighting Direction").
This can be an interative process depending on the complexity of the model you're trying to hollow, but it can save on printing time as well as $$ if you're only interested in the external surface. Play around with lighting directions to select the surfaces you want and as always, SAVE meshes along the way in case the program crashes or you make a mistake!
Top Orbital and Skull 3D Model STL Files on embodi3D®
In our day-to-day lives, we rely on vision more than any of the other four senses, so it only makes sense that human anatomy has adapted to include several features which keep our eyes safe: tear ducts, eyelids, and of course the orbital bone. The orbit (also known as the "eye socket") provides a rigid form of support and protection for some of the most sensitive parts of the eye including the central retinal artery, maeula, retina, choroid, and sclera.
The orbit has such complex anatomical features that modeling can prove difficult, and in many instances, the finer features of the orbital bone have been simply been averaged out. The orbital structure isn't one bone, but seven: the frontal, lacrimal, ethmoid, zygomatic, maxillary, and palatine, and sphenoid bones. Can you think of any part of the human body where seven bones converge to fulfill a singular purpose?
In recognition of this phenomenal feature of the human anatomy (and one of the most recognizable parts of the human skull), this week's embodi3D® Top Uploads articles, we are featuring several standout uploads — all of which can be used to create an orbital and skull 3D model. As detailed in the scholarly article "Clinical application of three-dimensional printing technology in craniofacial plastic surgery" 3D printing techniques are being used in craniofacial surgeries and especially in reconstruction procedures the require complex modeling. Using the latest 3D printing technology and the STL files converted using democratiz3D®, the contralateral orbit can serve as a point of reference for those in the medical field since the ipsilateral structures taken with a CT scan can be easily converted into an STL file and then fed to a 3D printer. These technologies improve patient consultations, increase the quality of diagnostic information while also helping to improve the planning stage of the surgical process. During surgery, a 3D-printed model of the orbital can be used to orient surgical staff and serve as a guide for surgical resectioning procedures.
While these files are available for free on the website, you must register with embodi3D® before you can begin uploading and converting your own CT scans into STL files as well as downloading and 3D printing anatomical models from other users. Every day the collection of anatomical models grows on the embodi3D® website. This is but one of the many ways embodi3D® is seeking to revolutionize medical practices.
#1. An Awesome Model of the Orbit's Acute Anatomy
The orbits are conical structures dividing the upper facial skeleton from the middle face and surround the organs of vision. Seven bones conjoin to form the orbital structure as we can see in the example below.
#2. A 3D Model of the Orbit's Surface in STL Format
This excellent 3D model of embodi3D® shows the superficial bony margin of the orbit, which is rectangular with rounded corners. The margin is discontinuous at the lacrimal fossa. The supraorbital notch (seen in the image below) is within the supraorbital rim and is closed to form the supraorbital foramen in 25% of individuals. The supratrochlear notch is medial to the supraorbital notch.
#3. A CT Scan of an Orbital Floor Fracture
Hisham published this excellent ct scan on embodi3D®. Direct fractures of the orbital floor can extend from fractures of the inferior orbital rim. Indications for repair of the orbital floor in these cases are the same as those for indirect (blowout) fractures. Indirect fractures of the orbital floor are not associated with fracture of the inferior orbital rim.
#4. A 3D Model of an Orbital Fracture
CT scans with coronal or sagittal views and 3D models help guide treatment. They allow evaluation of fracture size and extraocular muscle relationships, providing information that can be used to help predict enophthalmos and muscle entrapment.
#5. 3D Model Showing an Orbital Fracture
Dropbear upload this excellent example of a right orbit fracture.
#6. An Orbit 3D Model (Printable) Showing Fibrous Dysplasia (FD) for Surgical Demonstration
The FD is a benign slowly progressive disorder of bone, where normal cancellous bone is replaced by fibrous tissue and immature woven bone. This entity constitutes about 2.5 % of all bone tumors.
Choi, J. W., & Kim, N. (2015). Clinical application of three-dimensional printing technology in craniofacial plastic surgery. Archives of plastic surgery, 42(3), 267.
Bibby, K., & McFadzean, R. (1994). Fibrous dysplasia of the orbit. British journal of ophthalmology, 78(4), 266-270.
3D-Printed Models of the Spine
In this week's post, we want to share with you some of the best 3D-printed models of the spine uploaded by embodi3D® members. We will explore features of this unique anatomy and some of the main uses of 3D printing as it relates to the spine . To convert your own scans and download and 3D-print STL files from other users, all you have to do is register with embodi3D®. It's quick, easy, and costs absolutely nothing to join.
Anatomical models have applications in clinical training and surgical planning as well as in medical imaging research. The Wall Street Journal recently ran an article to discuss the many ways 3D printing is changing the face of healthcare. The article also highlighted a case where a 3D model of a pelvis was used to plan a surgical operation on a young female patient.
A full-scale, anatomical model of a human lumbar vertebra created with embodi3D®.
In terms of clinical applications, the physical interaction with models facilitates learning anatomy and how different structures interact spatially in the body. Simulation-based training with anatomical models reduces the risks of surgical interventions, which are directly linked to patient experience and healthcare costs.
3D printing (3DP) is most frequently utilised in spinal surgery in the pre-operative planning stage. A full-scale, stereoscopic understanding of the pathology allows for more detailed planning and simulation of the procedure. Assessing complex pathologies on a model overcomes many of the issues associated with traditional 3D imaging, such as the lack of realistic anatomical representation and the associated complexity of computer-related skills and techniques.
Summary of 3DP in spinal surgery planning
1999 D’Urso et al. (4) Osteogenesis imperfecta, cervicothoracic deformity, lumbar spinal fusion, cervical osteoblastoma
1999 D’Urso et al. (5) Craniofacial, maxillofacial and skull base cervical spine pathologies.
2005 D’Urso et al. (6) Complex spinal disorders.
2007 Guarino et al. (7) Multiplane spinal and pelvic deformities.
2007 Izatt et al. (8) Deformities, spinal tumours.
2007 Paiva et al. (9) Cervical Ewing Sarcoma.
2008 Mizutani et al. (10)Rheumatoid cervical spine.
2009 Madrazo et al. (11)Degenerative cervical disease.
2010 Mao et al. (12) Kyphoscoliosis, congenital malformations, neuromuscular disease.
2010 Yang et al. (13) Kyphoscoliosis.
2011 Wu et al.(14) Severe congenital scoliosis.
2013 Toyoda et al. (15) Atlantoaxial subluxation.
2014 Yang et al. (16) Atlantoaxial instability.
2015 Li et al.(17) Revision lumbar discectomy.
2015 Kim et al. (18)Thoracic tumours.
2015 Sugimoto et al. (19) Congenital kyphosis.
2015 Yang et al. (20) Adolescent idiopathic scoliosis.
2016 Goel et al. (21) Craniovertebral junction anomalies.
2016 Wang et al. (22) Congenital scoliosis, atlas neoplasm, atlantoaxial dislocation.
2016 Xiao et al. (23) Cervical bone tumours.
2017 Guo et al. (24) Cervical spine diseases.
There are 33 spinal vertebrae, which comprise two components: A cylindrical ventral bone mass, which is the vertebral body,and the dorsal arch.
7 cervical, 12 thoracic, 5 lumbar bodies
• 5 fused elements form the sacrum
• 4-5 irregular ossicles form the coccyx
• 2 pedicles, 2 laminae, 7 processes (1 spinous, 4 articular,
• Pedicles attach to the dorsolateral aspect of the body
• Pedicles unite with a pair of arched flat laminae
• Lamina capped by dorsal projection called the spinous process
• Transverse processes arise from the sides of the arches
The two articular processes (zygapophyses) are diarthrodial joints.
• (1) Superior process bearing a facet with the surface directed dorsally
• (2) Inferior process bearing a facet with the surface directed ventrally
Pars interarticularis is the part of the arch that lies between the superior and inferior articular facets of all subatlantal movable elements. The pars are positioned to receive biomechanical stresses of translational forces displacing superior facets ventrally, whereas inferior facets remain attached to dorsal arch (spondylolysis). C2 exhibits a unique anterior relation between the superior facet and the posteriorly placed inferior facet. This relationship leads to an elongated C2 pars interarticularis, which is the site of the
1. An Exceptional Human Lumbar Vertebra Converted from a CT Scan with embodi3D®
An anatomically accurate full-size human lumbar vertebra created from a real CT scan. The lumbar vertebral bodies are large, wide and thick, and lack a transverse foramen or costal articular facets. The pedicles are strong and directed posteriorly. The superior articular processes are directed dorsomedially and almost face each other. The inferior articular processes are directed anteriorly and laterally.
2. Create Your Own Lumbar Spine Model with a 3D-Printable STL File
A 3D printable STL file and medical model of the lumbar spine was generated from real CT scan data and is thus anatomically accurate as it comes from a real person. It shows the detailed anatomy of the lumbar (lower back) spine, including the vertebral bodies, facets, neural foramina and spinous proceses.
3. A 3D Printer-Ready Spinal Column in Amazing Detail
Thoracic bodies are heart-shaped and increase in size from superior to inferior. Facets are present for rib articulation and the laminae are broad and thick. Spinous processes are long, directed obliquely caudally. Superior facets are thin and directed posteriorly. The T1 vertebral body shows a complete facet for the capitulum of the first rib, and an inferior demifacet for capitulum of second rib. The T12 body has transitional anatomy, and resembles the upper lumbar bodies with the inferior facet directed more laterally
4. Create a 3D-Printed Model of Lumbar Vertebrae
The lumbar spine is formed by 5 lumbar vertebrae labelled L1-L5 and the intervening discs. Its main function is to provide stability and permits movement. The lumbar vertebral body is formed of 3 parts : Body, arch and spinal processes.
The body of the lumbar vertebrae is large, its transverse diameter is larger than is AP diameter, and is more thickened anteriorly.
The arch of the lumbar vertebra on the other hand is formed of pedicle, a strong structure that is projected from the back of the upper part of the vertebrae, and lamina which forms the posterior portion of the arch.
Another well reported benefit of 3DP models is improved patient education. A physical model is much easier for a patient to understand than complex MRI and CT scans.
5. An NRRD File Showing the Whole Spine — See the Future of Medical 3D Printing
A Whole Spine (Dorsal-Lumbar-Sacral) and Aorta NRRD file from CT Scan for Medical 3D Printing As 3DP technology continues to become cheaper, faster and more accurate, its use in the setting of spinal surgery is likely to become routine, and in a greater number of procedures.
6. Download a 3D-Printable Thoracic Spine with Prevalent Scoliosis
A 3D printable STL file contains a model of the thoracic spine derived from a CT. The spine has significant scoliosis. In a recent embodi3D® article, we touched on the topic of how medical 3D printing is being used to plan spinal surgeries, such as in correcting the spinal curvature in scoliosis patients.
Scoliosis is considered to be present when there is a coronal plane curvature of the spine measuring at least 10°. However, treatment is not generally instituted unless the curvature is > 20-25°. The curvature may be balanced (returning to midline) or unbalanced. The vertebrae at the ends of the curve are designated the terminal (or end) vertebrae, while the apical vertebra is at the curve apex. Curvatures are described by the side to which they deviate. A dextroscoliosis is convex to the right, with its apex to the right of midline. A levoscoliosis is convex to the left, with its apex to the left of midline.
Curvatures can be categorized as flexible (normalizing with lateral bending toward the side of the curve) or structural (failing to correct). Most scoliotic curvatures are associated with abnormal curvature in the sagittal plane. These are described as kyphosis (apex dorsal) or lordosis (apex ventral).
Morphology of the Curvature
Scoliosis due to fracture, congenital anomaly, or infection typically has an angular configuration. Other causes of scoliosis tend to have a smooth curvature. Scoliosis most commonly involves the thoracic spine, followed by the thoracolumbar spine. In the past, curves were categorized as
primary and secondary (compensatory), but it is often difficult to make the distinction and so these designations are no longer commonly used.
Measurement of Scoliosis
The Cobb method is most commonly used to measure scoliosis. The vertebrae at each end of the curve (the terminal vertebrae) are chosen. These are the endplates with the greatest deviation from the horizontal. The curvature is the angle between a line drawn along the superior endplate of superior terminal vertebra and a line along the inferior endplate of the inferior terminal vertebra. In severe curvatures, the endplates are often difficult to see. In that case, the inferior cortex of the pedicle can be used as the landmark for making the measurement. If measurements are made on hard copy radiographs, it is usually necessary to draw lines perpendicular to the endplates and measure the angle between the perpendicular lines.
Scoliosis is almost always associated with abnormal curvature in the sagittal plane. The most common finding is loss of normal thoracic kyphosis. The Cobb method can be used to determine sagittal plane deformity. Rotational deformity is often present but can only be grossly assessed on radiographs. It can be measured on CT scan by superimposing the apical and terminal vertebrae.
Normally, the T1 vertebra is centered over the L5 vertebra in both the coronal and sagittal planes. Coronal or sagittal plane imbalance can be measured as the horizontal distance between the center of the L5 vertebral body and a plumb line drawn through the center of the T1 vertebral body.
7. Dr. Mike's Excellent Tutorial on Converting CT Scans to 3D Printer-Ready STL Models
An excellent tutorial of A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes which allows you to follow along with the tutorial. Included is an anonymized chest abdomen pelvis CT in both DICOM and NRRD formats.
8. An MRI of a Lumbar Spine with Disc Bulge at L4-L5 and L5-S1
The term bulge is used to describe a generalized extension greater than 50% of the circumference of the disc tissues, extending a short distance (< 3 mm) beyond the edges of the adjacent apophyses. A bulge is not a herniation, although 1 portion of the disc may be bulging and another portion of the
disc may herniate. A bulge is often a normal variant, particularly in children in whom all normal discs appear to extend slightly beyond the vertebral body margin. Bulge may also be associated with disc degeneration or may occur as a response to axial loading or angular motion with ligamentous laxity. Occasionally, a bulge in 1 plane is really a central subligamentous disc herniation in another plane. Asymmetric bulging of disc tissue greater than 25% of the disc circumference may be seen as an adaptation to adjacent deformity, and is not considered a form of herniation. Herniations are a localized displacement of disc material beyond the limits of the intervertebral disc space in any direction.
9. Using 3D Modeling to Understand the Severity of a Scoliosis Case
A 3D model of a severe scoliosis. CT scan should always be performed with reformatted images. Angled reformatted images and 3D reformations are often useful in assessment of severe curvatures. Some physicians find it useful to obtain both SPECT and CT images of degenerative scoliosis. An area of arthritis on CT scan, which shows increased uptake on SPECT, is probably a pain generator.
MR can be difficult to interpret when scoliosis is severe. Angled axial images should be obtained based on both sagittal and coronal scout images and angled along the plane of the vertebral endplate on both scouts. Sagittal images should be angled along each segment of the curvature. The coronal plane is often the most useful for evaluating bony anomalies, spondylolysis, or degeneration of the discs and facet joints.
1. Bücking, T. M., Hill, E. R., Robertson, J. L., Maneas, E., Plumb, A. A., & Nikitichev, D. I. (2017). From medical imaging data to 3D printed anatomical models. PloS one, 12(5), e0178540.
2. Wilcox, B., Mobbs, R. J., Wu, A. M., & Phan, K. (2017). Systematic review of 3D printing in spinal surgery: the current state of play. Journal of Spine Surgery, 3(3), 433.
3. Ross, J. S., Moore, K. R., Bryson Borg, M. D., Julia Crim, M. D., & Shah, L. M. (2010). Diagnostic imaging: spine: published by Amirsys®. Lippincott Williams & Wilkins, Baltimore.
4. D'Urso PS, Askin G, Earwaker JS, et al. Spinal biomodeling.Spine (Phila Pa 1976) 1999;24:1247-51. 10.1097/00007632-199906150-00013.
5. D'Urso PS, Barker TM, Earwaker WJ, et al. Stereolithographic biomodelling in cranio-maxillofacial surgery: a prospective trial. J Craniomaxillofac Surg 1999;27:30-7. 10.1016/S1010-5182(99)80007-9
6. D'Urso PS, Williamson OD, Thompson RG. Biomodeling as an aid to spinal instrumentation. Spine (Phila Pa 1976) 2005;30:2841-5. 10.1097/01.brs.0000190886.56895.3d
7. Guarino J, Tennyson S, McCain G, et al. Rapid prototyping technology for surgeries of the pediatric spine and pelvis: benefits analysis. J Pediatr Orthop 2007;27:955-60. 10.1097/bpo.0b013e3181594ced
8. Izatt MT, Thorpe PL, Thompson RG, et al. The use of physical biomodelling in complex spinal surgery. Eur Spine J 2007;16:1507-18. 10.1007/s00586-006-0289-3
9. Paiva WS, Amorim R, Bezerra DA, et al. Aplication of the stereolithography technique in complex spine surgery. Arq Neuropsiquiatr 2007;65:443-5. 10.1590/S0004-282X2007000300015
10. Mizutani J, Matsubara T, Fukuoka M, et al. Application of full-scale three-dimensional models in patients with rheumatoid cervical spine. Eur Spine J 2008;17:644-9. 10.1007/s00586-008-0611-3
11. Mao K, Wang Y, Xiao S, et al. Clinical application of computer-designed polystyrene models in complex severe spinal deformities: a pilot study. Eur Spine J 2010;19:797-802. 10.1007/s00586-010-1359-0
12. Yang JC, Ma XY, Lin J, et al. Personalised modified osteotomy using computer-aided design-rapid prototyping to correct thoracic deformities. Int Orthop 2011;35:1827-32. 10.1007/s00264-010-1155-9
13. Wu ZX, Huang LY, Sang HX, et al. Accuracy and safety assessment of pedicle screw placement using the rapid prototyping technique in severe congenital scoliosis. J Spinal Disord Tech2011;24:444-50. 10.1097/BSD.0b013e318201be2a
14. Toyoda K, Urasaki E, Yamakawa Y. Novel approach for the efficient use of a full-scale, 3-dimensional model for cervical posterior fixation: a technical case report. Spine (Phila Pa 1976)2013;38:E1357-60. 10.1097/BRS.0b013e3182a1f1bd
15. Yang JC, Ma XY, Xia H, et al. Clinical application of computer-aided design-rapid prototyping in C1-C2 operation techniques for complex atlantoaxial instability. J Spinal Disord Tech 2014;27:E143-50.
16. Li C, Yang M, Xie Y, et al. Application of the polystyrene model made by 3-D printing rapid prototyping technology for operation planning in revision lumbar discectomy. J Orthop Sci 2015;20:475-80. 10.1007/s00776-015-0706-8
17. Kim MP, Ta AH, Ellsworth WA, 4th, et al. Three dimensional model for surgical planning in resection of thoracic tumors. Int J Surg Case Rep 2015;16:127-9. 10.1016/j.ijscr.2015.09.037
18. Sugimoto Y, Tanaka M, Nakahara R, et al. Surgical treatment for congenital kyphosis correction using both spinal navigation and a 3-dimensional model. Acta Med Okayama 2012;66:499-502.
19. Yang M, Li C, Li Y, et al. Application of 3D rapid prototyping technology in posterior corrective surgery for Lenke 1 adolescent idiopathic scoliosis patients. Medicine (Baltimore) 2015;94:e582. 10.1097/MD.0000000000000582
20. Goel A, Jankharia B, Shah A, et al. Three-dimensional models: an emerging investigational revolution for craniovertebral junction surgery. J Neurosurg Spine 2016;25:740-4. 10.3171/2016.4.SPINE151268
21. Wang YT, Yang XJ, Yan B, et al. Clinical application of three-dimensional printing in the personalized treatment of complex spinal disorders. Chin J Traumatol 2016;19:31-4. 10.1016/j.cjtee.2015.09.009
22. Xiao JR, Huang WD, Yang XH, et al. En Bloc Resection of Primary Malignant Bone Tumor in the Cervical Spine Based on 3-Dimensional Printing Technology. Orthop Surg 2016;8:171-8. 10.1111/os.12234
23. Guo F, Dai J, Zhang J, et al. Individualized 3D printing navigation template for pedicle screw fixation in upper cervical spine. PLoS One 2017;12:e0171509. 10.1371/journal.pone.0171509
This week we would like to share the most downloaded 3D models and resources from our site. These may be good resources for educational purposes as they demonstrate the detailed anatomy of the human body. We have a list of the top human heart STL files and another list of free human anatomy STL files.
The 1st place is for Dr. Mike’s tutorial on how to create 3D printable bone models. 3D printing is an evolving technology that enables the creation of unique organic and inorganic structures with high precision. In medicine, this technology has demonstrated potential uses for both patient treatment and education as well as in clinical practice. Learning how to create 3D models and taking this technology as a great advantage for medical education and practice is important for all of us as physicians and this tutorial makes it easy to learn.
The list also includes other great 3D models, like skull and heart. Let’s then take a look into this ten awesome models. Don’t forget to register in order to download the models, you can do it by clicking here.
1. 2.952 Downloads An improved tutorial that shows you how to create 3D printable bone models even more easily and for free on any operating system. Try it! https://www.embodi3d.com/files/file/115-file-pack-for-3d-printing-with-osirix-tutorial/
2. 913 Downloads 3D printable model of a human heart was generated from a contrast enhanced CT scan. https://www.embodi3d.com/files/file/64-3d-printable-human-heart-model-with-stackable-slices/
3. 893 Downloads 3D printable brain is from an MRI scan of a 24 year old human female.
4. 714 Downloads This full-size skull with web-like texture was created from a real CT scan.
5. 648 Downloads 3D printable model of stroke.
6. 609 Downloads Skull with web-like texture was created from a real CT scan.
7. 422 Downloads Anatomically accurate heart and pulmonary artery tree was extracted from a CT angiogram.
8. 396 Downloads Tutorial: "3D Printing of Bones from CT Scans: A Tutorial on Quickly Correcting Extensive Mesh Errors using Blender and MeshMixer”
9. 392 Downloads Tutorial A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes
10. 373 Downloads Bony anatomy and skin surface of the L and R feet.
1. Colaco, M., Igel, D. A., & Atala, A. (2018). The potential of 3D printing in urological research and patient care. Nature Reviews Urology.
The protection of the intellectual property of the 3D models can be a serious issue for every 3D modeler. It sucks when your model is posted for selling at a webside without your consent with a juicy price and you're gaining NOTHING from it. Some 3D artists are adding watermarks to their models, which can be easily removed by an amateur with a free surface modelling program (Meshmixer, Meshlab etc.). But there is an easy solution for this injustice - an invisible watermark. On Watermark3D you can add such watermark, incorporated into the mesh of your 3D model itself, which is hard for removing and can be checked on the same website during an intellectual property dispute. For the removing of the watermark you have to remesh the whole model, which will decrease the overall quality of the model substantially. I hope that I'll spare you the pain, which I experienced recently. Enjoy
Hello the Biomedical 3D Printing community, it's Devarsh Vyas here writing after a really long time!
This time i'd like to share my personal experience and challenges faced with respect to medical 3D Printing from the MRI data. This can be a knowledge sharing and a debatable topic and I am looking forward to hear and know what other experts here think of this as well with utmost respect.
In the Just recently concluded RSNA conference at Chicago had a wave of technology advancements like AI and 3D Printing in radiology. Apart from that the shift of radiologists using more and more MR studies for investigations and the advancements with the MRI technology have forced radiologists and radiology centers (Private or Hospitals) to rely heavily on MRI studies.
We are seeing medical 3D Printing becoming mainstream and gaining traction and excitement in the entire medical fraternity, for designers who use the dicom to 3D softwares, whether opensource or FDA approved software know that designing from CT is fairly automated because of the segmentation based on the CT hounsifield units however seldom we see the community discuss designing from MRI, Automation of segmentation from MRI data, Protocols for MRI scan for 3D Printing, Segmentation of soft tissues or organs from MRI data or working on an MRI scan for accurate 3D modeling.
Currently designing from MRI is feasible, but implementation is challenging and time consuming. We should also note reading a MRI scan is a lot different than reading a CT scan, MRI requires high level of anatomical knowledge and expertise to be able to read, differentiate and understand the ROI to be 3D Printed. MRI shows a lot more detailed data which maybe unwanted in the model that we design. Although few MRI studies like the contrast MRI of the brain, Heart and MRI angiograms can be automatically segmented but scans like MRI of the spine or MRI of the liver, Kidney or MRI of knee for example would involve a lot of efforts, expertise and manual work to be done in order to reconstruct and 3D Print it just like how the surgeon would want it.
Another challenge MRI 3D printing faces is the scan protocols, In CT the demand of high quality thin slices are met quite easily but in MRI if we go for protocols for T1 & T2 weighted isotropic data with equal matrix size and less than 1mm cuts, it would increase the scan time drastically which the patient has to bear in the gantry and the efficiency of the radiology department or center is affected.
There is a lot of excitement to create 3D printed anatomical models from the ultrasound data as well and a lot of research is already being carried out in that direction, What i strongly believe is the community also need advancements in terms of MRI segmentation for 3D printing. MRI, in particular, holds great potential for 3D printing, given its excellent tissue characterization and lack of ionizing radiation but model accuracy, manual efforts in segmentation, scan protocols and expertise in reading and understanding the data for engineers have come up as a challenge the biomedical 3D printing community needs to address.
These are all my personal views and experiences I've had with 3D Printing from MRI data. I'm open to and welcome any tips, discussions and knowledge sharing from all the other members, experts or enthusiasts who read this.
Thank you very much!
Hello everybody it's Dr. Mike here again with another medical 3D printing tutorial. In this tutorial we are going to be going over freeware and open-source software options for medical 3D printing. This tutorial is based on a workshop I am giving at the 2017 Radiological Society of North America (RSNA) Annual Meeting in Chicago Illinois, November 2017. In this tutorial we will be going over desktop software that can be used to create 3D printable anatomic models from medical scans, as well as a free online automated conversion service. At the end of this tutorial you should be able to make high-quality 3D printable models from a medical imaging scan using free software or services.
Do I need to use FDA-approved software for Medical 3D Printing?
Before I dive into the tutorial I'd like to take a minute to talk to learners from the United States about the US Food and Drug Administration (FDA) and how this federal agency impacts medical 3D printing. Many healthcare professionals are confused and concerned about the ability to use non-FDA-approved software for medical 3D printing. Software vendors sell software that has been FDA-approved, but the software is usually quite expensive, to the tune of many thousands of dollars per year in license fees. There has been a lot of confusion about whether non-FDA-approved free software can be used for medical applications.
In August 2017 a meeting was held at the main FDA campus between FDA staff and representatives from RSNA. During this meeting the FDA clarified its stance on the issue (Figure 1). Basically the FDA indicated that if a doctor needs a 3D printed model for patient care, the doctor does NOT need to use FDA-approved software, as this is a medical decision and the FDA does not regulate the practice of medicine. FDA-approved software is not required even if the doctor is using the model for diagnostic use (Figure 2). If a company or other organization is marketing or designing software for diagnostic use, then that company or organization is required to seek FDA approval for that product. Basically if you are a physician or working on behalf of the physician and require a model, FDA-approved software is not required as long as you are not running a commercial service or company. Despite this leeway granted by the FDA's interpretation, I encourage anyone considering using freeware to create models for diagnostic use to use common sense and double check your findings before making any critical decision that could impact patient care. I also encourage you to look at the slides from the FDA presentation directly at the link below. Of course, none of this applies if you are not creating models for medical use.
Figure 1: Title slide from the FDA presentation
Figure 2: The relevant slide from the FDA presentation. Doctors creating 3D printable models for clinical and diagnostic use do not need to use FDA-approved software as this is considered practice of medicine, which the FDA does not regulate.
Medical 3D Printing Overview
In this tutorial we're going to go over two different ways to use free and open-source software to convert a medical imaging scan to a 3D printable model. This can be done using free desktop software or a free online service. The desktop software requires more steps and more of a learning curve, but also allows more control for customized models. The online service is fast, easy, and automated. However, if you want to design customized elements into your model, you'll not be able to. The overall workflow of the session is shown in Figure 3.
Figure 3: Workflow overview
Part 1: Free online service – embodi3D.com
Step 1: Download the scan
Please download the scan for this tutorial from the embodi3D.com website at the link below. You have to have a free embodi3D.com account in order to download. If you don't have an account go ahead and register by clicking on the "Sign Up" button on the upper right-hand portion of the page. Registration is easy and only takes about one minute. You will have to confirm your email address before your account is active, so make sure you have access to your email.
Step 2: Inspect the scan
If you don't already have it, download and install the desktop software program 3D Slicer from slicer.org (http://www.slicer.org/). Slicer is a free medical image viewing and research software application. We are going to use Slicer to view our scan. Once Slicer is installed, open the application. Drag-and-drop the file "CTA Head.nrrd" onto the Slicer window. Slicer will ask if you want to add the file, click OK. The scan should now show in Figure 4. If your window doesn't look this then select the Four Up layout from the Layouts drop-down menu.
Figure 4: The 4 panel view and Slicer
You can navigate and manipulate the images with Slicer using the various mouse buttons. Your left mouse button to adjust the window/level settings as shown in Figure 5.
Figure 5: Use the left mouse button to adjust window/level.
The right mouse button allows you to zoom into a specific panel, as shown in Figure 6.
Figure 6: The right mouse button controls zoom.
The scroll wheel allows you to move through the various slices of the scan, as shown in Figure 7.
Figure 7: The mouse wheel controls scrolling
Step 3: Upload the scan to embodi3D.com
Now that we have an idea about what's in the scan, you can upload it to embodi3D.com for automatic processing into a 3D printable model. Go to https://www.embodi3d.com/. If you don't yet have a free embodi3D.com user account, you will need one now. Go ahead and register. The process only takes a minute. Under the democratiz3D menu, click Launch App, as shown in Figure 8.
Figure 8: Launching the democratiz3D medical scan to 3D printable model automated conversion service.
Drag and drop the file "CTA Head.nrrd" onto the upload panel, as shown in Figure 9. The NRRD file format is an anonymized file format so this transfer is HIPAA compliant. If you want to know more about how to create an NRRD file from a DICOM data set, please see my tutorial on the topic here.
Figure 9: Drag-and-drop the scan file "CTA Head.nrrd" onto the highlighted upload panel
A submission form will open up. The first part of the form will ask you questions about the source file you're uploading. The second part will ask about the new model being generated. Start with the first part of the form, as shown in Figure 10, and fill in information about your uploaded scan file, including a filename, short description, any tags you wish to use to help people identify your file, whether you wish to share the file with the community or keep it private, and whether you want to make the file free for download or for sale. Obviously if you keep the file private this last setting doesn't matter as nobody will be able to see the file except you.
Figure 10: The first part of the form relates to information about your uploaded scan file. Make sure you fill in at least the required elements.
In the second part of the form fill in information about your model file that will be generated, as shown in Figure 11. First of all, make sure democratized processing is turned on. The slider should be green in color, as shown in Figure 11. This is very important because if processing is turned off, you will not generate an output model file!
Specify what operation you would like to perform on the scan, and whether you would like to generate a bone, muscle, or skin model. Also, specify the desired quality of the output model (low, medium, high, etc.) and whether you want the output model to be shared with the community (recommended) or private. If your file is going to be shared, choose a Creative Commons license that people can use it under. When you're satisfied with your parameters, click the Submit button.
Figure 11: The second part of the form relates to information about your 3D printable model to be generated. Choose an operation, quality level, as well as privacy settings.
Step 4: Download your finished 3D printable model.
After anywhere between 5 to 20 minutes you should receive an email saying that your model processing is complete. The exact time depends on a variety of factors including the complexity of your model, the quality that you've chosen, as well as server load. Once you receive the email follow the link to the model download page. Alternatively you can find the model by clicking on your username at the upper right-hand corner of any embodi3D.com webpage and selecting My Files. Once you find your model page you can inspect the thumbnails to make sure the model meets your criteria, as shown in Figure 12. When you are ready click the download button, agree to the terms, and your model STL file will download to your computer.
Figure 12: Download your file after processing is complete.
That's it! Your 3D printable model is ready to send to a printer. The process takes about 2 to 3 minutes to enter the data, plus 5 to 15 minutes to wait for the processing to be done. The embodi3D.com service is batchable, so it is possible for you to upload multiple files simultaneously. The service will crank out models as fast as you can upload them.
Part 2: Free desktop software – 3D Slicer and Meshmixer
You can use the free software program 3D slicer and Meshmixer to generate 3D printable models. The benefit of using desktop software is that you have more control over the appearance of the model and which structures you want included and excluded. The downside of using desktop software is that software is complicated and somewhat time-consuming to learn. If you haven't already download 3D Slicer and Meshmixer from the links below. Be sure to choose the appropriate operating system for your computer.
Step 1: Download the tutorial scan file and load into Slicer as described above in Part 1 Steps 1 and 2.
Step 2: Create a surface model from the scan data.
From within Slicer, open the Grayscale Model Maker module. In the Modules menu at the top now bar, select All Modules and choose the Grayscale Model Maker item, as shown in Figure 13.
Figure 13: Selecting the Grayscale Model Maker module.
You will now be taken to the Grayscale Model Maker module, which will convert the volumetric data in the CT scan to a surface model that can be used to create a STL file for 3D printing. In the parameters panel on the left side of the screen, make sure that the parameter set value is set to "Grayscale Model Maker", and the Input Volume is set to "CTA Head." Under Output Geometry, choose Create a New Model, since we wish to create a new output model. These parameters are shown in Figure 14.
Figure 14: Input parameters for the Grayscale Model Maker module
Set the Threshold value to 150 Hounsfield units. Also, set the Decimate value to 0.8 and make sure the Split Normals checkbox is unchecked. These are shown in Figure 15. When you're happy with your parameters, check Apply, and the grayscale model maker will work for a minute or so to create your surface model.
Figure 15: Additional input parameters for the Grayscale Model Maker module
Step 3: Save the surface model to an STL file.
Now that you have generated a surface model, you are ready to export it to an STL file. Click on the Save button on the upper left-hand corner of the 3D Slicer window. A Save dialog box will pop up, as shown in Figure 16. Find the row that contains the item "Output Geometry.vtk." Make sure that the checkbox next to this item is checked. All other rows should be unchecked. In the File Format column, make sure that the file shows as STL. Finally, make sure that the directory specified in the third column is the one you wish to save the file to. When everything is correct go ahead and click Save. Your surface model will now be exported and STL file saved in the directory specified.
Figure 16: The Save dialog box
Step 4: Repair the model in Meshmixer
The model is in STL format, but it has multiple errors in it which need to be corrected prior to 3D printing. We will do this in the freeware software program Meshmixer. Open Meshmixer, and drag-and-drop the just-created STL file "Output Geometry.stl" onto the Meshmixer window. The model will now open in Meshmixer. You will notice that the model is quite large, having about 300,000 polygons, as shown in Figure 17.
Figure 17: Open the model in Meshmixer
Navigating in Meshmixer is quite intuitive. The left mouse button uses tools and selects structures. The right mouse button is used to rotate the model. The scroll wheel is used to zoom in and out, as shown in Figure 18.
Figure 18: Navigating in Meshmixer
Run an initial repair on the model using the Inspector tool
We will be able to get rid of most (but not all) errors using the automated Inspector tool. Click on the Analysis button on the left navigation pane and choose the Inspector tool. Inspector will run and highlight all of the problems with the model, as shown in Figure 19. As you can see there are many hundreds of errors. Click on the Auto Repair All button to automatically attempt to fix these. At least one error will remain after the end of the process, but don't worry we will fix that later. Click on the Done button.
Figure 19: The Inspector tool shows errors in the mesh
Remesh the model
The Remesh operation recalculates all the polygons in the model, adjusting their size, and giving the model in more natural and less faceted look. Remesh and can also help to fix lingering mesh errors. First, select all the polygons in the model by hitting control-A. The entire model should turn orange, as shown in Figure 20.
Figure 20: Selecting all the polygons in the model.
Next, run the Remesh operation. Hit the R key, or choose Select-> Edit-> Remesh. The Remesh operation will now run, and will take approximately 1.5 to 2 minutes, depending on the power of your computer. This is shown in Figure 21.
Figure 21: The Remesh operation.
At the end of the Remesh operation, your model should have a much smoother and more natural appearance. You can adjust some of the Remesh parameters in the visualized pane, and the operation will recalculate. When you're happy with the result, click on the Accept button. This is shown in Figure 22.
Figure 22: The model after the Remesh operation.
Repeat the Inspector tool operation
Now that we have re-mashed the model, we can rerun the Inspector tool to clean up any residual errors. Click on Analysis and then the Inspector menu item. Click Auto Repair All, and inspector should repair any problems that still remain. When you're finished, click the Done button, as shown in Figure 23.
Figure 23: Running the Inspector tool a second time
Expose the cerebral vessels.
We are now going to take an extra step and make a cut through the crowd of the skull to expose the cerebral vessels. This can be easily achieved in about one minute. First, make sure to select all the vertices in the model by hitting control-A or using the menus Select-> Modify-> Select all, as shown in Figure 24. The entire model should turn orange to indicate that it is selected.
Figure 24: Selecting all the polygons in the model prior to performing a cut.
Next, start a plane cut by choosing Select-> Edit-> Plane cut. The plane cut will show on the screen. The portion of the model that is transparent will be cut off. The portion of the model that is opaque will be left behind. Move the plane by using the purple and green arrow handles. Rotate the plane by using the red arc handle, as shown in Figure 25.
Figure 25: Move and rotate the plane cut using the arrow and arc handles.
In this case we wish to move the plane cut to the four head, and rotated 180° so that the transparent portion of the cut is at the top of the head, and the opaque portion encompasses the face, jaw, and lower part of the skull. After you have finished positioning the plane, your model should look similar to Figure 26. When you're happy with position, click Accept.
Figure 26: The best position of the plane cut tool
The crown of the skull will now be cut off, exposing the cerebral vessels within the brain. This includes the anterior, posterior, and middle cerebral arteries as well as the venous structures such as the straight sinus and sigmoid sinuses, as shown in Figure 27. As you can see, this is a highly detailed model and excellent for educational purposes and teaching neurovascular anatomy.
Figure 27: The final model
In this tutorial we learn how to create a 3D printable skull and vascular model utilizing the free online service from embodi3D.com, as well as free desktop software 3D Slicer and Meshmixer. Both methods have their advantages and disadvantages. Embodi3D.com has a very fast and easy to use service. The desktop software is more difficult to use and learn, but gives more flexibility in terms of customization. Alternatively, you can use a combination of the two techniques, for example generating your model on the embodi3D.com website and then performing custom modifications, such as the plane cut we did in this tutorial, utilizing Meshmixer.
I hope you found this tutorial helpful and entertaining. Please give the tutorial a like. If you are engaged in medical 3D printing, please consider sharing your work on the embodi3D.com website. Thank you very much and happy 3D printing!
Here is my video review of the Ultimaker 3 Extended for medical 3D printing. It was 4 months in the making. Medical anatomical models can be challenging to 3D print because of complex anatomy and large size. This 3D printer has a couple of features which help overcome these challenges. Ultimaker 3 Extended specfications and pricing.
First, the Ultimaker 3 is a dual extrusion printer which allows for two different materials to be used during a single print. This video shows 3D printing with one water soluble material for support and another material for printing anatomical structures. I show how water soluble PVA provides support during the build and can be easily dissolved in tap water once the build is complete.
Second, the Ultimaker has a large build volume compared to most 3D printers in this price range. This allows for anatomical structures to be created in one print rather than having to do several prints and putting the pieces together.
While there are several good features of this 3D printer, there is still room for improvement. In this review I successfully 3D print small structures like a vertebra, but struggle with large and more complex structures like human brain and lumbar vertebrae. Watch this video review and follow along as I provide the pros and cons of medical 3D printing with the Ultimaker 3 Extended.
Medical Three-dimensional (3D) printing has a variety of uses and is becoming an integral part of dentistry, oral surgery and dental lab workflows. 3D printing in dentistry is the natural progression from computer-aided design (CAD) and computer-aided manufacturing (CAM) technology which has been used for years by dental labs to create crowns, veneers, bridges and implants. Now, 3D printing is taking its place with 3D printing solutions for dental, orthodontic, and maxillofacial applications. Several 3D printer manufacturers, including Stratasys and EnvisionTEC, offer specialized materials and printers as part of their dental 3D printing solutions. Anyone can create 3D printed dental models and embodi3D has created a dental 3D printing tutorial which guides readers through the process of 3D printing teeth and mandible.
Interested in Dental 3D Printing? Here are some resources:
Free downloads of hundreds of 3D printable dental models.
Automatically generate your own 3D printable dental models from CT or CBCT scans.
Have a question? Post a question or comment in the dental forum.
What is Dental 3D Printing?
Three-dimensional printing begins with a special scanner. The mouth of the patient can be scanned using contact or non-contact scanning technology. The device works by creating a super accurate, patient specific digital image of a dental surface that is then saved as a computer file. Using specialized software, the scan is translated into a 3D digital representation. The resulting digital model may be a tooth, several teeth or the jaw. This digital imaging is not only replacing CAD/CAM technology, but it is also replacing some of the old plaster impressions traditionally used.
Once the scan is complete and a 3D image has been created, the specialized software will prepare it for physical model creation. There are two popular methods for creating a physical model from the digital representation.
The first method involves using a technique called slicing. With the help of specialized computer software, the original three-dimensional image is divided into thin horizontal layers. These layers are then transmitted to the 3D printer. The physical model is then printed layer by layer until the physical 3D model is complete.
The second method is CNC milling. In this case, the complete digital image is transferred to a milling machine. Rather than print a model layer by layer, the milling machine starts with a solid piece of material. The machine then carves the new 3D physical model out of that block of material.
As techniques become more advanced, 3D models become more accurate and the technology becomes more readily available, the first method is used more often in dental diagnosis, treatment planning and construction of dental appliances such as dental implants, orthodontics, denture bases and bite guards.
Advantages of 3D Printing Teeth, Crowns, Dentures and Other Dental Anatomy
3D imaging has been used in dentistry for many years, however, the traditional method of model creation involves dental plaster models. While these models are accurate, so are 3D printed oral models. In fact, dental 3D printing is not only accurate, it is quick and a lot less messy. Patients who have undergone fitting for a crown or other dental appliance generally do not remember the process fondly. Plaster is messy and it has been necessary for patients to be fitted with a temporary appliance only to return for a second visit. This is both inconvenient and time-consuming. 3D imaging and printing can alleviate this problem. In dental offices with the capability, the process is fast and patients can often be fitted with their permanent appliance in a single visit without the plaster mess. This makes the entire process far more convenient for patients.
Dentists also benefit from 3D printing and imaging. Imaging files are far easier to store than bulky plaster casts. By going digital, dentists and maxillofacial surgeons can store patient information indefinitely. This makes it easier to refer to files time and again for comparison, planning and treatment.
As the 3D printer technology becomes more accessible, the cost of use is going down. Patients can have these procedures performed at prices comparable to traditional methods, and these costs will continue to decrease as 3D printer prices decrease.
Advances in 3D printing technology are constantly improving. Whereas manual creation of implants, crowns and prosthetics required a high degree of specialization, 3D printing can quickly and easily create highly accurate models. This provides better fitting, more personalized appliances improving both comfort and efficacy of prosthetics.
3D Printing in Maxillofacial and Oral Surgery
Maxillofacial and oral surgery is an area where 3D printing is currently being utilized for a variety of reasons including cancer, birth defects, injury or receding bone. Corrective surgery is often needed in cases like these. A prosthesis, implant, dental mesh, surgical stent and more can be created through the 3D scanning and printing process to aid patients.
In addition to creating the actual prosthetics, three-dimensional printing is also helpful as part of the planning process. Three-dimensional printing can be used to create prototypes of the planned devices prior to surgery. Having the ability to simulate devices prior to implantation can help surgeons work out complex reconstructions and ensure that devices fit well. This allows the entire surgical process to be safer and easier.
3D Printed Dental Implants
As with maxillofacial surgery, 3D scanning and 3D printing improve the fit, comfort and ease of dental implant surgery. 3D scans of the patient’s teeth, gums and jaw allow dentists to have a high degree of accuracy and as a result 3D printed dental anatomy is patient specific. There are many advantages to using 3D printing for dental implant surgery including:
Determine depth and width of bone
Accurate sizing for implants
Determine the location of sinuses and nerves
Three dimensional printing creates accurate models that ensure a good fit. It is used to address issues such as location, angle and depth of the implant prior to surgery. This same technology allows dentists to create templates and surgical drill guides for permanent implants. Many dentists use these guides to improve surgical safety as they guide the surgeon’s hand, ensure correct placement and restrict the depth of the drill.
How 3D Printing is Used for Crowns
With 3D scanning and printing, dentists and patients can forgo the plaster dental mold and the need to rely on a lab for crown creation. With 3D technology, dentists can use a scanning camera and specialized software to create an exact three-dimensional image of the tooth that needs to be crowned if the tooth has not broken below the gum line. This image is then transmitted to a 3D printer or milling machine that carves a porcelain crown to exact specifications. The entire process can be completed in about an hour allowing patients to leave the dental office with a permanent crown on the same day.
Three-dimensional imaging is one more tool in the dentists’ and oral surgeons’ arsenal to provide better oral health care. With three-dimensional imaging and printing, dentists can gain more complete information for diagnosis and treatment, ensure safer procedures and provide a more comfortable fit for oral devices.
We had a file sharing contest in May of 2017, where those members who uploaded and shared a file were entered to win. We had many good entries and it was a tough choice, but we found a winner! Michael Platt is our winner! He submitted and shared two STL downloads; a thoracic vertebra and a renal cortex. We selected the renal cortex because the download contains two STL files: an intact renal cortex and another STL with the cortex sliced in half.
Michael is a medical physicist with a passion for 3D printing and design. His research involves 3D printing and scanning in radiation oncology. He loves 3D printing and thinks that it has wonderful potential in medicine. We couldn't agree more!
We are having a file review contest in June with a $50 prize. All that is required is to download a file and write a review. Each file you review in June 2017 will be an entry in our contest. There is no limit to the number of files you can review. To learn more and see complete rules please visit our contest page.
In this tutorial we will learn how to easily create a 3D printable dental, orthodontic, or maxillofacial bone model quickly and easily using the free democratiz3D® file conversion service on the embodi3D.com website. Creating the 3D printable dental model takes about 10 minutes and requires no prior experience or specialized knowledge. Dental 3D printing is one of the many uses for democratiz3D. You can 3D print teeth, braces, dental implants and so much more.
Step 1: Download the CT scan file for dental 3D printing.
Go to the navigation bar on the embodi3D.com website and click on the Download menu. This is shown in Figure 1.
Figure 1: The Download menu
This will take you to the download section of the website, which has a very large and extensive library of 3D printable anatomy files and source medical scan files. Look for the category along the right side of the page that says Medical Scan Files. Click on the section within that that says Dental, Orthodontic, Maxillofacial, as shown in Figure 2.
Figure 2: Viewing the medical scan library on the embodi3D website
This section contains anonymized CT scans of the teeth and face. Many of the scans in this section are perfect for 3D printing dental models. For this tutorial we will use the file openbiteupdated by member gcross, although you can use any source CT scan. This particular scan is a good one to choose because the patient does not have metallic fillings which can create streak artifact which can lower the quality of the model. Click on the link below to go to the file download page.
Step 2: Preview the Dental CT scan file.
Once you've downloaded the file you can inspect the CT scan using 3D Slicer. If you don't know about 3D Slicer, it is a free open source medical image viewing software package that can be downloaded from slicer.org. Once you have installed and opened Slicer, you can drag-and-drop the downloaded NRRD file onto the slicer window and it will open for you to view. You can see as shown in Figure 3 that the file appears to be quite good, without any dental fillings that cause streak artifact.
Figure 3: Viewing the dental CT scan in Slicer.
Step 3: Upload your dental CT scan NRRD file to the democratiz3D online service.
Now that we are happy with our NRRD source file, we can upload it to the democratiz3D service for conversion into a 3D printable STL file. On the embodi3D website click on the democratiz3D navigation menu and Launch App, as shown in Figure 4.
Figure 4: Launching the democratiz3D service.
Once the online application opens, you will be asked to drag-and-drop your file onto the webpage. Go ahead and do this. Make sure that the file you are adding is an NRRD file and corresponds to a dental CT scan. An MRI will not work. This is shown in Figure 5.
Figure 5: Dragging and dropping the CT scan NRRD file onto the democratiz3D application page.
Step 4: Fill in basic information about your uploaded scan and generated model file
While the file is uploading you can begin to fill out some of the required form fields. There are two main sections to the form. The section labeled 3 pertains to the file currently being uploaded, the NRRD file. Section 4 pertains to the generated STL file that democratiz3D will create. In Section 3 fill out a filename and a short description of your uploaded NRRD file. Specify whether you want the file to be private or shared, and whether this is a free file or a paid file that you wish to sell. You must choose a license type, although this is only really applicable if your file is shared as if it is private nobody will be able to download it. This portion of the form is shown in Figure 6.
Figure 6: Filling out the submission form, part 1. Enter in information related to the uploaded NRRD file.
Next proceed to section 4, the portion of the form related to the file you wish to generate. Make sure that democratiz3D processing is turned on and the slider shows green. Choose the appropriate operation. For creation of dental files, the best operation is "CT NRRD to Bone STL Detailed." This takes a CT scan in NRRD file format and converts it to a bone STL file using maximum detail. Leave the threshold at the default value of 150. Set quality to high. Make sure that you specify whether you want the file to be private or shared, and free versus paid. Make sure you specify file license. The steps are shown in Figure 7.
Figure 7: Filling out the submission form, part 2. Enter in information related to the generated STL file.
Figure 8: The file download page for your newly created dental model.
Step 5: Check your dental STL file for errors and send it to your dental 3D printer!
Once you have downloaded the STL file open it in Meshmixer. Meshmixer is a free 3D software program available from meshmixer.com that has many handy 3D printing related features. The democratized service is a good job of creating error-free files, but occasionally a few errors will sneak through, which can be easily fixed and Meshmixer. Click on the analysis button and then select Inspector as shown in Figure 9. Click on the Auto Repair All button and any minor defects that are remaining will be automatically fixed. Make sure to save your repaired and finalized 3D printable model by clicking on the menu File -> Export.
You can now send your STL file to the 3D printer of your choice. Here is an example of the model when printed on a Form 1+ using white resin. You can see that the level of detail is very good. Formlabs has several examples of 3d printing teeth and other dental applications on their website.
Thank you very much. I hope this tutorial was helpful. If you are not already a member, please consider joining the embodi3D community of medical 3D printing enthusiasts. If you have any questions or comments, please feel free to post them below.
Welcome to our May 2017 newsletter! Read on to learn how you can participate in our file sharing contest and win an Amazon gift certificate, what improvements we have made to democratiz3D, and where you can find source medical files for 3D printing.
democratiz3D: New NRRD & STL Thumbnail Creation
democratiz3D(TM), our online tool which converts a medical scan study to a 3D printable file, has had an exciting upgrade: it now automatically creates thumbnails for NRRD files. As a reminder, the NRRD files are created from the original DICOM files from CT scans. Thumbnails are now automatically generated for all newly uploaded files. Once you submit a file for processing the thumbnails images will be available almost immediately. Simply refresh your browser window to see the thumbnails.
You can make thumbnails for your existing NRRD and STL files by clicking "Generate Thumbnails" on the file detail page. NRRD thumbnail generation takes a few seconds. Please note thumbnails are generated for STL files as well, but these take several minutes to process.
A Collection of Medical Scan Files
A new category called Medical Scan Files has been added to our Download area. This is a collection of NRRD source files uploaded and shared by members. Check it out, and please share your files so we can continue to grow our medical file library.
May Medical 3D Printing File Sharing Contest
Speaking of sharing, we are now running a contest for the best shared file with the winner receiving a $50 Amazon gift certificate. Share a file when you upload and you are automatically entered to win. The contest runs the month of May.
April 3D Printable STL File Review Contest Winner
Congratulations to Cris, who won our April file review contest! Cris is CEO and cofounder of Tenere Technology, a medical software development company, based in Madrid, Spain. Cris and her team are working to discover the world of 3D printing and excited about the amazing possibilities.
She reviewed an anatomically accurate scapula STL file. She wrote a nice review including an image of the scapula she printed using a file contributed by member health_physics.
In her review Cris also includes a picture of her 3D printer and helpful 3D printing details like wall thickness, print speed and type of material used.
Meet Dr. Mike
Dr. Mike will be speaking at FUSE 2017, Formlabs User Conference in Boston on June 6. If you are attending the conference, please seek out Dr. Mike. It is a unique opportunity to let him know how you use embodi3D and how we can improve.
We Want Your Feedback
We would like to thank our members who have provided feedback and thus contributed to the improvements we covered in this newsletter. Please keep sending us your feedback and making the experience better for everyone!
Let's grow our community together! The Embodi3D Team
If you are planning on using the democratiz3D service to automatically convert a medical scan to a 3D printable STL model, or you just happen to be working with medical scans for another reason, it is important to know if you are working with a CT (Computed Tomography or CAT) or MRI (Magnetic Resonance Imaging) scan. In this tutorial I'll show you how to quickly and easily tell the difference between a CT and MRI.
I am a board-certified radiologist, and spent years mastering the subtleties of radiology physics for my board examinations and clinical practice. My goal here is not to bore you with unnecessary detail, although I am capable of that, but rather to give you a quick, easy, and practical way to understand the difference between CT and MRI if you are a non-medical person.
Interested in Medical 3D Printing? Here are some resources:
Free downloads of hundreds of 3D printable medical models.
Automatically generate your own 3D printable medical models from CT scans.
Have a question? Post a question or comment in the medical imaging forum.
A Brief Overview of How CT and MRI Works
For both CT (left) and MRI (right) scans you will lie on a moving table and be put into a circular machine that looks like a big doughnut. The table will move your body into the doughnut hole. The scan will then be performed. You may or may not get IV contrast through an IV. The machines look very similar but the scan pictures are totally different!
CT and CAT Scans are the Same
A CT scan, from Computed Tomography, and a CAT scan from Computed Axial Tomography are the same thing. CT scans are based on x-rays. A CT scanner is basically a rotating x-ray machine that takes sequential x-ray pictures of your body as it spins around. A computer then takes the data from the individual images, combines that with the known angle and position of the image at the time of exposure, and re-creates a three-dimensional representation of the body. Because CT scans are based on x-rays, bones are white and air is black on a CT scan just as it is on an x-ray as shown in Figure 1 below. Modern CT scanners are very fast, and usually the scan is performed in less than five minutes.
Figure 1: A standard chest x-ray. Note that bones are white and air is black. Miscle and fat are shades of gray. CT scans are based on x-ray so body structures have the same color as they don on an x-ray.
How does MRI Work?
MRI uses a totally different mechanism to generate an image. MRI images are made using hydrogen atoms in your body and magnets. Yes, super strong magnets. Hydrogen is present in water, fat, protein, and most of the "soft tissue" structures of the body. The doughnut of an MRI does not house a rotating x-ray machine as it does in a CT scanner. Rather, it houses a superconducting electromagnet, basically a super strong magnet. The hydrogen atoms in your body line up with the magnetic field. Don't worry, this is perfectly safe and you won't feel anything. A radio transmitter, yes just like an FM radio station transmitter, will send some radio waves into your body, which will knock some of the hydrogen atoms out of alignment. As the hydrogen nuclei return back to their baseline position they emit a signal that can be measured and used to generate an image.
MRI Pulse Sequences Differ Among Manufacturers
The frequency, intensity, and timing of the radio waves used to excite the hydrogen atoms, called a "pulse sequence," can be modified so that only certain hydrogen atoms are excited and emit a signal. For example, when using a Short Tau Inversion Recovery (STIR) pulse sequence hydrogen atoms attached to fat molecules are turned off. When using a Fluid Attenuation Inversion Recovery (FLAIR) pulse sequence, hydrogen atoms attached to water molecules are turned off. Because there are so many variables that can be tweaked there are literally hundreds if not thousands of ways that pulse sequences can be constructed, each generating a slightly different type of image. To further complicate the matter, medical scanner manufacturers develop their own custom flavors of pulse sequences and give them specific brand names. So a balanced gradient echo pulse sequence is called True FISP on a Siemens scanner, FIESTA on a GE scanner, Balanced FFE on Philips, BASG on Hitachi, and True SSFP on Toshiba machines. Here is a list of pulse sequence names from various MRI manufacturers. This Radiographics article gives more detail about MRI physics if you want to get into the nitty-gritty.
Figure 2: Examples of MRI images from the same patient. From left to right, T1, T2, FLAIR, and T1 post-contrast images of the brain in a patient with a right frontal lobe brain tumor. Note that tissue types (fat, water, blood vessels) can appear differently depending on the pulse sequence and presence of IV contrast.
How to Tell the Difference Between a CT Scan and an MRI Scan? A Step by Step Guide
Step 1: Read the Radiologist's Report
The easiest way to tell what kind of a scan you had is to read the radiologist's report. All reports began with a formal title that will say what kind of scan you had, what body part was imaged, and whether IV contrast was used, for example "MRI brain with and without IV contrast," or "CT abdomen and pelvis without contrast."
Step 2: Remember Your Experience in the MRI or CT (CAT) Scanner
Were you on the scanner table for less than 10 minutes? If so you probably had a CT scan as MRIs take much longer. Did you have to wear earmuffs to protect your hearing from loud banging during the scan? If so, that was an MRI as the shifting magnetic fields cause the internal components of the machine to make noise. Did you have to drink lots of nasty flavored liquid a few hours before the scan? If so, this is oral contrast and is almost always for a CT.
How to tell the difference between CT and MRI by looking at the pictures
If you don't have access to the radiology report and don't remember the experience in the scanner because the scan was A) not done on you, or you were to drunk/high/sedated to remember, then you may have to figure out what kind of scan you had by looking at the pictures. This can be complicated, but don't fear I'll show you how to figure it out in this section.
First, you need to get a copy of your scan. You can usually get this from the radiology or imaging department at the hospital or clinic where you had the scan performed. Typically these come on a CD or DVD. The disc may already have a program that will allow you to view the scan. If it doesn't, you'll have to download a program capable of reading DICOM files, such as 3D Slicer. Open your scan according to the instructions of your specific program. You may notice that your scan is composed of several sets of images, called series. Each series contains a stack of images. For CT scans these are usually images in different planes (axial, coronal, and sagittal) or before and after administration of IV contrast. For MRI each series is usually a different pulse sequence, which may also be before or after IV contrast.
Step 3: Does the medical imaging software program tell you what kind of scan you have?
Most imaging software programs will tell you what kind of scan you have under a field called "modality." The picture below shows a screen capture from 3D Slicer. Looking at the Modality column makes it pretty obvious that this is a CT scan.
Figure 3: A screen capture from the 3D Slicer program shows the kind of scan under the modality column.
Step 4: Can you see the CAT scan or MRI table the patient is laying on?
If you can see the table that the patient is laying on or a brace that their head or other body part is secured in, you probably have a CT scan. MRI tables and braces are designed of materials that don't give off a signal in the MRI machine, so they are invisible. CT scan tables absorb some of the x-ray photons used to make the picture, so they are visible on the scan.
Figure 4: A CT scan (left) and MRI (right) that show the patient table visible on the CT but not the MRI.
Step 5: Is fat or water white? MRI usually shows fat and water as white.
In MRI scans the fat underneath the skin or reservoirs of water in the body can be either white or dark in appearance, depending on the pulse sequence. For CT however, fat and water are almost never white. Look for fat just underneath the skin in almost any part of the body. Structures that contained mostly water include the cerebrospinal fluid around the spinal cord in the spinal canal and around the brain, the vitreous humor inside the eyeballs, bile within the gallbladder and biliary tree of the liver, urine within the bladder and collecting systems of the kidneys, and in some abnormal states such as pleural fluid in the thorax and ascites in the abdomen. It should be noted that water-containing structures can be made to look white on CT scans by intentional mixing of contrast in the structures in highly specialized scans, such as in a CT urogram or CT myelogram. But in general if either fat or fluid in the body looks white, you are dealing with an MRI.
Step 6: Is the bone black? CT never shows bones as black.
If you can see bony structures on your scan and they are black or dark gray in coloration, you are dealing with an MRI. On CT scans the bone is always white because the calcium blocks (attenuates) the x-ray photons. The calcium does not emit a signal in MRI scans, and thus appears dark. Bone marrow can be made to also appear dark on certain MRI pulse sequences, such as STIR sequences. If your scan shows dark bones and bone marrow, you are dealing with an MRI.
A question I am often asked is "If bones are white on CT scans, if I see white bones can I assume it is a CT?" Unfortunately not. The calcium in bones does not emit signal on MRI and thus appears black. However, many bones also contain bone marrow which has a great deal of fat. Certain MRI sequences like T1 and T2 depict fat as bright white, and thus bone marrow-containing bone will look white on the scans. An expert can look carefully at the bone and discriminate between the calcium containing cortical bone and fat containing medullary bone, but this is beyond what a layperson will notice without specialized training.
Self Test: Examples of CT and MRI Scans
Here are some examples for you to test your newfound knowledge.
Figure 5A: A mystery scan of the brain
Look at the scan above. Can you see the table that the patient is laying on? No, so this is probably an MRI. Let's not be hasty in our judgment and find further evidence to confirm our suspicion. Is the cerebrospinal fluid surrounding the brain and in the ventricles of the brain white? No, on this scan the CSF appears black. Both CT scans and MRIs can have dark appearing CSF, so this doesn't help us. Is the skin and thin layer of subcutaneous fat on the scalp white? Yes it is. That means this is an MRI. Well, if this is an MRI than the bones of the skull, the calvarium, should be dark, right? Yes, and indeed the calvarium is as shown in Figure 5B. You can see the black egg shaped oval around the brain, which is the calcium containing skull. The only portion of the skull that is white is in the frontal area where fat containing bone marrow is present between two thin layers of calcium containing bony cortex. This is an MRI.
Figure 5B: The mystery scan is a T1 spoiled gradient echo MRI image of the brain. Incidentally this person has a brain tumor involving the left frontal lobe.
Figure 6A: Another mystery scan of the brain
Look at the scan above. Let's go through our process to determine if this is a CT or MRI. First of all, can you see the table the patient is lying on or brace? Yes you can, there is a U-shaped brace keeping the head in position for the scan. We can conclude that this is a CT scan. Let's investigate further to confirm our conclusion. Is fat or water white? If either is white, then this is an MRI. In this scan we can see both fat underneath the skin of the cheeks which appears dark gray to black. Additionally, the material in the eyeball is a dark gray, immediately behind the relatively white appearing lenses of the eye. Finally, the cerebrospinal fluid surrounding the brainstem appears gray. This is not clearly an MRI, which further confirms our suspicion that it is a CT. If indeed this is a CT, then the bones of the skull should be white, and indeed they are. You can see the bright white shaped skull surrounding the brain. You can even see part of the cheekbones, the zygomatic arch, extending forward just outside the eyes. This is a CT scan.
Figure 6B: The mystery scan is a CT brain without IV contrast.
Figure 7A: A mystery scan of the abdomen
In this example we see an image through the upper abdomen depicting multiple intra-abdominal organs. Let's use our methodology to try and figure out what kind of scan this is. First of all, can you see the table that the patient is laying on? Yes you can. That means we are dealing with the CT. Let's go ahead and look for some additional evidence to confirm our suspicion. Do the bones appear white? Yes they do. You can see the white colored thoracic vertebrae in the center of the image, and multiple ribs are present, also white. If this is indeed a CT scan than any water-containing structures should not be white, and indeed they are not. In this image there are three water-containing structures. The spinal canal contains cerebrospinal fluid (CSF). The pickle shaped gallbladder can be seen just underneath the liver. Also, this patient has a large (and benign) left kidney cyst. All of these structures appear a dark gray. Also, the fat underneath the skin is a dark gray color. This is not in MRI. It is a CT.
Figure 7B: The mystery scan is a CT of the abdomen with IV contrast
Figure 8A: A mystery scan of the left thigh
Identifying this scan is challenging. Let's first look for the presence of the table. We don't see one but the image may have been trimmed to exclude it, or the image area may just not be big enough to see the table. We can't be sure a table is in present but just outside the image. Is the fat under the skin or any fluid-filled structures white? If so, this would indicate it is an MRI. The large white colored structure in the middle of the picture is a tumor. The fat underneath the skin is not white, it is dark gray in color. Also, the picture is through the mid thigh and there are no normal water containing structures in this area, so we can't use this to help us. Well, if this is a CT scan than the bone should be white. Is it? The answer is no. We can see a dark donut-shaped structure just to the right of the large white tumor. This is the femur bone, the major bone of the thigh and it is black. This cannot be a CT. It must be an MRI. This example is tricky because a fat suppression pulse sequence was used to turn the normally white colored fat a dark gray. Additionally no normal water containing structures are present on this image. The large tumor in the mid thigh is lighting up like a lightbulb and can be confusing and distracting. But, the presence of black colored bone is a dead giveaway.
Figure 8B: The mystery scan is a contrast-enhanced T2 fat-suppressed MRI
Conclusion: Now You Can Determine is a Scan is CT or MRI
This tutorial outlines a simple process that anybody can use to identify whether a scan is a CT or MRI. The democratiz3D service on this website can be used to convert any CT scan into a 3D printable bone model. Soon, a feature will be added that will allow you to convert a brain MRI into a 3D printable model. Additional features will be forthcoming. The service is free and easy to use, but you do need to tell it what kind of scan your uploading. Hopefully this tutorial will help you identify your scan.
If you'd like to learn more about the democratiz3D service click here. Thank you very much and I hope you found this tutorial to be helpful.
Nothing in this article should be considered medical advice. If you have a medical question, ask your doctor.
In April 2017, embodi3D held its first review writing contest. Many great reviews were posted and we selected a review by Cris as the winner. She is the recipient of the $25 Amazon gift certificate. Congratulations Cris!
She reviewed an anatomically accurate scapula STL file. She wrote a nice review including an image of the scapula she printed using the file uploaded by health_physics. In her review Cris also includes a picture of her 3D printer and helpful 3D printing details like wall thickness, print speed and type of material used.
We are having a file sharing contest in May and have increased the prize to $50. All that is required is to upload a file, share the file and write a brief description. Each shared file you upload in May 2017 will be an entry in our contest. There is no limit to the number of files you can upload and share. To learn more and see complete rules please visit our contest page.
The Embodi3D website offers a large and ever-growing library of 3D printable files that are available for free to anyone who signs up for a free account. Images include files from normal anatomy to those related to paleontology to complex musculoskeletal tumors. This site was founded by a practicing interventional radiologist with a passion for 3D printing and perfecting an easier method for converting files into those that may be downloaded and printed—a medical 3D printing application called democratiz3D.
Commercial Medical 3D Printing Software
Three-dimensional printing has become a popular research and industrial interest in the orthopaedic surgery world. International companies such as Stryker (www.stryker.com) and DePuy Synthes (www.depuysynthes.com) are now marketing designs in craniofacial reconstruction, arthroplasty, and spine deformity surgery that utilize 3D printing in order to individualize implants and surgical techniques. Specialized software for 3D printing in healthcare is sold by Materialise in an offering called Mimics. Vital Images, a medical imaging and informatics company, has partnered with Stratsys, a 3D printer manufacturer, to provide a segmentation and healthcare 3D printing solution. However, these technologies are costly, and may be cost-prohibitive for the average patient or surgeon.
Three-Dimensional Printing for Patient Education and Surgical Planning
Although most radiology departments currently have the capability to quickly convert a CT (computer tomography) scan to a three-dimensional image for better understanding of a patient’s anatomy, visualized anatomy cannot replace the ability to feel and manipulate a model. Three-dimensional printing can, however, bring these images to life. Printers have the capability to use differing materials, such as polymers, plastics, ceramics, metals, and biologics to create models. These models can be an excellent tool for patient and trainee education as well as surgical planning. In procedures such as complex tumors or difficult pelvic fractures, the surgeon could practice different techniques on an exact replica of the patient’s anatomy so that they have a better grasp of their approach to the patient. Furthermore, trainees currently learn and practice their surgical skills on cadaveric specimens, which can also be costly. Having access to a 3D printer that could create models could potentially decrease the utilization of cadavers.
Free and Easy Medical Three-Dimensional Printing
Creating files from CT scans that can be used in 3D printing is easy with the use of the Embodi3d website. Detailed instructions are available on the tutorial pages of the website, but a brief overview will be described here. CT scans may be obtained from the radiology department in DICOM format. Free software available online at www.slicer.org can be used to review the DICOM imaging, isolate the area of interest and convert to an .nrrd file. This .nrrd file may then be loaded onto the democratiz3D application and formatted in a number of ways based on threshold as shown in the images below.
Files may be opened through the application or dragged and dropped into the file area (Figure 1, Figure 2). Details of the file, such as the title, description of the anatomy or pathology, and keywords are placed beneath the upload (Figure 3). Different thresholds are available to be automatically placed on the uploaded file, including bone, detailed bone, muscle, and skin (Figure 4). These files as well as the final, processed, files may be shared or remain private, free or at a fee to download by the community.
Figure 1. The link to the democratiz3D application is located at the top menu bar of the main page at https://www.embodi3d.com.
Figure 2. Once on the democratiz3D application, you may upload the .nrrd file or drag and drop the .nrrd file into the uploading area.
Figure 3. While the .nrrd file is processing, you may edit the details of the file, such as the title, tags, and description.
Figure 4. The application allows for thresholding of bone, detailed bone, muscle, and skin from the uploaded CT scan.
Once the file has been processed, you receive a notification and may view the file as well as automatically created screen shots (Figure 5). This is now an STL file that may be downloaded by clicking “Download this file”. If this is a file that you have downloaded, you may also edit the details of the file, move it to another category or upload a new version of the STL file directly onto the page (Figure 6). Although the democratiz3D application is a powerful and quick tool to convert .nrrd files to STL files, it is limited by the quality of the CT scan. Therefore, users may wish to clean up the model using free software such as Meshmixer or Blender. Once the files have been edited, they are maintained as an STL file that may be directly uploaded onto the page as a new version (Figure 7). These may then be placed in a category that is most descriptive of the file (Figure 8).
Figure 5. After about 5-20 minutes of processing (depending on the size of the file), you will get a notification and e-mail that the file has processed. The democrati3D application has converted the file into an STL file is now available for downloading and use in 3D printing.
Figure 6. If you would like to change the details, or upload new files or screen shots, you may choose from the drop-down menu.
Figure 7. In order to upload a new version of the file, such as after it is edited in the free software Meshmixer or Blender, you may choose from the drop-down menu and drag and drop a new STL file.
Figure 8. Because Embodi3D has created a library divided into different categories, you may move your file into the appropriate category to allow for ease of sharing with the community.
Alternatively, files that have been downloaded and edited may be uploaded as new files using the “Create” selection on the top menu (Figure 9). Once you have chosen the most accurate category (Figure 10), you can upload the new file by selecting the file or drag and drop into the proper area (Figure 11). This will then take you to similar section as outlined above in order to edit the details and sharing options for your file.
Figure 9. Upload an STL file by selecting the “Create” menu at the top of the webpage.
Figure 10. Select the category under which the file most accurately fits.
Figure 11. Upload the STL file by dragging and dropping or selecting the file.
As you can see, creating STL files from individual CT scans is an easy, 15-20 minute process that is reasonable for the busy orthopaedic surgeon to utilize in their practice.
For educational purposes, however, not every trainee, surgeon, or radiologist has access to patients with such a wide array of pathologies. The Embodi3D community provides an ever-growing diverse library of normal anatomy and pathology that may be downloaded for free and used for 3D printing. The files are divided into categories including: Bones, Muscles, Cardiac and Vascular, Brain and nervous system, Organs of the Body, Veterinary, Paleontology, Anthropology, Research and Miscellaneous.
In order to access these files, click “Download” from the top menu (Figure 12), which will take you to the main Downloads page (Figure 13). The categories available are listed on the right side of the page, and will bring you to each category page. There, the number of files available within each category is listed. Once the desired file is selected, the file may be downloaded as described above.
Figure 12. In order to access the library of files, click “Download” from the top menu on the main page.
Figure 13. The Downloads page has a listing of the available categories to browse and explore for the desired files.
Creating and printing 3D models of CT scans will be useful in the future of medicine and the era of individualized medicine. The free library of medical 3D printing files available at embodi3D.com as well as the free conversion application democratiz3D will be an invaluable resource for education as well as for the private orthopaedic surgeon with limited resources. Furthermore, because healthcare costs are a main focus in the United States, having the ability to download and create models for a much lower price than through commercial 3D printing companies will be useful to decrease the cost of individualized care.
For more information about 3D printing in orthopaedic surgery, please see the following references:
Cai H. Application of 3D printing in orthopedics: status quo and opportunities in China. Ann Transl Med. 2015;3(Suppl 1):S12.
Eltorai AEM, Nguyen E, Daniels AH. Three-Dimensional Printing in Orthopedic Surgery. Orthopedics. 2015;38(11):684-687.
Mulford JS, Babazadeh S, Mackay N. Three-dimensional printing in orthopaedic surgery: review of current and future applications. ANZ J Surg. 2016;86(9):648-653.
Tack P, Victor J, Gemmel P, Annemans L. 3D-printing techniques in a medical setting: a systematic literature review. Biomed Eng Online. 2016;15(1):115.
Welcome to our April 2017 newsletter! Read on to learn how you can participate in our review writing contest and win an Amazon gift certificate, what improvements we have made to democratiz3D, and what our medical device development service offers.
3D Printable File Review Writing Contest
Download a file, post a review and you are automatically entered to win a $25 Amazon gift certificate. We will award the prize to the writer of the best review. The contest runs the month of April.
democratiz3D: Medical 3D Printing for All
democratiz3D(TM), our online tool which converts a medical scan study to a 3D printable file, has had an upgrade that allows for improved processing of dental, and face bone models. Lung CT scans with hard (sharpened) reconstruction kernels also have improved performance. Additionally, there are new materials that are shown in thumbnail renders for muscle and skin files. Going forward, thumbnails are now three colors white (bone), redish-brown (muscle) and gray (skin). Check it out, and let us know how you like it.
Custom 3D Printing for Medical Device Development
Embodi3D creates customized and highly detailed 3D printed medical models from real patient medical scans. You are assured the anatomy is realistic because it comes from a real patient. We can create sets of models, meeting your specifications for age/gender/pathology, thus giving you the most accurate picture of anatomic variability in your target patient population.
A Collection of Medical Scan Files
Prior to model creation we perform a consultation to understand your needs in detail, so that the models are precisely tailored to test your device. Reply to this email for more information.
We Want Your Feedback
We would like to thank our members who have provided feedback and thus contributed to the improvements we covered in this newsletter. Please keep sending us your feedback and making the experience better for everyone!
Let's grow our community together!
The Embodi3D Team
So I have seen some questions here on embodi3D asking how to work with MRI data. I believe the main issue to be with attempting to segment the data using a threshold method. The democratiz3D feature of the website simplifies the segmentation process but as far as I can tell relies on thresholding which can work somewhat well for CT scans but for MRI is almost certain to fail. Using 3DSlicer I show the advantage of using a region growing method (FastGrowCut) vs threshold.
The scan I am using is of a middle aged woman's foot available here
The scan was optimized for segmenting bone and was performed on a 1.5T scanner. While a patient doesn't really have control of scan settings if you are a physician or researcher who does; picking the right settings is critical. Some of these different settings can be found on one of Dr. Mike's blog entries.
For comparison purposes I first showed the kind of results achievable when segmenting an MRI using thresholds.
With the goal of separating the bones out the result is obviously pretty worthless. To get the bones out of that resultant clump would take a ridiculous amount of effort in blender or similar software:
If you read a previous blog entry of mine on using a region growing method I really don't like using thresholding for segmenting anatomy. So once again using a region growing method (FastGrowCut in this case) allows decent results even from an MRI scan.
Now this was a relatively quick and rough segmentation of just the hindfoot but already it is much closer to having bones that could be printed. A further step of label map smoothing can further improve the rough results.
The above shows just the calcaneous volume smoothed with its associated surface generated. Now I had done a more proper segmentation of this foot in the past where I spent more time to get the below result
If the volume above is smoothed (in my case I used some of my matlab code) I can get the below result.
Which looks much better. Segmenting a CT scan will still give better results for bone as the cortical bone doesn't show up well in MRI's (why the metatarsals and phalanges get a bit skinny), but CT scans are not always an option.
So if you have been trying to segment an MRI scan and only get a messy clump I would encourage you to try a method a bit more modern than thresholding. However, keep in mind there are limits to what can be done with bad data. If the image is really noisy, has large voxels, or is optimized for the wrong type of anatomy there may be no way to get the results you want.
3D printing technologies have opened up the capabilities for customization in a wide variety of applications in the medical field. Using bio-compatible and drug-contact materials, medical devices can be produced that are perfectly suited for a particular individual. Another trend enabled by 3D printing is mass customization, in that multiple individualized items can be produced simultaneously, saving time and energy while improving manufacturing efficiency.
3D printers are used to manufacture a variety of medical devices, including those with complex geometry or features that match a patient’s unique anatomy.
Some devices are printed from a standard design to make multiple identical copies of the same device. Other devices, called patient-matched or patient-specific devices, are created from a specific patient’s imaging data.
Commercially available 3D printed medical devices include:
Instrumentation (e.g., guides to assist with proper surgical placement of a device)
Implants (e.g., cranial plates or hip joints)
External prostheses (e.g., hands)
In summary, the 3D Printing medical device market looks exciting and promising, Various Reports and surveys suggest the unexpected growth and demand for 3D Printing in medical device industry and it is expected to blossom more but a number of existing application areas for 3D printing in healthcare sector require specialized materials that meet rigid and stringent bio-compatibility standards, Future 3D printing applications for the medical device field will certainly emerge with the development of suitable additional materials for diagnostic and therapeutic use that meet CE and FDA guidelines.
Very few infectious diseases in recent years have commanded the kind of attention and concern that Zika Virus has. Although Zika outbreaks have been reported in Africa, Southeast Asia and other parts of the world since the 1952, recent announcement by the Center for Disease Control and Prevention (CDC) confirming its link with microcephaly has forced everyone to sit up and take notice. The CDC estimates that the current pandemic is widespread with at least 50 countries reporting active Zika transmissions at this time. Most people with Zika virus infection will not have any symptoms though some may experience mild fever, conjunctivitis, muscle and joint pain, and headaches.
The virus is primarily transmitted by the Aedes mosquito. However, pregnant women may pass the infection to their babies, which may lead to microcephaly, a neurological condition associated with an abnormally small brain in the infant. The condition can lead to birth defects ranging from hearing loss to poor vision and impaired growth. Prompt diagnosis and treatment of Zika virus infections in pregnant women can, nonetheless, lower the risk of microcephaly to a great extent. Researchers have, therefore, put in a lot of time, money and effort to find a solution, and as always, three-dimensional (3D) medical printing and bioprinting technologies are leading the way.
Understanding the Disease
To begin with, 3D printing has played a crucial role in conclusively establishing the link between Zika virus and microcephaly. Researchers at John Hopkins Medicine used 3D bioprinting technology to develop realistic models of brain that revealed how the virus infects specialized stem cells in the outer layers of the organ, also known as the cortex. The bioprinted models allowed researchers to study the effects of Zika exposure on fetal brain during different stages of pregnancy. The models are also helping the scientists with drug testing, which is the obvious next stage of their research.
Zika Test Kit
Engineers at Penn’s School of Engineering and Applied Science, under the leadership of Professor Changchun Liu and Professor Haim Bau, have developed a simple genetic testing device that helps detect Zika virus in saliva samples. It consists of an embedded genetic assay chip that identifies the virus and turns the color of the paper in the 3D printed lid of the device to blue. This can prompt healthcare professionals to send the patient for further testing and to initiate treatment. Unlike other Zika testing techniques, this screening method does not require complex lab equipment. Each device costs about $2, making Zika screening accessible to pregnant women from the poorest parts of the world.
The scientists at the Autonomous University of the State of Morelos (UAEM) in Mexico are relying on the additive printing technology to create a microvalve that may help treat microcephaly in infants. The valve reduces the impact of the neurological disease and slows its progression by draining out excessive cerebrospinal fluid associated with this disorder. It can be inserted into the infant brain through a small incision to relieve fluid pressure and provide space for normal development. Researchers estimate the device will be available for patient use by 2017. These examples clearly demonstrate the impact of 3D printing on every aspect of the fight against Zika virus from diagnosing the disease to treating it. The results have been extremely promising, and both researchers and healthcare professionals are immensely hopeful that additive printing technology will help them overcome the infection quickly and effectively.
So I began to develop some pain in my right wrist which was later diagnosed as tendinitis. At the same time I had been looking at the CT scan of my abdomen and noticed they also captured my right hand as it was resting on my stomach during the scan (I had injured my right shoulder again).
I recalled a concept project a while back I had seen: the CORTEX brace. It presented the idea of replacing the typical plaster cast with a 3D printed one which would prevent the issues of sweating and itchiness… as well as be much more stylish (though not allowing people to sign your cast).
I had wanted to apply this to prosthesis sockets initially but never got past the idea stage. Looking around for how to create the ‘webbing’ style I found that meshmixer had the necessary capabilities. So I now had all the tools needed to make my own brace to partially immobilize my wrist.
Once the surface model is created and loaded into meshmixer the first step is to cut off anatomy that you don't want in the model using 'plane cut'.
Once the general shape of the brace is created the next step is to consider how the brace will be taken on and off. For my design I wanted to have one piece that is flexible enough to slide my wrist in. To create the 'slot' I found that I did a boolean in blender as meshmixer would crash when I tried to create the slot.
With the brace model and slot in place the next step was to offset the surface since creating the voroni mesh would generate the tubes on both sides of the surface. This is done back in meshmixer and is fairly computationally intensive so partially reducing the mesh density first is a good idea.
The next step is to further decimate the mesh to get the desired voroni mesh pattern. This takes a bit of playing around to get the desired style. Too dense and the resulting web structure will not have many openings which will be stronger but not as breathable. Too rough and the model may not conform to the surface well causing pressure points.
The final step is to take the reduced mesh and web like structure using the 'make pattern' feature within meshmixer. There are various settings to be applied within this feature but setting 'Dual Edges' then adjusting the pipe size to double your offset will result in the inner edge of the webbing to just touch the skin of the initial model.
Having never made a brace/cast before it took me a few iterations to get a design which I could easily don and doff (put on and take off). I also found that I could make a brace that held my wrist very rigidly but would be too restrictive.
Also material selection became important. Initially I used ABS which is more flexible than PLA and I had it in a nice pink skin color. It turned out to be too rigid for the style I was designing. I found PETT (taulman t-glass) to work well as it had a lower modulus of elasticity meaning it was more flexible than ABS.
After using the brace on and off for a few weeks I have found that it fits well and is surprisingly comfortable. I have taken a shower with it on as well as slept with it on. It doesn’t seem to smell as bad as the cheap and common cloth type braces. The main downsides have been taking it on and off is a bit challenging still and it is more restrictive of my motion as it behaves somewhere between a brace and a cast. There is definitely a great deal of potential for this type of cast though widespread adoption would require further technical development to simplify the process.
Physicians across the globe have relied on surgical interventions for centuries to treat complex illnesses and injuries. High quality surgical instruments have played an important role in their success. Nonetheless, healthcare professionals are constantly looking for tools that would improve patient outcomes and minimize the risk of unwanted complications. In recent times, three-dimensional (3D) medical printing and bioprinting technologies have allowed doctors and engineers to develop innovative tools that help perform invasive procedures with greater ease.
Robotic Surgical Tools
Mechanical engineering students at Brigham Young University (BYU), under the guidance of their professors Barry Howell, Spencer Magleby, and Brian Jensen, combined additive printing technology and the ancient art of Origami to create surgical tools that can fit through 3mm wide incisions. Inside the body, the tools can unfold and expand into complex devices such as D-core tools. Minute incisions allow for quick healing eliminating the need for sutures and scars. The tools are highly precise and effective as well. Researchers at BYU are now collaborating with California-based Intuitive Surgicals to manufacture their products. The company is using 3D printing to develop both the prototypes and the actual tools. The 3D printing technology is also helping Intuitive Surgicals to create instruments with fewer parts making the entire process more cost-effective and stable.
The Pathfinder ACL Guide
Orthopedic surgeon Dr. Dana Piasecki of the OrthoCarolina Sports Medicine has developed a 3D printed surgical tool to conduct ACL surgeries with improved success. Currently, most surgeons drill a hole in the patient’s tibia to remove the torn anterior cruciate ligament and replace it with a graft. The procedure is painful, and the graft often fails to anchor properly. The Pathfinder ACL Guide, created by Dr. Piasecki in collaboration with Strasys Direct Manufacturing, has a 95 percent chance of placing the graft at the right position and helping it withstand the stress associated with extensive movement. The surgical tool is made from a biocompatible and flexible metal and is significantly cheaper than the existing devices. The Pathfinder ACL Guide has been registered with the FDA as a class I medical device and can now help thousands of amateur and professional athletes to continue playing their game in spite of an ACL tear.
Eyelid Wands and Forceps
Similarly, Dr. Bret Kotlus, a New York-based cosmetic surgeon, has used 3D printing technology to create customized tools for eyelid surgeries. His stainless steel Eyelid Wand helps surgeons lift excess eyelid skin and point it to various facial structures as per the needs of the patient. The handle of the tool consists of a ruler for accurate measurements.
Dr. Kotlus has also developed 3D printed Pinch Blepharoplasty Marking Forceps that allow surgeons to mark excessive skin with a gentle ink. It comes with a round tip and a built-in ruler handle for additional patient comfort. These tools also add some sophistication to the doctor’s office at an affordable price. Close to 50 million surgical inpatient procedures are performed across the United States each year. While recent times have seen a significant improvement in the way these interventions are carried out, a lot can be done to make the process more efficient and safe. This is where 3D printing is bound to make a huge impact in the near future.
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3d printed eyelid instrument designed by Dr. Kotlus
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