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Musings about biomedical 3D printing

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Dr. Mike

large.intro.JPGHello 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!

Dr. Mike

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.



Dr. Mike

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.


Make sure you check the checkbox that states you agree to the terms of use, and click the submit button. Your file will now start processing. In approximately 10 minutes or so you should receive an email stating that the file has been processed and your newly created 3D printable STL model is ready for download. The email should contain a link that will take you to your file download page, which should look something like the page in Figure 8. There should be several thumbnails which show you what the model looks like. To download the file click on the Download button.



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.

Dr. Mike

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.


large.5ad153c584686_skullbig.jpg Interested in Medical 3D Printing? Here are some resources:

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 B) 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.

Example 1


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.


Example 2


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.


Example 3


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


Example 4


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.

Dr. Mike

Note: This tutorial accompanies a workshop I presented at the 2016 Radiological Society of North America (RSNA) meeting. The workflow and techniques presented in this tutorial and the conference workshop are identical.




In this tutorial we will be using two different ways to create a 3-D printable medical model of a head and neck which will be derived from a real contrast-enhanced CT scan. The model will show detailed anatomy of the bones, as well as the veins and arteries. We will independently create this model using two separate methods. First, we will automatically generate the model using the free online service embodi3D.com. Next, we will create the same file using free desktop software programs 3D Slicer and Meshmixer.


If you haven't already, please download the associated file pack which contains the files you'll need to follow along with this tutorial. Following along with the actual files used here will make learning these techniques much easier. The file pack is free. You need to be logged into your embodi3D account to download, but registration is also free and only takes a minute. Also, you'll need an embodi3D.com account in order to use the online service. Registration is worth it, so if you haven't already go ahead and register now.




Online Service: embodi3D.com



Step 1: Go to the embodi3D.com website and click on the democratiz3D menu item in the naw bar. Click on the "Launch democratizD" link, as shown in Figure 1.



Figure 1: Opening the free online 3D model making service service democratiz3D.


Step 2: Now you have to upload your imaging file. Drag and drop the file MANIX Angio CT.nrrd from the File Pack, as shown in Figure 2. This contains the CT scan of the head and neck in NRRD file format. If you are using a file other NRRD that provided by the file pack, please be aware the file must contain a CT scan (NOT MRI!) and the file must be in NRRD format. If you don't know how to create an NRRD file, here is a simple tutorial that explains how.



Figure 2: Dragging and dropping the NRRD file to start uploading.


Step 3: Type in basic information on the file being uploaded, including File name, file description, and whether you want to share the file or keep it private. Bear in mind that this information pertains to the uploaded file, not the file that will be generated by the service.

Step 4: Type in basic parameters for file processing. Turn on the processing slider. Here you will enter in basic information about how you would like the file to be processed. Under Operation, select CT NRRD to Bone STL Detailed, as shown in Figure 3. This will convert a CT scan in NRRD format to a bone STL with high detail. You also have the option to create muscle and skin STL files. The standard operation, CT NRRD to Bone STL sacrifices some detail for a smoother output model. Leave the default threshold at 150.



Figure 3: Selecting an operation for file conversion.


Next, choose the quality of your output file. Low-quality files process quickly and are appropriate for structures with simple geometry. High quality files take longer to process and are appropriate for very complex geometry. The geometry of our model will be quite complex, so choose high quality. This may take a long time to process however, sometimes up to 40 minutes. If you don't wish to wait so long, you can choose medium quality, as shown in Figure 4, and have a pretty decent output file in about 12 minutes or so.




Figure 4: Choosing a quality setting.


Finally, specify whether you want your processed file to be shared with the community (encouraged) or private and accessible only to you. If you do decide to share you will need to fill out a few items, such as which CreativeCommons license to share under. If you're not sure, the defaults are appropriate for most people. If you do decide to share thanks very much! The 3D printing community thanks you!


Click on the submit button and your file will be submitted for processing! Now all you have to do is wait. The service will do all the work for you!


Step 5: Download your file. In 5 to 40 minutes you should receive an email indicating that your file is done and is ready for download. Follow the link in the email message or, if you are already on the embodi3D.com website, click on your profile to view your latest activity, including files belonging to you. Open the download page for your file and click on the "Download this file" button to download your newly created STL file!



Figure 5: Downloading your newly completed STL file.



Desktop software

If you haven't already, download 3D Slicer and Meshmixer. Both of these programs are available on Macintosh and Windows platforms.


Step 1: Create an STL file with 3D Slicer. Open 3D Slicer. Drag and drop the file MANIX Angio CT.nrrd from the file pack onto the 3D Slicer window. This should load the file into 3D Slicer, as shown in Figure 6. When Slicer asks you to confirm whether you want to add the file, click OK.



Figure 6: Opening the NRRD file in 3D Slicer using drag-and-drop.


Step 2: Convert the CT scan into an STL file. From within Slicer, open the Modules menu item and choose All Modules, Grayscale Model Maker, as shown in Figure 7.



Figure 7: Opening the Grayscale Model Maker module.


Next, enter the conversion parameters for Grayscale Model Maker in the parameters window on the left. Under Input Volume select MANIX Angio CT. Under Output Geometry choose "Create new model." Slicer will create a new model with the default name such as "Output Geometry. If you wish to rename this to something more descriptive, choose Rename current model under the same menu. For this tutorial I am calling the model "RSNA model."


For Threshold, set the value to 150. Under Decimate, set the value to 0.75. Double check your settings to make sure everything is correct. When everything is filled in correctly click the Apply button, as shown in Figure 8. Slicer will process for about a minute.



Figure 8: Filling in the Grayscale Model Maker parameters.


Step 3: Save the new model to STL file format. Now it is time to create an STL file from our digital model. Click on the Save button on the upper left-hand corner of the Slicer window. The Save Scene pop-up window is now shown. Find the row that corresponds to the model name you have given the model. In my case it is called "RSNA model." Make sure that the checkbox next to this row is checked, and all other rows are unchecked. Next, under the File Format column make sure to specify STL. Finally, specify the directory that the new STL file is to be saved into. Double check everything. When you are ready, click Saved. This is all shown in Figure 9. Now that you've created an STL file, we need to postprocessing in Meshmixer.



Figure 9: Saving your file to STL format.


Step 4: Open Meshmixer, and drag-and-drop the newly created STL file onto the Meshmixer window to open it. Once the model opens, you will notice that there are many red dots scattered throughout the model. These represent errors in the mesh and need to be corrected, as shown in Figure 10.


Figure 10: Errors in the mesh as shown in Meshmixer. Each red dot corresponds to an error.


Step 5: Remove disconnected elements from the mesh. There are many disconnected elements in this model that we do not want in our final model. An example of unwanted mesh are the flat plates on either side of the head from the pillow that was used to secure the head during the CT scan. Let's get rid of this unwanted mesh.


First use the select tool and place the cursor over the four head of the model and left click. The area under the cursor should turn orange, indicating that those polygons have been selected, as shown in Figure 11.



Figure 11: Selecting a small zone on the forehead.


Next, we are going to expand the selection to encompass all geometry that is attached to the area that we currently have selected. Go to the Modify menu item and select Expand to Connected. Alternatively, you can use the keyboard shortcut and select the E key. This operation is shown in Figure 12.



Figure 12: Expanding the selection to all connected parts.


You will notice that the right clavicle and right scapula have not been selected. This is because these parts are not directly connected to the rest of the skeleton, as shown in Figure 13. We wish to include these in our model, so using the select tool left click on each of these parts to highlight a small area. Then expand the selection to connected again by hitting the E key.



Figure 13: The right clavicle and right scapula are not included in the selection because they are not connected to the rest of the skeleton. Individually select these parts and expand the selection again to include them.


At this point you should have all the geometry we want included in the model selected in orange, as shown in Figure 14.



Figure 14: All the desired geometry is selected in orange


Next we are going to delete all the unwanted geometry that is currently unselected. To start this we will first invert the selection. Under the modify menu, select Invert. Alternatively, you can use the keyboard shortcut I, as shown in Figure 15.



Figure 15: Inverting the selection.


At this point only the undesired geometry should be highlighted in orange, as shown in Figure 16. This unwanted geometry cannot be deleted by going to the Edit menu and selecting Discard. Alternatively you can use the keyboard shortcut X.


Figure 16: Only the unwanted geometry is highlighted in orange. This is ready to delete.


Step 6: Correcting mesh errors using the Inspector tool. Meshmixer has a nice tool that will automatically fix many mesh errors. Click on the Analysis button and choose Inspector. Meshmixer will now identify all of the errors currently in the mesh. These are indicated by red, blue, and pink balls with lines pointing to the location of the error. As you can see from Figure 17, there are hundreds of errors still within our mesh. We can attempt to auto repair them by clicking on the Auto Repair All button. At the end of the operation most of the errors have been fixed, but if you remain. This can be seen in Figure 18.



Figure 17: Errors in the mesh. Most of these can be corrected using the Inspector tool.



Figure 18: Only a few errors remain after auto correction with the Inspector tool.


Step 7: Correcting the remaining errors using the Remesh tool. Click on the select button to turn on the select tool. Expand the selection to connected parts by choosing Modify, Expand to Connected. The entire model should now be highlighted and origin color. Next under the edit menu choose Remesh, or use the R keyboard shortcut, as shown in Figure 19. This operation will take some time, six or eight minutes depending on the speed of your computer. What remesh does is it recalculates the surface topography of the model and replaces each of the surface triangles with new triangles that are more regular and uniform in appearance. Since our model has a considerable amount of surface area and polygons, the remesh operation takes some time. Remesh also has the ability to eliminate some geometric problems that can prevent all errors from being automatically fixed in Inspector.


Figure 19: Using the Remesh tool.


Step 8: Fixing the remaining errors using the Inspector tool. Once the remesh operation is completed we will go back and repeat Step 6 and run the Inspector tool again. Click on Analysis and choose Inspector. Inspector will highlight the errors. Currently there are only two, as shown in Figure 20. These two remaining errors can be easily auto repair using the Auto Repair All button. Go ahead and click on this.


Figure 20: running the Inspector tool again.


At this point the model is now completed and ready for 3D printing as shown in Figure 21. The mesh is error-free and ready to go! Congratulations!


Figure 21: The final, error-free model ready for 3D printing.


Complex bone and vascular models, such as the head and neck model we created in this tutorial, can be created using either the free online service at embodi3D.com or using free desktop software. Each approach has its benefits. The online service is easier to use, faster, and produces high quality models with minimal user input. Additionally, multiple models can be processed simultaneously so it is possible to batch process multiple files at once. The desktop approach using 3D Slicer and Meshmixer requires more user input and thus more time, however the user has greater control over individual design decisions about the model. Both methods are viable for creating high quality 3D printable medical models.


Thank you very much for reading this tutorial. Please share your medical 3D printing designs on the embodi3D.com website. Happy 3D printing!

Dr. Mike

In this brief tutorial we will go over how to use Meshmixer to create a hollow shell from a medical 3D printable STL file. Hollowing out the shell, as shown in the pictures below, can allow you to 3D print the model using much less material that printing a solid piece. The print will take less time and cost less money.


For this tutorial we will use a head that we created from a real medical CT scan in a prior tutorial, " Easily Create 3D Printable Muscle and Skin STL Files from Medical CT Scans" If you haven't seen the prior tutorial, please check it out.




To follow along with the tutorial, please download the accompanying file. This will enable you to replicate the process exactly as it is shown in the tutorial. 






Dr. Mike

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.




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.


While the file is uploading, fill in the required fields, including the name of the uploaded file, a brief description, file privacy, and license type. Except the terms of use. next, turn on Imag3D processing.  Under operation, select "CT NRRD to Muscle STL."  Leave the threshold value unchanged. Under quality, select medium or high. Specify your privacy preference for your output STL file. If you are going to share this file, you can choose to share it for free or sell it. Please see my separate tutorial on how to share and sell your files on the embodi3D.com website for additional details. When you're happy with your choices, save the file, as shown in Figure 15:


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!


Dr. Mike

Please note that any references to “Imag3D” in this tutorial should be replaced with “democratiz3D”


In this tutorial we will discuss how to share, sell, organize, and reprocess 3D printable medical models you make using the free online democratiz3D service from embodi3D. democratiz3D is a powerful tool that automatically converts a medical CT scan into a 3D printable file in minutes with minimal user input. It is no longer necessary to master complicated desktop software and spend hours manually segmenting to create a 3D printable model. Learn how to make high quality medical 3D models with democratiz3D by following my introductory guide to creating medical 3D printing files and my more advanced 3D printing file processing tutorial. Once you create your medical masterpiece, you can share, sell, organize, or tweak your model to make it perfect. This tutorial will show you how.





Resubmit your CT Scan for Reprocessing into Bone STL

If you are trying to learn the basics of how to convert CT scans into 3D printable STL models, please see my earlier tutorials on basic creation of 3D printable models and more advanced multiprocessing. If you are not 100% satisfied with the quality of your STL model, you can resubmit the input scan file for repeat processing. To do this, go to the page for your input NRRD file. IMPORTANT: this is the NRRD file you originally uploaded to the website, NOT the STL file that was generated for you by the online service. Since both the original NRRD file and the processed STL file have similar titles, you can tell the difference by noting that the NRRD file you uploaded won't have any thumbnails, Figure 1. In most cases, the processed file will have the word "processed" appended to the file name.



Figure 1: Choose the original NRRD file, not the generated STL file.


You can find your files underneath your profile, as shown in Figure 2. That will show you your most recent activity, including recently uploaded files.



Figure 2: Finding your files under your profile.


If you uploaded the file long ago or contribute a lot of content to the site, your uploaded NRRD file may not be among the first content item shown. You can search specifically for your files by clicking on See My Activity under your Profile, and selecting Files from the left hand now bar, as shown in Figures 3 and 4.




Figure 3: Showing all your activity.


Figure 4: Showing the files you own.


Once you have found your original NRRD file, open the file page and select File Actions on the lower left-hand corner, as shown in Figure 5. Choose Edit Details as shown in Figure 6.



Figure 5: File Actions – start making changes to your file



Figure 6: Edit Details


Scroll down until you reach the democratiz3D Processing section. Make sure that the democratiz3D Processing slider is turned ON. Then, make whatever adjustments you want to the processing parameters Threshold and Quality, as shown in Figure 7. Threshold is the value in Hounsfield units to use when performing the initial segmentation.


Quality is a measure of the number of polygons in the output mesh. Low quality is quick to process and generates a small output file. Low quality is suitable for small and geometrically simple structures, such as a patella or single bone. High quality takes longer to process and produces a very large output file, sometimes with millions of polygons. This is useful for very large structures or complex anatomy, such as a model of an entire spine where you wish to capture every crack and crevice of the spine. Medium quality is a good balance and suitable in most cases.



Figure 7: Changing the processing parameters.


When you're happy with your parameter choices, click Save. The file will now be submitted for reprocessing. In 5 to 15 minutes you should receive an email saying that your file is ready. From this NRRD file, an entirely new STL file will be created using your updated parameters and saved under your account.


Sharing your 3D Printing File on embodi3D.com

Sharing your file with the embodi3D community is easy. You can quickly share the file by toggling the privacy setting on the file page underneath the File Information box on the lower right, as shown in Figure 8. If this setting says "Shared," then your file is visible and available for download by registered members of the community. If you wish to have more detailed control over how your file is shared, you can edit your file details by clicking on the File Actions button on the lower left-hand side of the file page, also shown in Figure 8. Click on the Edit Details menu item. This will bring you to the file editing page which will allow you to change the Privacy setting (shared versus private), License Type (several Creative Commons and a generic paid file license are available), and file Type (free versus paid). These are shown in detail in Figure 9. Click Save to save your settings.



Figure 8: Quick sharing your file, and the File Actions button



Figure 9: Setting the file type, privacy, and license type for your file.



Sell your Biomedical 3D Printing File and Generate Income

If you would like to sell your file and charge a fee for each download, you may do so by making your file a Paid File. If you have a specialized model that there is some demand for, you can generate income by selling your file in the marketplace. From the Edit Details page under File Actions, as shown in Figure 8, scroll down until you see Type. Choose Paid for the Type. Choose the price you wish to sell your file for in the Price field. This is in US dollars. Buyers will use PayPal to purchase the file where they can pay with Paypal funds or credit card. Make sure that the privacy setting is set to Shared. If you list your file for sale but keep it private and invisible to members, you won't sell anything. Finally, make sure you choose an appropriate license for users who will download your file. The General Paid File License is appropriate and most instances, but you have the option to include a customized license if you wish. This is shown in Figure 10.



Figure 10: Configuring settings to sell your file


The General Paid File License contains provisions appropriate for most sellers. It tells the purchaser of your file that they can download your file and create a single 3D print, but they can't resell your file or make more than one print without paying you additional license fees. All purchasers must agree to the license prior to download. If you wish to have your own customized license terms, you can select customized license and specify your terms in the description of the file.


Organize your file by moving it to a new category


If you share your file, you should move the file into an appropriate file category to allow people to find it easily. This is quite simple to do. From the file page, select File Actions and choose the Move item, as shown in Figure 11. You will be able to choose any of the file categories. Choose the one that best fits your particular file.


Figure 11: Moving your file to a new category.

That's it! Now you can share your amazing 3D printable medical models with the world.

Dr. Mike

large.57fc815d6d130_entrypic.pngPlease note that any references to “Imag3D” in this tutorial has been replaced with “democratiz3D”


In this tutorial you will learn how to create multiple 3D printable bone models simultaneously using the free online CT scan to bone STL converter, democratiz3D. We will use the free desktop program Slicer to convert our CT scan in DICOM format to NRRD format. We will also make a small section of the CT scan into its own NRRD file to create a second stand-alone model. The NRRD files will then be uploaded to the free democratiz3D online service to be converted into 3D printable STL models.


If you haven't already, please see the tutorial A Ridiculously Easy Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes, which provides a good overview of the democratiz3D service.


You should download the file pack that accompanies this tutorial. This contains an anonymized DICOM data set that will allow you to follow along with the tutorial.







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 NRRD Files from DICOM with Slicer


Open Slicer, which can be downloaded for free from www.slicer.org. Take the folder that contains your DICOM scan files and drag and drop it onto the slicer window, as shown in Figure 1. If you downloaded the tutorial file pack, a complete DICOM data set is included. 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. Remember, this only works with CT scans. MRIs cannot be converted at this time.



Figure 1: Dragging and dropping the DICOM folder onto the Slicer application. This will load the CT scan.


A NRRD file that encompasses the entire scan can easily be created by clicking the save button at this point. Before we do that however, we are going to create a second NRRD file that only contains the lumbar spine, which will allow us to create a second 3D printable bone model of the lumbar spine. Open the CT scan by clicking on the Show DICOM Browser button, selecting the scan and series within the scan, and clicking the Load button. The CT scan will then load within the multipanel viewer.


From the drop-down menu at the top left of the Slicer window, select All Modules and then Crop Volume, as shown in Figure 2. You will now want to create a Region Of Interest (ROI) to encompass the smaller volume we want to make. Turn on the ROI visibility button and then under the Input ROI drop-down menu, select "Create new AnnotationROI," As shown in Figure 3.



Figure 2: Choosing the Crop Volume module



Figure 3: Turn on ROI visibility and Create a new AnnotationROI under the Input ROI drop-down menu.


A small cube will then be displayed in the blue volume window. This represents the sub volume that will be made. In its default position, the cube may not overlay the body, and may need to be dragged downward. Grab a control point on the cube and drag it downward (inferiorly) as shown in Figure 4.

Figure 4: Grab the sub volume ROI and drag it downwards until it overlaps with the body.


Next, use the control points on the volume box to position the volume box over the portion of the scan you wish to be included in the small 3D printable model, as shown in Figure 5.


Figure 5: Adjusting the control points on the crop volume box.


Once you have the box position where you want it, initiate the volume crop by clicking the Crop! button, as shown in Figure 6.


Figure 6: The Crop! button


You have now have two scan volumes that can be 3D printed. The first is the entire scan, and the second is the smaller sub volume that contains only the lumbar spine. We are now going to save those individual volumes as NRRD files. Click the Save button in the upper left-hand corner. In the Save Scene window, uncheck all items that do not have NRRD as the file format, as shown in Figure 7. Only NRRD file should be checked. Be sure to specify the directory that you want each file to be saved in.



Figure 7: The Save Scene window


Your NRRD files should now be saved in the directory you specified.


Step 3: Upload your NRRD files and Convert to STL Files Using the Free democratiz3D Service


Launch your web browser and go to www.embodi3d.com. If you haven't already register for a account. Registration is free and only takes a minute. Click on the democratiz3D navigation item and select Launch App, as shown in Figure 8.



Figure 8: launching the democratiz3D application.


Drag-and-drop both of your NRRD files onto the upload panel. Fill in the required fields, including a title, short description, privacy setting (private versus shared), and license type. You must agree to the terms of use. Please note that even though license type is a required field, it only matters if the file is shared. If you keep the file private and thus not available to other members on the site, they will not see it nor be able to download it.


Be sure to turn on the democratiz3D Processing slider! If you don't turn this on your file will not be processed but will just be saved in your account on the website. It should be green when turned on. Once you turn on democratiz3D Processing, you'll be presented with some basic processing options, as shown in Figure 9. Leave the default operation as "CT NRRD to Bone STL," which is the operation that creates a basic bone model from a CT scan in NRRD format. Threshold is the Hounsfield attenuation to use for selecting the bones. The default value of 150 is good for most applications, but if you have a specialized model you wish to create, you can adjust this value. Quality denotes the number of polygons in your output file. High-quality may take longer to process and produce larger files. These are more appropriate for very large or detailed structures, such as an entire spinal column. Low quality is best for small structures that are geometrically simple, such as a patella. Medium quality is balanced, and is appropriate for most circumstances.



Figure 9: The democratiz3D File Processing Parameters.


Once you are satisfied with your processing parameters, click submit. Both of your nrrd files will be processed in two separate bone STL files, as shown in Figure 10. The process takes 10 to 20 minutes and you will receive an email notifying you that your files are ready. Please note, the stl processing will finish first followed by the images. Click on the thumbnails for each model to access the file for download or click the title.



Figure 10:  Two files have been processed simultaneously and are ready for download


Step 4: CT scan conversion is complete your STL bone model files are ready for 3D Printing

That's it! Both of your bone models are ready for 3D printing. I hope you enjoyed this tutorial. Please use the democratiz3D service and  SHARE the files you create with the community by changing their status from private or shared. Thank you very much and happy 3D printing!

Dr. Mike


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.



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

To complete basic information about your NRRD file. Do you want it to be private or do you want to share it with the community? Click on the Private File button if the former. If you are planning on sharing it, do you want it to be a free or a paid (licensed) file? Click the appropriate setting. Also select the License Type. If you are keeping the file private, these settings don't matter as the file will remain private. Make sure you accepted the Terms of Use, as shown in Figure 9.




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!


Dr. Mike

NRRD is a file format for storing and visualizing medical image data. Its main benefit over DICOM, the standard file format for medical imaging, is that NRRD files are anonymized and contain no sensitive patient information. Furthermore NRRD files can store a medical scan in a single file, whereas DICOM data sets are usually comprised of a directory or directories that contain dozens if not hundreds of individual files. NRRD is thus a good file for transferring medical scan data while protecting patient privacy. This tutorial will teach you how to create an NRRD file from a DICOM data set generated from a medical scan, such as a CT, MRI, ultrasound, or x-rays.


To complete this tutorial you will need a CD or DVD with your medical imaging scan, or a downloaded DICOM data set from one of many online repositories. If you had a medical scan at a hospital or clinic you can usually obtain a CD or DVD from the radiology department after signing a waiver and paying a small copying fee.


Step 1: Download Slicer


Slicer is a free software program for medical imaging. It can be downloaded from the www.slicer.org. Once on the Slicer homepage, click on the Download link as shown in Figure 1.



Figure 1


Slicer is available for Windows, Mac, and Linux. Choose your operating system and download the latest stable release as shown in Figure 2.



Figure 2: Download Slicer


Step 2: Copy the DICOM files into Slicer.


Insert your CD or DVD containing your medical scan data into your CD or DVD drive, or open the folder containing your DICOM files if you have a downloaded data set. If you navigate into the folder directory, you will notice that there are usually multiple DICOM files in one or more directories, as shown in Figure 3. Navigate to the highest level folder containing all the DICOM files.


Figure 3: There are many DICOM files in a study


Open Slicer. The welcome screen will show, as demonstrated in Figure 4. Left click on the folder that contains the DICOM files and drop it onto the Welcome panel in Slicer. Slicer will ask you if you want to load the DICOM files into the DICOM database, as shown in Figure 5. Click OK Slicer will then ask you if you want to copy the files or merely add links. Click Copy as shown in Figure 6.


Figure 4: Drag and drop the DICOM folder onto the Slicer Welcome window.



Figures 5 and 6


After working for a minute or two, Slicer will tell you that the DICOM import was successful, as shown in Figure 7. Click OK


Figure 7


Step 3: Open the Medical Scan in Slicer.


At this point you should see a window called the DICOM Browser, as shown in Figure 8. The browser has three panels, which show the patient information, study information, and the individual series within each study. If you close the DICOM Browser and need to open it again, you can do so under the Modules menu, as shown in Figure 9.


Figure 8: DICOM Browser



Figure 9: Finding the DICOM browser


Each series in a medical imaging scan is comprised of a stack of images that together make a volume. This volume can be used to make the NRRD file. Modern CT and MRI scans typically have multiple series and different orientations that were collected using different techniques. These multiple views of the same structures allow the doctors reading the scan to have the best chance of making the correct diagnosis. A detailed explanation of the different types of CT and MRI series is beyond the scope of this article, but will be covered in a future tutorial.


Click on the single patient, study, and a series of interest. Click the Load button as shown in Figure 8. The series will then begin to load as shown in Figure 10.


Figure 10: The study is loading


Step 4: Save the Imaging Data in NRRD Format

Once the series loads you will see the imaging data displayed in the Slicer windows. Click the Save button on the upper left-hand corner, as shown in Figure 11.


Figure 11: Click the Save button


The Save Scene dialog box will then appear. Two or more rows may be shown. Put a checkmark next to the row that has a name that ends in ".nrrd". Uncheck all other rows. Click the directory button for the nrrd file and specify the directory to save the file into. Then click the save button, as shown in Figure 12.


Figure 12: Check the NRRD file and specify save directory.


The NRRD file will now be saved in the directory you specified!

Dr. Mike


I was recently contacted by another doctor who asked if I could help him to create a 3D printed replicate of his spine to visualize pinched nerves in his low back and aid with planning a future back surgery. In order to work this doctor has to stand for long hours while performing surgical procedures. Excruciating low back pain had limited his ability to stand to only 30 minutes. As you can imagine, this means he couldn't work. Things only got worse after he had low back surgery.


A CT scan of his lumbar spine (the low back portion of the spine) was performed. It showed that his fifth lumbar vertebra was partially sacralized. This means it looked more like a sacral vertebra than a lumbar vertebra. Was this causing his problem? On the image slices of the CT scan it was difficult to tell.


How the Spine is Organized
First, a word about the different vertebrae (bones) in the spine. There are four main sections of spinal bones. The seven cervical vertebrae are in the neck and support the head. They are generally small but flexible, and allow rotation of the head. The 12 thoracic vertebrae are in the chest. Their most distinctive characteristic is they all have associated ribs, which make up the rib cage. The five lumbar vertebrae are in the low back. These are large and strong, and designed for supporting lots of weight. They do not have associated ribs. The five sacral vertebrae are in the pelvis. In adults, they are fused together and effectively form a single bone, the sacrum. The coccyx, or tailbone, which is a tiny bone at the bottom end of the vertebral column, can be considered a fifth spinal section. This is the bone that is often injured when you fallen your behind. Figure 1 shows the different sections of the vertebral column.


Figure 1. Sections of the vertebral column. Source:aimisspine.com


Although the bones of the individual sections of the spine usually have their own unique features, it is not uncommon for vertebrae in one section to have features typically associated with an adjacent section. This is particularly true of the vertebrae that are immediately adjacent to a neighboring section. These hybrids are a mix between both sections, are called transitional vertebrae. Do you recall that only thoracic vertebrae have associated ribs? Occasionally the highest lumbar vertebra, L1, will have tiny ribs attached to it. This is a normal variant and is usually harmless. Radiologists who are interpreting medical scans need to be careful to not confuse an L1 vertebra which may have tiny ribs for the adjacent T12 vertebra which normally has ribs. Similarly, the lowest lumbar vertebra, L5, which is normally unfused, can exhibit fusion. As you recall, fusion is a characteristic of sacral vertebrae.


A Congenital Spine Abnormality
This was the situation with our physician. His lowest lumbar vertebra, L5, has partially fused with S1, the highest sacral vertebra. This condition is congenital. He has had it all his life. The fusion can have the side effect of creating a very narrow bony canal through which the L5 nerve roots can exit the spine. Normally, these nerve roots would have much more space as a large gap would exist between the normally unfused L5 and S1 vertebrae. Was this the problem? The CT scan showed the sacralization of L5, but it was difficult to get a sense for how tight the holes through which the nerves exit, the neural foramina, were. See Figures 2 and 3.


Figure 2


Figure 2: Coronal CT image through the L5 and S1 vertebral bodies. Is this the cause of the problem? It is very difficult to get an intuitive sense of what is going on with these flat image slices.


Figure 3


Figure 3: Image from Figure 2 with the neural foramina marked.


Seeking help through Embodi3D
The doctor contacted me through the Embodi3D website and asked if I could create a 3D model design and 3D print of his lumbar spine to help him and his team of spinal specialists understand his unique anatomy better. Of course, I was happy to help. The CT scan was of high quality and allowed me to extract the bones and metallic spinal fusion implants with little trouble. The individual nerves, however, were very difficult to see even on a high quality CT scan. I had to manually segment them one image at a time, which was a very tedious and time-consuming process. After fusing everything together, I had a very good digital model of the lumbar spine. I created some photorealistic 3D renders to illustrate the key findings.


Figures 4 and 5 show the very tight L5-S1 bony neural foramina. The inter-vertebral disc sits within the gap between the two vertebral bodies, and you can see how a lateral bulge from this disc would significantly pinch these exiting nerve roots.


Figure 4


Figure 4: Right L5 nerve root (yellow) exiting the tight neural foramen caused by the fused L5 and S1 lateral processes.


Figure 5


Figure 5: Left L5 nerve root (yellow) exiting the tight neural foramen caused by the fused L5 and S1 lateral processes.


Additionally, I showed that a bone screw that had been placed during the last surgery had partially exited the L4 vertebral body and was in very close proximity, and probably touching, the adjacent nerve root. Ouch! This can be seen in Figure 6. This may explain why the pain seem to get worse after the last surgery.


Figure 6


Figure 6: Transpedicular orthopedic screw which has partially exited the L4 vertebral body and is in very close proximity or in contact with the right L3 nerve root.


The Final 3D Printed Spine Model
The doctor wanted his spine 3D printed in transparent material, so I used a stereolithographic printer with transparent resin. I printed the spine in two separate parts that could be separated and fit together. When separated, the nerves exiting through the neural foramina can be inspected from inside the spinal canal, which gives an added degree of understanding.


Final pictures of the transparent 3D printed model are shown below.



Figure 7


Figure 8



Figure 9



Figure 11



Figure 12




I just recently shipped the model to this doctor and don't yet know how his back problems will be resolved. With this 3D printed model in hand however, he will be able to have much more meaningful discussions with his spinal surgeons about the best way to definitively fix his low back problems. I hope that the 3D printed spine model will literally help to get this good doctor back on his feet again.

Dr. Mike


Hello Dr. Mike here and welcome to my review of the Form 2 3D printer by Formlabs. The Form 2 is Formlabs newest desktop stereolithography printer. It is a great asset for medical 3D printing with many user friendly features and an acceptable price.


My full review is included here in both video and text. You can download the splenic artery aneurysm file shown in the video. The Form 2 printer is available to purchase. The previous generation Form 1+ can be purchased on Amazon. However, the Form 2 represents a better value.


Stereolithography is a 3D printing method where a laser hardens liquid resin in a vat one layer at a time. This is different from fused deposition modeling (FDM) where plastic filament is heated and extruded through a nozzle to make the 3-D print. Stereolithography is capable of producing highly detailed 3-D prints with a layer thickness of 25 µm. This is four times finer than the 100 µm layer thickness for the latest MakerBot Replicator. q?_encoding=UTF8&MarketPlace=US&ASIN=B00ir?t=embform2-20&l=am2&o=1&a=B00SNM8VIK



Form 2 Unboxing and Set Up
My Form 2 arrived in a series of boxes at my front door. I do a lot of 3-D printing so I ordered extra bill platforms and resin tanks. Resin cartridges came in their own separate box. As you can see I also ordered extra resin cartridges.


The Form 2 printer came in a large box that contained a quick start guide, another resin tank, build platform, and accessories. The printer itself was well secured in the box and had convenient pullout handles. Once the printer was in its final location next to my old form 1+ printers I had to remove the extensive tape used to secure the printer during shipping. A thin plastic protective film is present over the touchscreen. I tend to get my printers dirty so I left this in place.


Next I plugged in the printer, and it immediately started to initialize. The printer immediately gave me a warning that it was not level. I had the printer set up on the same table that my older Form 1+ printers were on but they do not have a leveling sensor, and apparently I have been printing with them leveled all this time.


Fortunately leveling the Form 2 printer is very easy. It has screw type legs that can be raised or lowered, much the same way that restaurant tables can be adjusted. A simple disc like leveling tool comes with the printer and can be used to adjust the legs easily. Adjust the legs until the leveling circle is within the bull's-eye shown on the main screen. This is a pretty cool feature. The printer is now ready to print.


You can connect to the printer over a USB cable, but I prefer Wi-Fi as my main computer is in a different room than the printer. To do this turn on Wi-Fi settings and select your network. The older Form 1+ printer resin came in bottles that you had to pour into the resin tank. The Form 2 printer comes with a printer cartridge that slides into the back of the printer. When you're resin tank is low the printer automatically fills the tank from the cartridge. This is quite handy especially with larger prints that may require the tank to otherwise be refilled in the middle of a print.


A new resin tank fits easily into the printer and snaps in place. Resin tanks are considered to be consumables and are thrown out after about 2 L of printing when the floor of the tank becomes foggy and starts to inhibit the laser. Each resin tank comes with a wiper arm which snaps into place. This wiper arm is a new feature for the form to and can prevent cured resin from sticking to the bottom of the tank, a situation that in older printers could cause total print failure. With the new wiper arm this situation is much less likely to happen.
The new build platform slides and easily.


Inserting a resin cartridges a snap. There's a cap on the top of the resin cartridge that should be opened to allow resin to drain into the printer. At this point the printer should be ready to print. You can see that the display shows that a resin tank and cartridge have been inserted. Also the display indicates the internal temperature. During printing a heater will warm the internal temperature to the appropriate level to achieve best results.


This is the result of my first print, which is a hollow vascular model. This is my second print which is a section of lumbar spine printed in clear resin.


This is the new removal tool, which is used to remove the three printed model from the build platform. Form labs has recently released firmware update which makes removal of the parts much easier. The removal tool can slip under the edges and with gentle twisting will separate from the bill platform. This is a significant improvement over the older support structure. It is also an example of how form labs continues to improve its products even after sale through the use of software upgrades.


Once removed from the bill platform the support structures need to be removed. This can be done either before or after cleaning the part in an alcohol bath. The model will be covered in sticky resin so you need to wear disposable gloves and be able to clean the parts with alcohol, which requires decent ventilation. Using the flush cutters that come with the kit the base can be cut and the support structures can be gently worked off the model.


Here's an example of a splenic artery aneurysm model that I printed and clear. You can see that the quality of the print is excellent. If you would like to 3-D print this model yourself I have made it free for download at the link in the description below. It is available in both STL and Form labs Preform software format. This is an example of some of the parts that are produced with the Form 2 printer. As you can see they are a very high quality.


Purchase and material options, and other features
The Form 2 comes with many upgrades and improvements over its predecessor, the Form 1+. This includes:

  • Larger build volume, 14.5 x 14.5 x 17.5 cm
  • Heated tank
  • slide peeled
  • resin wiper
  • dust protection
  • automated resin system
  • wireless connectivity

The cost of the Form 2 printer is $3499, which includes the printer, resin tank, build platform, finishing kit, and one liter of resin of your choice. The printer comes with a one-year warranty.


Standard resins are available in black, gray, white, and clear. Functional resins include flexible, castable, and tough. A biocompatible resin is available for dental purposes.


Form 2 For Medical 3D Printing Review Conclusion
The Form 2 is an outstanding desktop stereolithography 3-D printer for the price. It produces very high quality parts. It is expensive for a consumer grade desktop printer but is significantly cheaper than other printers used for medical purposes. The free Preform software makes setting up a print easy. Cons of the printer are it is messy, requiring gloves and isopropyl alcohol to clean the sticky resin from the parts. This can be a problem in a poorly ventilated office environment. Also the build volume, while larger than its predecessor, is still smaller than many FDM printers.
Overall the form two is an outstanding value and I recommend it highly particularly for medical 3-D printing. Thank you very much for watching if you like this video subscribe below and happy 3-D printing.

Dr. Mike

If you have a 3D printable file you would like to share with the Embodi3D community the process is very easy.


1) First, get your files ready. STL files are best and have good compatibility with most printers. Make sure your files are of good quality as Embodi3D's file library contains high quality files. If you think you files may have errors in them, you can check them using the Inspector function in MeshMixer. Be sure to compress your files if possible using a compression program like WinZip.


2) Take photographs or screenshots of your model, and have the image files ready to upload.


3) Now we are ready to upload. From anywhere in the Embodi3D site, click on the Marketplace nav menu. Make sure you are logged into your member account.

Figure 1 click marketplace


4) Click the Upload File button in yellow.

Figure 2 click Upload file


5) Select a category that most appropriately describes your file.

Figure 3 choose category


6) Upload you files. Click on the "Click to Upload Files" button and navigate to the folder that contains the files you want to upload. Please compress your files using a file format like ZIP beforehand to make downloading easier for users. Uploads are limited to 30 MB in size, so compressing large STL files is important. You can upload a file as large as 100 MB if compression is used.

Figure 4 Select files


7) Upload pictures or screenshots. Click the button and navigate to the folder that contains pictures of your model.

Figure 5 select screenshots


8) Add details about your files. Put in a descriptive title. This is very important to attract people to your file page. Type in descriptive file tags to help search engines find your files. In the Description section, describe your model. You can even embed youtube links. To include media that you have uploaded to your Gallery click the My Media button. Choose whether you want the file to be free or paid. If you want the file to be a paid file (i.e. downloadable for a fee), see the selling page for more information on how to sell your files. Finally, choose a license type. Free files are distributed with Creative Commons licenses. Choose the one that you like the the best and click "Add Submission."


Figure 6 Add details


9) View your newly shared file! Thanks a bunch! By sharing your file you are helping other Embodi3D members with research, education, and a variety of other worthy causes.


Figure 7 final view


If you would like to download the splenic artery aneurysm file shown in this tutorial, you can do so here.

Dr. Mike


If you attended my open-source 3D printing didactic talk or open-source 3D printing workshop at this year's RSNA meeting and are interested in a having a copy of my slides (I have been asked several times), or if you are not at the meeting and are just interested, you can find them here. They are an attached PDFs and links.


Manual for Open-Source 3D printing workshop (PDF)


Other resources to help you get 3D Printing the Embodi3D tutorials page: http://www.embodi3d.com/tutorials.html


Additional specific resources I mentioned in my talk:


3D printing with Osirix (Mac only)


3D printing with Slicer (Windows, Mac, Linux)


5-minute modeling with Slicer



Good luck! Contact me if you need any help.


Dr. Mike

Open source software RSNA 2015 v1.1.pdf

Dr. Mike



UPDATED TUTORIAL: A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes

Hello, it's Dr. Mike here again with another tutorial on 3D printing. Proprietary software that creates 3D printable models from medical scans typically costs tens of thousands of dollars to license. But, did you know that you can do the same thing using freeware? It's true! In this tutorial I'm going to show you exactly how to do this.


We will be using the free, open-source program 3D Slicer to convert a CT scan of a skull into an STL file ready for 3D model printing. We will also use the freeware software programs Blender and Meshmixer to perform some final cleanup of the STL files before sending them to the printer. All three software programs are available on Windows, Macintosh, and Linux, so you can use the methods described here on almost all personal computers.


If you master this workflow you can create 3D printable models very quickly, as illustrated in my brief tutorial on Creating a 3D Printable Skull in 5 Minutes. If you are on a Mac and prefer to use Osirix, see my tutorial on Creating 3D Printable Models with Osirix. Once you have completed your 3D printable model, be sure to share it with the community via the File Vault, or if you prefer, you can sell it on this website.


Before you began I highly recommend you download the free associated file pack. The file pack contains files that will allow you to follow along with the tutorial, making it easier and faster to learn. This includes the same CT scan used here. The download is free for registered members, and registration is also free and only takes a moment.






Creating a Skull STL File for Medical 3D Printing using 3D Slicer


If you haven't already, download 3D Slicer from slicer.org. Open Slicer.

01 slicer icon

Drag and drop the folder that contains your DICOM images onto the slicer welcome window, Figure 1. If you downloaded the file pack, the DICOM folder is the one that begins with "1.3.6" followed by a whole bunch of numbers.


Fig 01 drag dicom Set

Figure 1: Loading your DICOM data set by dragging and dropping the DICOM folder onto 3D Slicer.


Slicer will ask you to select a reader to use for your data. Leave the default setting selected, "Load directory into DICOM database" and click OK. Slicer will ask you if you want to copy the DICOM files into the Slicer database or just add links to the DICOM files. Click Copy, Figure 2.


Fig 02 copy files

Figure 2: Telling Slicer to copy the DICOM files into the Slicer database.


Slicer will now take a minute or two to load your DICOM data. Once the data has loaded you should get a pop-up box telling you that the study imported successfully. Click OK. At this point a window titled "DICOM Browser" should be showing. Select the study with patient ID TCGA-06-5410. Click on the Load button in the lower left-hand corner, Figure 3.


Fig 03 select study from DICOM browser

Figure 3: Loading the CT scan into the active seen within Slicer.


At this point you should see a matrix with four boxes in the right half of the Slicer window. In three of the boxes you will see the axial (transverse), sagittal, and coronal views of your imaging study. If you don't see this, you can adjust the viewport layout using the viewport button.

6a view button

Select the Four-Up viewport layout as shown in Figure 4.


Fig 04 Four Up view

Figure 4: Selecting the Four-up viewport layout.


Next, go to the Volume Rendering module. You can access this from the drop-down menu at the top now bar as shown in Figure 5.


Fig 05 open volume rendering

Figure 5: Selecting the Volume Rendering module.


Once you are in Volume Rendering, turn on volume rendering by clicking the small eyeball to the left of the Volume drop-down menu, as shown in Figure 6. The 3D volume should now be displayed in the fourth square on the right part of the Slicer window. However, the volume is likely not centered. To center the volume click on the small crosshairs at the upper left corner of the volume screen, as shown in Figure 6.


Fig 06 turn On volume And center

Figure 6: Turning on volume rendering and centering the volume view.


You now need to adjust the appearance of your 3D volume. Under the Display section, select a Preset. For this model, select the third icon from the left on the top row, which should be CT-Bone. Slide the Shift slider to the right until the 3D volume looks good. These actions are shown in Figure 7.


Fig 07 bone preset

Figure 7: Selecting and adjusting a 3D display Preset.


Now we are going to start actually constructing our 3D surface model. From the module drop-down menu, Editor, as shown in Figure 8. When asked to create a merge label map, use the default selection GenericAnatomyColors, and click Apply, as shown in Figure 9.


Fig 08 open editor

Figure 8: Selecting the Editor module.


Fig 09 select label Map

Figure 9: Choose the default merge label map.


First, we're going to create a label map that denotes the skull. Click on the Threshold Effect Tool button. It looks like this.

12 threshold effect button

The threshold effect tool will then open as shown in Figure 10. We want to select bone, so click on the green rectangle to bring up a choice of label maps. Select 2 – bone. The blinking area should turn a yellow-orange color. Next, define the minimum Threshold Range. If you are using the DICOM data set from the file pack, set this to 1250. If you are using your own scan, this will be a different number, probably closer to 300. Experiment with the values until the blinking region seems to encompass the structures you want to 3D print. Leave the default maximum Threshold Range at 4095. The settings that you need to modify are shown in Figure 11. When you are satisfied with your selection, click Apply.


Fig 10 threshold effect tool

Figure 10: The Threshold Effect Tool.


Fig 11 threshold effect settings

Figure 11: The Threshold Effect parameters to set.


Now you have created a "label map" that encompasses the bony skull we wish to 3D print. We need to generate a surface model. Click on the Make Model Effect button, which looks like this.

12 make model effect button

Make sure that the target label is still set to 2 (bone). Click Apply, as shown in Figure 12. 3D Slicer will take about 10 seconds to generate the surface model. When it is completed, you will notice a slight change in the appearance of the 3D rendered image in the upper right view box.


Fig 12 make model effect tool

Figure 12: The Make Model Effect tool.


You now have a 3D surface model, and need to save it in STL file format. Click on the save button on the left portion of the upper toolbar. 3D Slicer asks you what you want to save. The only thing we are interested in is the bone surface model, so uncheck everything except "bone.vtk." Choose STL for file format and specify the directory you want the file to be saved, as shown in Figure 13.


Fig 13 save Stl file

Figure 13: Saving your 3D surface model as an STL file.


You should now have a file called bone.STL. Although tempting to send your new STL file directly to a 3D printer, don't do it. Your file is not yet ready for 3D printing. Fortunately, we can fix most problems with our next software program, Blender.


Performing Additional Skull STL File Cleanup in Blender


If you haven't already, download the free Blender software program from blender.org. Install it and open Blender.

02 blender icon

Delete the default cube that is shown in Blender by hitting the X key followed by the D key. Import the STL file by going to the File menu -> Import -> STL, as shown in Figure 14. Blender may take 10 to 15 seconds to import the file as it is fairly large.


Fig 14 import STL into blender

Figure 14: Importing the STL file into Blender.


Next, you need to center the skull object in the field of view. Select the Object menu in the lower left-hand corner, then click Transform -> Geometry to Origin, as shown in Figure 15.


Fig 15 center model

Figure 15: Centering the object in the field of view using the Geometry to Origin function.


You will notice that the imported skull appears quite large. Don't worry about this. Simply use your scroll wheel on the mouse to scroll out. If you have a middle mouse button, you can use it to rotate the skull. Next, we are going to delete the innumerable disconnected mesh islands in our skull object. Go to Edit Mode, as shown in Figure 16.


Fig 16 Edit mode

Figure 16: Entering Edit Mode.


When you are in Edit Mode, you can directly edit the mesh of your object. Initially, the entire mesh is selected, thus the skull appears orange. Right click somewhere on the skull. It does not matter where as long as it is not one of the disconnected mesh islands. By right clicking, you will select a single vertex. Expand the selection to include all connected vertices by clicking Control-L on your keyboard. You will notice that the skull has turned orange, but the disconnected mesh islands are still black. Next, we want to invert the selection by hitting Control-I on your keyboard. The selection is now inverted, and only the disconnected mesh islands should be shown highlighted in orange, as shown in Figure 17.


Fig 17 free islands selected

Figure 17: Selecting the disconnected mesh islands.


With the disconnected mesh islands selected, delete them by hitting the X key on the keyboard. A menu of deletion choices is presented. Type "V" for Vertices. This is shown in Figure 18. The disconnected mesh islands are now deleted.


Fig 18 delete vertices

Figure 18: Deleting the vertices of the disconnected mesh islands.


Go back to Object Mode by selecting it from the mode button on the lower left as shown in Figure 19.


Fig 19 object mode

Figure 19: Returning to Object Mode.


From Object Mode select the Modifiers toolbar. It has a button that looks like a small wrench and is located in the right tool column. Modifiers are functions that you can apply to your mesh to change its appearance. In this case, we are going to smooth out our mesh. Click on the Add Modifier menu and select Smooth from the Deform column. DO NOT select Laplacian Smooth. That is a different modifier. The correct selection is shown in Figure 20.


Fig 20 smooth modifier

Figure 20: Opening the Smooth Modifier.


Set the Repeat field to 30. Blender may take a few seconds to perform the smoothing function. Then, click Apply, as shown in Figure 21.


Fig 21 smooth modifier applied

Figure 21: Settings for the Smooth Modifier.


You are now ready to save your smoothed and cleaned-up STL file. From the File menu, select Export -> STL, as shown in Figure 22. Navigate to the folder you want the file to be saved in and type a file name. In this case, we are going to call the file "bone smoothed.stl." Close Blender.


Fig 22 save STL

Figure 22: Saving your cleaned-up STL file.
Performing a Final File Check in Meshmixer Before 3D Bioprinting


If you haven't already, download Meshmixer from Meshmixer.com. Open Meshmixer.

03 meshmixer icon

Click on the Import button as shown in Figure 23. Select your smoothed STL file that you just created in Blender.


Fig 23 meshmixer import

Figure 23: Meshmixer's Import button.


Meshmixer will take 10 to 15 seconds to import the file. Once imported, you can rotate the orientation of your skull object by using the right mouse button. Click on the Analysis button and choose Inspector as shown in Figure 24. The Inspector tool will check your mesh for the defects that could cause problems during 3D printing. Any problem areas will be highlighted by red, blue, or pink lines. In this case, our mesh looks great, without any errors as shown in Figure 25.


Fig 24 meshmixer inspector

Figure 24: Opening the Inspector tool.


Fig 25 meshmixer inspector done

Figure 25: A clean mesh ready to 3D print!


That's it! You have now created a defect-free high quality STL file of the skull from a CT scan using free software. You can take the money you saved by not buying proprietary software to do the same thing, and by yourself a new car or something.


Fig 26 final model

Figure 26: The Final 3D printed product.


I hope you found this tutorial helpful, and you will begin designing 3D printable medical models from medical scans yourself. Embodi3D is here to help you. If you have questions, post them in the comments below or in the Forums. Share 3D printable models you have designed in the File Vault, or download models that others have shared. You can even sell your 3D printable creations! If you want to learn more about how to create 3D printable medical models, there are many more helpful and free tutorials.

Dr. Mike


UPDATED TUTORIAL: A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes


Hello and welcome back. I hope you enjoyed my last tutorial on creating 3D printable medical models using free software on Macintosh computers. In this brief video tutorial I'll show you how to create a 3D printable skull STL file from a CT scan in FIVE minutes using only free and open source software. In the video I use a program called 3D Slicer, which is available from slicer.org. 3D Slicer works on Windows, Macintosh, and Linux operating systems. Also, I use Blender, which is available from blender.org, to perform some mesh cleanup. Finally, I check my model prior to 3D printing using Meshmixer from Autodesk. This is available at meshmixer.com. All software programs are free.


If you like this, view my complete tutorial where I go through each step shown here in detail. I hope you enjoy the video.



Dr. Mike


UPDATED TUTORIAL: A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes


Hello, it's Dr. Mike here again with another tutorial and video on medical 3D printing. In this tutorial we're going to learn how to take a DICOM-based medical imaging scan, such as a CT scan, and convert into an STL file in preparation for 3D printing. We will use the free, open-source software program Osirix to do this. Once the file is converted into STL format, we will use the free software packages Blender and Meshmixer to prepare the file for 3D bioprinting. If mastered, this material should easily allow you to make a high-quality 3D printed medical model in less than 30 minutes using free software. Expensive, proprietary software is not needed. This tutorial is designed primarily for Macintosh users since Osirix is a Macintosh-only program. If you use Windows or Linux, please stay tuned for my upcoming tutorial on using free, open-source 3D Slicer to create medical and anatomic models.
If you haven't already done so, please see my tutorial on selecting the best medical scan to create a 3D printed model. If you start your 3D printed model project with the wrong kind of scan, your model will not turn out well. Selecting the right kind of scan is critically important and will save you a lot of frustration. Take a few minutes to look over this brief tutorial. It will be well worth your time.


Before you start, DOWNLOAD THE FILE PACK that accompanies this video so you can follow along on your own computer. When you finish the tutorial, you will have your very own 3D printable skull STL file. Download is free for members, and registration for membership is also free and only takes a minute.



Video 1: The video version of this tutorial. It takes you from start to finish in 30 minutes. The written version here has more detail though.
A Few Brief Definitions


What is Osirix?


Osirix is a Macintosh-only software package for reading medical imaging scans (Figure 1). There are several versions. There is an FDA-approved version designed for doctors reading scans in clinics and hospitals, a 64-bit version for research and other nonclinical activities, and a free, 32-bit version. The main difference between the free 32-bit version and the paid 64-bit version is the 64-bit version can open very large imaging studies, such as MRI exams with thousands of images. The 32-bit version is limited to about 500 images. Additionally, there is a performance boost with the paid versions. If you are just getting into 3D bioprinting, the free, 32-bit version is a great place to start. It can be downloaded at the Osirix website here.


Figure 1 osirix

Figure 1: An example of Osirix being used to read a CT scan.


What is DICOM?


DICOM stands for Digital Imaging and Communications in Medicine. It is the standard file format for most medical imaging scans, such as Computed Tomography (CT), Magnetic Residence Imaging (MRI), ultrasound, and x-ray imaging studies.


What is STL?


STL, or STereoLithography format , is an engineering file format created by 3D Systems for use with Computer Aided Design software (CAD). The file format is primarily used in engineering, and has become the standard file format for 3D printing.


The Problem with 3D Printing Anatomic Structures


The major problem with trying to 3D print anatomic structures from medical scans is that the medical scan data is in DICOM format and 3D printers require files in STL format. The two formats are incompatible. There are very expensive, proprietary software packages that can perform the conversion between DICOM and STL. A little-known secret is that this can also be done using free, open-source software. Osirix is the best solution for Macintosh. 3D Slicer is the best solution for Windows and Linux. I will discuss 3D Slicer in an upcoming tutorial.


If you haven't already, please download the DICOM data set we will be using in this tutorial. This data set is from a high quality CT scan of the brain and skull. It has been anonymized and has been put in the public domain for research by the US National Cancer Institute. Also included with the download packet are other files we will use for this tutorial, including the final STL file of the skull. The download is free for members, and registration for membership is also free and only takes a minute.


From the Macintosh Finder navigate to the folder with the downloaded tutorial file pack and double-click on the file TCGA-06-5410 sharp.zip.


Opening the CT scan with Osirix


Open Osirix. From the File menu, click Import, Import Files. Click Open. (Figure 2)


Figure 2 open DICOM folder

Figure 2: Importing the CT scan into Osirix


Navigate to the folder that contains your DICOM data set. Click the Open button.


Osirix will ask you if you want to copy the DICOM files into the Osirix database, or only copy the links to these files. Click "Copy Files."


Osirix will begin to copy the files into the database. A progress bar will be shown on the lower left-hand corner. When the data is imported you'll see a small orange circle with a "+" in it. This orange circle will eventually go away when Osirix is finished analyzing the study, but you can open the study and work with it while Osirix does some cleanup postprocessing. Left click on the study.


You will see an icon with a label "FIDUCIALS 1.0 SPO cor, 216 Images." This is a CT scan of the head with coronal slices at 1 mm intervals. Double-click on this icon, Figure 3.


Figure 3

Figure 3: The study when opened


Osirix will remind you that you're not supposed to be using it for diagnostic scan reading on real patients unless you are using the more expensive FDA approved version, Osirix MD we're just using it to create a 3D model, so click "I agree."


At this point, the study will load. Use the mouse wheel or the bar on the top of the screen to scroll.


You can see that this is a pretty decent CT scan of the head for 3D printing. There is not much artifact from metallic dental implants because the maxilla and mandible have been cut off.


Segmenting the bony skull and creating a new series


We can measure the density of the bony structures using the Region Of Interest or ROI tool. This measures the Hounsfield density, or CT density, of the target area. Select the oval tool from the drop-down menu, Figure 4.


Figure 4 ROI tool

Figure 4: The ROI tool.


Choose a region of bone using the oval tool. You will see that information about this region is displayed. What we are interested in is the mean density, which in this case is 1753.194, Figure 5.


Figure 5 skull hounsfield

Figure 5: Density measurement using ROI tool. The mean density is 1753.194, as shown in maroon field.


Use the ROI tool to select another region in the brain. You will see that the mean attenuation, or density, is much less, in this case 1059.137, Figure 6.


Figure 6 brain hounsfield

Figure 6: Density measurement of the brain tissue.


Finally, use the oval tool to choose an area in the air adjacent to the head. You can see that the mean attenuation of this region is 38.514, Figure 7.


Figure 7 Air hounsfield

Figure 7: Density measurement of air.


In this scan the Hounsfield attenuation numbers have been shifted. In a typical scan, air measures about -1000, soft tissue between 30 and 70, and bone typically greater than 300. In this scan those numbers have been increased by 1000. Since we were thorough enough to check the Hounsfield attenuation before moving on, we can easily correct for this shift.


Under ROI menu select Grow Region 2D/3D Segmentation, Figure 8.


Figure 8 select segmentation

Figure 8: The Grow Region tool


In the Segmentation Parameters window that pops up, set the following:
Lower Threshold 1150
Upper Threshold 3000.
Generate a new series with:
Inside pixels 1000
Outside pixels 0


Be sure to check the checkbox next to the Set Inside Pixels, and Set Outside Pixels fields, Figure 9.


Figure 9 Set segmentation parameters

Figure 9: Setting up the Segmentation Parameters window.


Next, make sure you select a starting point for the algorithm. Left click on one of the skull bones. Green crosshairs will show. All of the bone that is contiguous with point you clicked will now be highlighted in green, Figure 10.


Figure 10 select bone For segmentation

Figure 10: Setting the starting point for segmentation. The target region turns green.


Click the Compute button


Osirix will generate a new series with the bones being a single white color with a value of 1000, and everything else being a black color with a value of zero, Figure 11. Creating a separate series just for 3D printing purposes is the secret to getting good 3D models from Osirix. Trying to generate a 3D surface model directly from the 3D Surface Rendering function underneath the 3D Viewer menu is tempting to use, however it will not work well for generating STL files. This is not obvious, and the source of much frustration for beginners trying to use Osirix for 3D printing.


Figure 11 New series

Figure 11: The new bitmapped series shown on right of screen. This series has only two colors, black and white. It is idea for conversion to and STL surface model.


Generating an STL file from the new bitmapped series


Now we are ready to create our 3D surface model. Make sure that your new bitmapped series is highlighted. Click on the 3D viewer menu and select 3D Surface Rendering, Figure 12. Leave the settings set to their default values. Click OK as shown in Figure 13.


Figure 12 surface rendering

Figure 12: Selecting 3D Surface Rendering


Figure 13 surface rendering settings

Figure 13: Setting 3D surface rendering settings


Osirix will then think for a few moments as it prepares the surface. You can see that a relatively good approximation of the skull has been generated. Use of the left mouse button to rotate the 3D model.


Next were going to export the 3D surface model to an STL file. Click Export 3D-SR and choose Export as STL as show in Figure 14. Type the file name "skull file." Click Save.


Figure 14 export At STL

Figure 14: Exporting model to STL file format.


Cleaning up the 3D model in Blender


You can see from the 3D rendering that there are many small islands of material that have been included with the STL file. Also, the skull has a very pixelated appearance. It does not have the smooth surface that would be expected on a real skull. In order to fix these problems, we're going to do a little postprocessing in Blender, a free open-source 3D software program.


If you don't already have Blender on your computer, you can download it free from blender.org. Blender is available for Windows, Macintosh, and Linux. Select your operating system, preferred installation method, and download mirror.


Once Blender is installed on your computer, open it. In the default scene there will be a cube. We don't need this. Right click on the cube to select it. Then delete it using the delete key on a full keyboard or the X key on a laptop keyboard. Blender will ask you to confirm you want to delete the object. Click Delete as shown in Figure 15.


Figure 15 delete cube In Blender

Figure 15: Deleting the default cube.


Next, we are going to import the skull STL file. From the File menu select Import, STL, as shown in Figure 16. Navigate to the skull STL file you saved from Osirix, and double-click it. Blender will think for a few seconds and then return to what appears to be an empty scene, as shown in Figure 17. Where is your skull? To find your skull, use the mouse scroll wheel to zoom out. If you zoom out far enough you will see the skull. The skull appears to be gigantic, as shown in Figure 18. This is because the default unit of measurement in the skull is 1 mm. In Blender, an arbitrary unit of measurement called a "blender unit" is used. When the skull was imported, 1 mm of real size was translated into 1 blender unit. Thus the skull appears to be hundreds of blender units large, and appears very big.


Figure 16 import STL

Figure 16: Importing the STL file into Blender


Figure 17 empty scene

Figure 17: The "empty" scene. Where is the skull?


Figure 18 zoom Out

Figure 18: Zoom out and the skull appears!


The skull is also offset from the origin. We are going to correct that. Make sure that the skull is still selected by right clicking on it. If it is selected it will have a orange halo. In the lower left corner of the window click on the Object menu. Select Transform, Geometry to Origin as shown in Figure 19. The skull is now centered on the middle of the scene.


Figure 19 Set Geometry To origin

Figure 19: Centering the skull in the scene.


Deleting Unwanted Mesh Islands


First, let's get rid of the extra mesh islands. There is a menu in the lower left-hand corner of the window that says Object Mode. Click on this and go to Edit Mode, as shown in Figure 20.


Figure 20 Edit Mode

Figure 20: Entering Edit mode in Blender.


Now we are in Edit Mode. In this mode we can edit individual edges and vertices of the model. Right now the entire model is selected because everything is orange. In edit mode you can select vertices, edges, or faces. This is controlled by the small panel of buttons on the bottom toolbar. Make sure that the leftmost or vertex selection mode is highlighted and then right click on a single vertex on the model, as shown in Figure 21. That vertex should become orange and everything else should become gray, because only that single vertex is now selected, Figure 22.


Figure 21 Vertex selection model

Figure 21: Vertex selection mode


Figure 22 single vertex selected

Figure 22: Select a single vertex by right clicking on it.


Under the Select menu, click Linked, as shown in Figure 23. Alternatively, you can hit Control-L. This selects every vertex that is connected to the initial vertex you selected. All the parts of the model that are contiguous with that first selection are now highlighted in orange. You can see that the many mesh islands we wish to get rid of are not selected.


Figure 23 linked selection

Figure 23: Selecting all linked vertices.
We are next going to invert the selection. Do this by again clicking on the Select menu and choosing Inverse, Figure 24. Alternatively, you can hit Control-I. Now, instead of the skull being selected, all of the unwanted mesh islands are selected, as shown in Figure 25. Now we can delete them. Hit the delete key, or alternatively the X key. Blender asks you what you want to delete. Click Vertices, Figure 26. Now all of those unwanted mesh islands have been deleted.


Figure 24 invert selection

Figure 24: Inverting the selection.


Figure 25 unwanted mesh selected

Figure 25: The result after inverting the selection. Only the unwanted mesh islands are selected!


Figure 26 delete vertices

Figure 26: Deleting the unwanted mesh islands.


Repairing Open Mesh Holes


We can see that on the top of the skull there is a large hole where the skull was cut off by the scanner. Because the bone surface was cut off, Osirix left a gaping defect, Figure 27. Before 3D printing, this will have to be corrected. This is what is called a manifold mesh defect. It is an area where the surface of the model is not intact. A 3D printer will not know what to do with this, such as whether it should be filled in or left hollow. Fortunately, it is relatively easy to correct.


Figure 27 hole In skull Top

Figure 27: A large open mesh hole at the top of the skull.


Using the Select menu in the lower left-hand corner, click on Non-Manifold. This will select all of the non-manifold mesh defects in your model. You can see that the edge of our large hole at the top of the skull has been selected and turned orange. This confirms that this defect has to be fixed.


Unselect by hitting the A key. Then, go to Edge select mode by clicking on the Edge Select button along the lower toolbar. Holding down the Alt key, right-click on one of the edges of the target defect, in this case the top of the skull. That familiar orange ring has formed. Your selection should look like Figure 28. Let's fill in this hole by creating a new face. Hit the F key. This creates a new face to close this hole, Figure 29.


Figure 28 hole selected

Figure 28: The edge of the hole is selected, as indicated by the orange color.


Figure 29 hole filled

Figure 29: The hole when filled with a new face.


Due to the innumerable polygons along the edges, the face is actually quite a complex polygon itself. Let's convert it to a simpler geometry. With the face still selected hit Control T. You can alternatively go to the Mesh menu and select Faces, Triangulate Faces as shown in Figure 30. This will convert the complicated face into simpler triangles. As you can see, some of these triangles are quite large relative to the other triangles along the skull surface. These large triangles may become apparent when smoothing algorithms are applied or 3D printing is performed. Let's reduce their size. Hit the W key and then select Subdivide Smooth, as shown in Figure 31. The triangles are now subdivided. Let's repeat that operation again so that they are even smaller. Hit the W key and again select Subdivide Smooth.


Figure 30 triangulate faces

Figure 30: Converting all faces into triangles.


Figure 31 subdivide smooth

Figure 31: Subdividing and smoothing the selected faces.


Smoothing the Model Surface


Next let's get rid of that pixelated appearance of the model surface. First, we need to convert all of the polygons in the model to triangles. The smoothing algorithms just work better with triangles. Staying in Edit mode, hit the A key. The A key toggles between selecting all and unselecting all. If you need to, hit the A key a second time until the entire model is orange, thus indicating that it is selected. Hit Control-T, or alternatively use the Mesh menu, Faces, Trangulate Faces. This will convert any remaining complex polygons to triangles.


Go back to Object mode by hitting the tab button or selecting Object Mode from the bottom toolbar. We are now going to apply a smoothing function, called a modifier, to the skull. Along the right of the screen you'll see a series of icons, one of which is a wrench, as shown in Figure 32. Click on that. This brings up the modifier panel, a series of tools that Blender uses to manipulate digital objects. Click on the Add Modifier button and select the Smooth modifier. Do not select the Laplacian Smooth modifier. That is different. We just want the regular Smooth modifier, as shown in Figure 33. Leaving the Factor value at 0.5, increase the Repeat factor until you are satisfied with the surface appearance of your model. For me, a factor of 20 seemed to work, Figure 34. At this point the modifier is only temporary, and has not been applied to the model. Click on the Apply button. Now the smoothing function has been applied to the model.


Figure 32 modifiers toolbar

Figure 32: The Modifiers toolbar on the right.


Figure 33 smooth modiifer

Figure 33: The Smooth modifier


Figure 34 smooth modifier 2

Figure 34: Setting the Smooth modifier to repeat 20 times.


Rotating and Adjusting the Model Orientation


When the model was originally exported from Osirix and opened in Blender, it was at a strange orientation. We can correct to this easily. Click on the View menu from the left portion of the lower now bar and select Front. This orients the model from the frontal view, and you can see that in this orientation we are looking at the top of the skull. To correct this, we will rotate the model along the X axis. First, make sure that the cursor is inside the model window. Then, Hit the R key and then the X key, and type "180." This will rotate the model on the X axis by 180°. Hit the return key to confirm the modification. Don't worry if the skull isn't facing the correct way right now, we will fix that later.


Now we are ready to export our cleaned up skull model. Go to the File menu, click Export, STL. Navigate to your desired folder and save your STL file. Since I corrected several defects in this mesh file, I called the file "skull file corrected.stl"


Performing a Final Inspection Using Meshmixer


If you haven't already done so, go to the Autodesk Meshmixer website at http://www.meshmixer.com/download.html and download and install Meshmixer. The software is free. Once installed open the program and select Import. Navigate to your STL file and double-click it. Meshmixer has a variety of nice features, and one of them is a mesh correction function. Once your file is open click on the Analysis button along the left nav bar. Click on Inspector as shown in Figure 35. Meshmixer will now analyze the STL file for obvious mesh defects. Anything that is detected will be highlighted by red, pink, or blue lines. You can see that our skull model appears to be defect free. Click on the done button and quit Meshmixer.


Figure 35 Meshmixer inspector

Figure 35: Running the inspector tool in MeshMixer
Your STL file of the skull is now ready for 3D printing!




In this tutorial you have learned how to take a DICOM data set from a CT scan and use it to create a 3D printable STL file using free software. First we used the Osirix to segment a CT scan and convert it to an STL file. Then we performed cleanup operations on the STL file using the Blender and Meshmixer, both free programs. For additional information on how to select an appropriate CT or MRI scan for 3D printing please see my previous tutorial. If you want to learn more about using Blender to fix more extensive defects in bone models, you can view to other tutorials I have created:

A variety of useful tutorials for 3D printing is available on the Tutorials page. If you are planning on attending the 2015 Radiological Society of North America (RSNA) meeting in Chicago this November, look for my hands-on course "3D Printing and 3D Modeling with Free and Open-Source Software." I will give more tips and tricks for creating great 3D printed medical models using freeware.


I hope you find this tutorial helpful in creating your own medical and anatomic models for 3D printing. Please stay tuned for my next tutorial on using the free, open-source program 3D Slicer to create medical 3D models on Windows and Linux platforms.


If you are creating your own 3D printed medical models, please share your models with the Embodi3D community in the File Vault. If you have questions or comments, please leave a comment below or start a discussion thread in the Forums.


Sample free downloads


Male skull from CT scan

A Collection of Free Downloadable STL Skulls for you to 3D print yourself.



3D printable human heart in stackable slices, shows amazing internal anatomy.


Lumbar spine

A Collection of Spine STL files to download and 3D print.





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Dr. Mike


Hello, it's Dr. Mike here again with another tutorial on medical 3D printing. In this tutorial we are going to learn what types of medical imaging scans can be used for 3D printing. We will also explore the characteristics those scans must have to ensure a high quality 3D print. This is one of a series of 3D printing tutorials that will teach you how to create 3D printed anatomical and medical models yourself. Open source and commercial software are covered in the tutorials along with 3D printer selection and setup. This tutorial is followed by a tutorial on Creating 3D Printable Medical Models in 30 minutes using free software: Osirix, Blender, and MeshMixer.


Introduction to Selecting a Medical Scan for 3D Printing


If you listen to the hype in the press, it sounds like any medical imaging scan can be easily converted into a high quality 3D printed anatomic model, and any structure of interest can be shown clearly and beautifully. This is simply not true. In fact, most conventional medical imaging scans are not suitable for 3D printing. Those few that are suitable will probably only produce high-quality 3D prints of a few anatomic structures. In this tutorial I will go over the basic elements that make a medical scan suitable for 3D printing. I will briefly discuss different imaging modalities such as CT, MRI, and ultrasound. By the end of this tutorial you should be able to recognize whether a medical scan is suitable for 3D printing. If you are planning on having a medical scan done with the intention of 3D printing from the scan, you will be able to protocol the scan appropriately to enable a high quality 3D print.


Imaging planes


I'd first like to take a moment to discuss the standard imaging planes used in medical scans. When a medical scan is performed, images of the body are usually captured and displayed in one of three standard imaging planes. These are the transverse plane (also called axial plane), the coronal plane, and the sagittal plane. Figure 1 demonstrates these planes. In layman's terms, the axial plane divides the body into top and bottom, the coronal plane front and back, and the sagittal plane right and left. CT and MRI scans are typically comprised of several series of images. Each series is comprised of a stack of images in the same plane spaced out evenly. When a medical scan is converted into a format suitable for 3D printing, such as an STL file, the computer takes this stack of images and extrapolates the volume of an object. A surface is then calculated around that volume. That surface is what becomes the 3D printed model.


planes Of The body

Figure 1: Standard imaging planes used in medical scans. Source: National Cancer Institute


Imaging Modality: CT versus MRI versus ultrasound


In order to understand what scans are best used for 3D printing, a very basic understanding of the types, or modalities, of medical scans is needed. The medical physics behind how these scans work can literally fill volumes. Radiology residents are required to take board examinations on the physics and engineering of medical scanners as part of their training. I will attempt to summarize only the most critical information about medical scans into a few short paragraphs to get you up and 3D printing as quickly as possible.


Computed Tomography, or CT scans, are created when an x-ray beam is rotated around the patient. An x-ray detector on the opposite side of the emitter records the strength of the beam that emerges from the other side of the patient. Knowing the angle and position of the x-ray emitter and the strength of the beam emerging from the other side of the patient, a computer can calculate the x-ray appearance of the body in three dimensions. An x-ray beam is generally absorbed or deflected by electrons in matter. Since the density of electrons in matter is more or less the same as the actual physical density of matter, a CT scan can be considered to be a density map of the patient. Things that are dense, such as bone or metal, will appear white. Things that are not dense, such as air, appear black. Figure 2 shows how the different densities of tissue appear on a standard CT scan. When intravenous contrast is given, which contains an iodine-containing chemical that is very dense, it appears white. Fat is not very dense and floats on water, thus it has a blackish appearance.


What else floats on water? Choices: bread, apples, very small rocks, cider, gravy, cherries, mud, churches, lead, a duck. (This is a joke. If you get the reference, please leave a comment and give yourself a star).


CT Brain noncon labelled

Figure 2: Effect of tissue density on CT scan appearance. This CT scan image of the head at the eyes shows fat in the temporal fossa as black (red arrow), intermediate density brain tissue as gray (green arrow) and dense calcium-laden bone in the skull as white (blue arrow).


Magnetic Residence Imaging, or MRI, is a type of imaging that uses very strong magnetic fields to generate an image. The hydrogen atoms that are part of almost all biological structures (water, fat, muscle, protein, etc.) align with the magnetic field. Radio waves can be sent into the scanner causing the hydrogen atoms to flip orientation. When the radio waves are turned off, the hydrogen atoms flip back and emit their own faint radio signal. Based on analysis of these faint radio emissions and by varying the magnetic field strength and timing of the radio wave pulses, a variety of images can be generated. These different pulse sequences can be used to highlight different types of tissue.


Take Figure 3 for example. Four different pulse sequences are shown of the same slice of brain: T1, T2, FLAIR, and T1 with gadolinium contrast. On the T1 image tissues with fat are a bright white, as shown by the fat in the skin (white arrow). The hard, calcium-filled tissue of the skull is black, with the exception of a small amount of bone marrow which is gray in color and sandwiched between the inner and outer skull plate (yellow arrow). The watery cerebral spinal fluid in the lateral ventricles are black (red arrow). However, on the T2 image the watery cerebral spinal fluid is bright white (red arrow). T2 images show water very well. In addition to the water in the ventricles, swelling of the brain tissue due to an adjacent brain tumor can be seen as a white appearance (blue arrow). FLAIR images are similar to T2 images except pure water has been subtracted from the image. Thus tissue swelling (blue arrow) is still clearly visible but the cerebral spinal fluid in the ventricle (red arrow) now appears black. Finally, in the T1 images with gadolinium IV contrast small blood vessels are visible. Additionally, you can actually see the brain tumor and meninges turning white from contrast enhancement (purple arrows).


Brain MRI labelled 2

Figure 3: MRI of the brain at the same level using four different pulse sequences. The patient has a left frontal lobe brain tumor.


When 3D printing from an MRI scan, it is important to select images from a pulse sequence that will highlight the structure you wish to visualize. Arteries, tumors, body fluid, bones, and general tissue are all best seen on different sequences. If you choose the wrong imaging sequence to generate your 3D model from, you will encounter only frustration.


Ultrasound images are generated when soundwaves are sent into the body by an ultrasound emitter. The waves then bounce off various structures and are detected by a receiver, typically built into the emitter. The concept is similar to sonar that is used on ships and submarines. Based on the strength and depth of the soundwave return, an image can be created. Ultrasound images can be used for 3D printing, however it is very difficult to do so because individual images are not registered in a fixed place in space. The images are acquired by sliding the ultrasound transducer on the skin. The exact location in space and angle of the transducer at the time of image acquisition is not known, which makes generation of a 3D volume difficult or impossible. In general, ultrasound is not recommended as a source of imaging data for 3D printing for the beginner.


Key features of medical imaging scans used in 3D printing


There are certain features common to all scan modalities that can help you to create a good 3D print. When considering making a 3D medical or anatomic model you must first decide what you want the model to show. Should it show bones, arteries, or organs? Having a model with unnecessary structures included not only makes it more difficult to manufacture, but it also diverts attention away from the important parts of the model. Give this careful thought. Once you have decided what you want to show, evaluate the medical scan you want to create your model from carefully. If the scan doesn't have the proper characteristics, you can exponentially increase the difficulty of getting a 3D printable model from it.


1. Presence of Intravenous contrast


Take a look at these two axial (transverse) images from CT scans of the upper abdomen (Figure 4). Both images show slices of the upper abdomen at the level of the tops of the kidneys and liver. What is the difference between the two? You'll notice that on the rightmost scan the aorta is white, whereas on the left scan the aorta is gray. Figure 5 is a zoomed image of this region and shows this in more detail. This is because the rightmost scan was performed with intravenous contrast and that contrast is causing the aorta and other vessels to turn a bright white color.



Figure 4: The effect of intravenous contrast.


Aortas labelled

Figure 5: Close-up view of the abdominal aorta with (right) and without (left) intravenous contrast.


Take a closer look at the kidneys. Figure 6 shows a zoomed-in image. The outer part of both kidneys on the contrast-enhanced scan on the right are a light shade of color. This is due to blood mixed with contrast going into the outer cortex of the kidney. With the contrast-enhanced scan you can clearly see the edge of the kidney, even where it touches the liver. On the noncontrast scan the border of the kidney is only discernible where it is adjacent to the darker colored fat. Where it touches the liver it is difficult to see where the kidney ends and the liver begins. If you want to make a print of the kidney, it will be very difficult to discern the edge of the kidney without IV contrast.


Kidneys labelled

Figure 6: Close-up view of the right kidney with (right) and without (left) intravenous contrast.


If you are trying to create a 3D printed model of a bone, it is best to create it from a scan without IV contrast. This is because the bone is the only thing that will be a white color in the scan. This allows your software to easily separate the bones from other tissues. The presence of intravenous contrast may trick the software into thinking that blood vessels or organ tissue is actually bone, and it may improperly include these structures in the 3D printable surface model. These unwanted structures can be manually removed, but this can be an incredibly time-consuming and laborious exercise. It is best to avoid this problem in the first place.


On the other hand, if you are trying to 3D print a blood vessel, tumor, or organ, then intravenous contrast is absolutely necessary. Vessels and tumors will light up, or enhance, with IV contrast, turning white on a CT scan. Which will make separation of these structures from background tissue more easy to perform.


2. Timing of intravenous contrast


If you are creating a 3D printed model of a blood vessel, tumor, or organ, merely having intravenous contrast in your scan is not sufficient. You also must have the proper contrast timing. Contrast injected into a vein before a medical scan is not static. It is a very dynamic entity, and flows through the blood vessels and tissues of the body at different times before being excreted by the kidneys.


Intravenous contrast is injected through an IV catheter, typically in the arm immediately before initiation of scanning. The contrast flows with the blood into the superior vena cava, the large vein in the chest, and then into the heart where it is then pumped into the pulmonary arteries. It is at this point, typically about 15 to 20 seconds, that is the best time to perform a scan to clearly visualize the pulmonary arteries. The contrast-filled blood then flows out of the lungs back to the heart where it is pumped into the aorta and its branches. This may be about 30 seconds after contrast injection, and is the best time to see the arteries. The contrast-filled blood then percolates into the capillaries of the tissues throughout the body. This is the point of maximal tissue enhancement, and is usually the best time to see tumors and organs. The blood then leaves the tissues and drains back into the veins, which is the best time to look at the veins. Finally, after about five minutes or so, the contrast begins to be excreted by the kidneys into the urine, and can be seen within the collecting system of the kidneys, the ureters, and the bladder.


Take a look at Figure 7. When the scan was performed in the arterial phase (left) you can clearly see the aorta, arteries of the intestine, and outer rim (cortex) of the kidneys have turned white with contrast-enhanced blood (green arrows). After about five minutes the scan was repeated (right), and on these delayed phase images only a small amount of contrast is left within the aorta and blood vessels. However, contrast can be seen concentrated within the central portions of the kidney (red arrow). This is urine mixed with contrast collecting in the renal pelvis and ureter.


contrast delay labelled

Figure 7: Transverse (axial) images from a contrast-enhanced CT scan from a patient with intravenous contrast in the arterial (left) phase and delayed urographic (right) phase.


The point I'm trying to make here is that merely having intravenous contrast is not good enough. When the scan was taken relative to the contrast injection, in other words the timing of the contrast, is critically important to visualizing the target structure.


3. Oral contrast


In addition to intravenous contrast it is very common for oral contrast to be given prior to CT scans of the abdomen or pelvis. This is that nasty stuff that you are asked to drink about two hours before your scan. Oral contrast is designed to stay within the intestines so they can be clearly seen and evaluated. Take a look at Figure 8. In this CT scan of the abdomen intravenous contrast has clearly been given as the right kidney is white and enhancing (red arrows). Oral contrast has also been given, as several loops of small intestine can be seen filled with a substance that appears white on the CT scan (green arrows).


Unless you are trying to 3D print the intestines, for the most part oral contrast is something you do not want in your source imaging scans. If you are trying to separate out bones, organs, or blood vessels for printing, the presence of oral contrast will increase the likelihood that intestines will be accidentally included in your 3D printable model.


Oral contrast labelled

Figure 8: The effects of oral contrast on a CT scan of the abdomen.


4. Slice thickness


Take a look at these two CT scans of the chest (Figure 9). What is the difference between them? Both of them have IV contrast and both of them are showing the heart. Obviously, the scan on the right is of higher quality than that on the left, but why? The reason has to do with the thickness of the image slices. When CT scans are performed they are reconstructed into slices in the axial (transverse) plane. The axial plane is the plane that is parallel to the ground if you are standing upright. When the axial slices are stacked on top of each other the data can be used to create images in a different plane, such as when viewed from the front (the coronal plane), as in these example images. The axial slices that were used to create the coronal image on the left were 5 mm thick, whereas the axial slices used to create the image on the right were only 1 mm thick. You can see that the thick slices in the leftmost image generate structures with a very coarse appearance. If you try to 3D print an anatomic model from a scan with thick slices, your model will have a similar rough appearance. It is very important to use scans with thin slices, preferably less than 1.25 mm in thickness, when creating a model for 3D printing.


slice thickness

Figure 9: The effect of slice thickness on three-dimensional reconstructions.


5. Imaging artifact


Finally, take a look at these two CT scans of the face (Figure 10). What is the difference between them? The scan on the left clearly shows the teeth of the upper jaw as well as the bones of the upper cervical spine. The scan on the right however has white and black lines crisscrossing the mouth and obscuring the teeth. This type of artifact, called a beam hardening artifact, was created by metallic fillings in the teeth. When the CT scan was performed, the x-ray beam could not penetrate the metal fillings in the teeth to reach the detector. Subsequently, the scanner has no information about the x-ray appearance of the tissues along that x-ray path. When it generates an image from the x-ray data, the x-ray path with the missing information is shown as a white or a black line. The same phenomenon can be seen with any metallic object within the body, such as an artificial hip or spine fixation rods. If the scan on the right were converted to an STL file for 3D printing, the white lines would be 3D printed as well and the print would look as if sharp spikes were coming out of the mouth. Metallic objects also cause imaging artifact in MRIs. Metal on MRIs typically looks like a big black blob that obscures everything around it.


beam hardening

Figure 10: Two CT scans through the face and jaw. What is the difference between the two?


6. Reconstruction kernel


Take a closer look at the two CT scans of the face (Figure 10). In particular, look closely at the muscle and fat tissue of the neck. The scan on the left shows the muscle and fat tissue as being somewhat noisy. It has a granular type of appearance. On the rightmost scan however, the muscle and fat tissues appear rather smooth. This is because the two scans use a different type of reconstruction kernel. Think of the reconstruction kernel as equivalent to a sharpening or blurring function in Photoshop. The sharper kernel on the left shows the edges of the bones very clearly at the expense of causing a speckled appearance of the muscles and fat. The softer kernel on the right shows the muscle and fat more accurately, at the expense of causing the bones to have a more indistinct edge. Sharp kernels are used to make it easier to find hairline fractures and other difficult to detect abnormalities in the bones. However, for 3D printing smoother reconstruction kernels are generally best. Reconstruction kernel is primarily a factor only in CT scans.


kernel zoom labeled

Figure 11: Zoomed image from Figure 10 of the angle of the jaw. Note how the sharp kernel has much more clearly defined bone edges, but also has a speckled, noisy appearance to the soft tissues.
Final thoughts


So there you have it. In this tutorial we have gone over the main types of imaging modalities used for 3D printing (CT, and MRI), as well as six very important factors to consider with any type of imaging scan you are thinking about using for 3D printing. There is a saying when it comes to medical 3D printing: "garbage in, garbage out." No matter what your skill level or amount of available free time, if you start the 3D printing process with a problem-laden medical scan, you will encounter nothing but frustration and probably end up with a bad 3D model assuming you can make the model at all. Do yourself a favor and carefully evaluate your medical scan prior to sinking the time and energy into creating a 3D model from it.


I hope you enjoyed this tutorial and found it helpful. If you liked this article please look see my next to tutorial on Creating a 3D Printable Medical Model in 30 Minutes Using Free Software: Osirix, Blender, and MeshMixer. Additionally, you may wish to check out the Tutorials section of the website.


Also consider registering as a member. Registration is free and allows you to post questions and comments both for blog articles and in the discussion forums. Additionally, you can download free 3D printable models from the file library.


Below are a few 3D models to download. If you wish to follow the latest medical 3D printing news, you can follow Embodi3D on various social media platforms.


Thank you very much and happy 3D printing!


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Male skull from CT scan

A Collection of Free Downloadable STL Skulls for you to 3D print yourself.




3D printable human heart in stackable slices, shows amazing internal anatomy.


Lumbar spine

A Collection of Spine STL files to download and 3D print.

Dr. Mike


Summary: 3D printing is making rapid advances in many areas of medical treatment. In this article, I'll describe how I used recent advances in 3D printing to save a patient from having to have her spleen removed. In the process I broke some new ground in use of 3D printing in surgical planning. The clinical case and 3D printing advances are described in a recently published peer-reviewed paper in the medical journal Diagnostic and Interventional Radiology.


Intro image: The author using 3D printed vascular models in the OR.


A clinical conundrum
I am a board-certified interventional radiologist, and specialize in the minimally-invasive treatment of vascular (involving blood vessels) disorders. My adventure in 3D printing started when a very nice 62-year-old lady was referred to me by another doctor. A CT scan done for another reason had incidentally detected aneurysms in her splenic artery. The splenic artery is the major artery going to the spleen. An aneurysm is a bulging of the artery wall. Aneurysms are dangerous because as they grow they stretch the artery wall, causing it to thin. Like a balloon, the more the aneurysm stretches, the thinner the artery wall becomes, until the wall is too thin to hold back the pressure of the blood and the aneurysm bursts. This can lead to sudden, acute, life-threatening internal bleeding.


Figure 1. Examples of aneurysms. The thin, stretched out walls of the aneurysm predispose it to rupture. The larger the aneurysm, the greater the risk of rupture and bleeding. Source Drugline.org.


Medical convention states that when a splenic artery aneurysm is 2 cm or larger, it is at risk for rupture and should be treated. My patient had two aneurysms in her splenic artery, each of which was 2 cm in size. Something needed to be done. A third, smaller aneurysm was also present but it didn't need to be treated at this time. The conventional treatment in this situation is a surgical splenectomy, in which a surgeon, either in an open fashion or laparoscopically, physically removes the splenic artery with its aneurysms. Because the spleen cannot survive without its artery, it must be taken out too. The spleen plays a critical role in the body's ability to fight infections, so after removal of the spleen, patients are at higher risk for certain infections.



Video 1. Digital rendering showing the two large splenic artery aneurysms arising from the splenic artery. The aneurysm are the sphere-like bulges arising from a small artery in the middle of the aorta. The large trunk is the abdominal aorta. Rendering done with Blender.


An alternative treatment to surgical removal is splenic artery embolization. In this procedure, a vascular surgeon or interventional radiologist, such as myself, will make a needle puncture in the artery of the hip and navigate a small plastic tube, called a catheter, into the splenic artery using x-ray guidance. A series of small metallic threads, called coils because they coil up once deployed, are then pushed through the catheter into the splenic artery, where they plug up the entire artery. In principle, the technique is similar to putting hair down your bathroom drain. The hair takes up space and eventually plugs the pipe. In the same way, fine thread-like platinum coils can be pushed into the artery one at a time until the artery is plugged up. Any blood in the artery clots, and without any blood flow there is no pressure on the aneurysm wall and thus no risk of the aneurysms rupturing. Unfortunately, the lack of blood flow also causes the spleen to die from insufficient oxygen. The process of the spleen dying from lack of blood flow results in pain for a day or two. Also, without a functional spleen, these patients also are at higher risk for infections.


My patient was a very intelligent and determined individual. I explained both options to her in detail, but she would not accept either of the conventional treatments. She did not want to lose her spleen and be at increased risk of future infections. She challenged me to find a way to treat her aneurysms while saving her spleen. I reviewed the case and imaging studies with several of my colleagues, all board-certified specialists in treating this type of problem. Everybody said the spleen couldn't be saved. It was "impossible." She either had to have her spleen removed or her splenic artery embolized. Do nothing and it was just a matter of time until an aneurysm ruptured, probably killing her. I was greatly moved by my patient's doggedness. She wasn't willing to accept the limits of conventional medical treatment, so I didn't think I should either. I kept searching for solutions.


I was aware of some specialized catheter equipment that had been specifically designed to treat aneurysms in the brain. Brain aneurysm treatments are very delicate affairs. If an aneurysm in the brain ruptures, it can result in intracranial bleeding, stroke, permanent disability, or death. Brain aneurysms can be treated with placement of metallic coils through a catheter, as long as the coils are only placed in the bulging, aneurysmal part of the artery. There, they cause blood to clot in the aneurysm, which reduces pressure on the aneurysm wall and prevents it from rupturing. These special coils and catheters are designed to treat the aneurysm while preserving blood flow in the parent artery. Because these aneurysms are in the brain, any disruption in the blood flow of the parent artery will result in stroke.


aneurysm coiling

Figure 2: How coils can be used to treat aneurysms in the brain. Using specialized equipment designed for the brain, coils are used to pack the aneurysm while preserving blood flow in the parent artery. (Image source: wix.com)


Could the specialized coils and catheters designed to treat aneurysms in the brain work in the splenic artery? Nobody seemed to know. The patient's splenic artery had an unusually large number of loops, which would complicate any procedure. A search of the published medical literature did not produce any useful results. There were many variables that were different. I discussed my thoughts with the patient. I thought there might be a way to treat her aneurysms while sparing her spleen using this specialized brain aneurysm equipment. But the only way to know if the equipment would work would be to try it during an actual procedure. She gave me a puzzled look. "Well isn't there a way for you to practice?," she said.


For generations doctors faced with difficult and complex surgical procedures have really had only one true way to know if they will work: try it in a real surgery. We do everything possible to maximize our chance of success, such as ordering scans, consulting colleagues, reading research articles, and imagining the procedure over and over again in our heads. We try to know everything possible about the intended surgical procedure beforehand. But, the only way to truly know how things will go is to actually do it. There really wasn't any way to know how the brain catheter equipment would work in the spleen because nobody had ever done a procedure quite like this before. Yet, I kept thinking about my patient's statement. Why wasn't there a way for me to practice this beforehand?


Finding a solution with 3D printing
At that point I had been looking into uses for 3D printing in medicine for about a year. There seemed to be great potential, but at the time few people were using 3D printing in real patient care. I had designed a few simple 3D printable body parts from medical imaging scans. Would it be possible to 3D print a replica of my patient's splenic artery, and practice doing this complex procedure in the 3D printed model? I had never 3D printed an arterial structure of such complexity. Another search of the medical literature revealed that nobody else had either. I was further hampered by the fact that as a private practice doctor, I don't have access to an expensive 3D printer or the costly proprietary software that is needed to create complex 3D printable anatomic models. Nobody was paying me for my time or expenses. I needed to find a solution that was practical but inexpensive.


I invested hundreds of hours testing free and open source software packages to see if they could be used to generate the detailed 3D printed splenic artery model I needed. I eventually found that a combination of the software packages Osirix and Blender, the latter of which is typically used for computer animation, would allow me to design a detailed anatomic model from my patient's CT scan. I could then use the low-cost online 3D printing services Shapeways and iMaterialise to actually print my models. I paid for everything out-of-pocket. When the models arrived in the mail I couldn't believe it. They were precise full-scale replicas of the patient's splenic artery.


The 3D printed model

Figure 3: A precise 3D printed replica of the patient's splenic artery.
I contacted representatives from the companies that manufactured the brain aneurysm equipment. They had never heard of anybody testing their equipment in a 3D printed model before, but enthusiastically supported it. They donated real guidewires, catheters, stents, and coils for use in testing. Several came over to my house and we replicated the entire procedure inside the 3D model. During this testing I learned that some of catheters and wires would work well in the complex curves of the patient's splenic artery, and others would not. I was able to get all of the trial and error done in the model, something that otherwise would have taken place during the actual procedure. The model wasn't exactly the same as a real patient, but I was able to learn a lot about how the catheters and wires handled in the complex and unique geometry of the patient's splenic artery.



Video 2: Time-lapse footage of endovascular wire and catheter testing in the 3D printed model. Numerous problems were encountered with the difficult geometry of the splenic artery, but with trial-and-error a combination of wires and catheters was found that could handle the difficult geometry.


With the optimal set of catheters, wires, stents, and coils preselected, I subsequently did the real procedure on the patient. I completed all the necessary paperwork including getting approval from my hospital's research review board. I brought the 3D models into the operating room as a reference, and referred to them many times during the procedure. All of the preselected equipment worked beautifully, just as it had in testing. I was successful in putting coils in the aneurysms while preserving blood flow to the spleen. Even without having to try out different equipment combinations, the procedure was still very difficult and took five hours. If I hadn't had the ability to practice the procedure in the 3D printed model and preselect my equipment, it easily could have taken twice as long. That is, assuming I didn't collapse from exhaustion and dehydration before finishing it. More importantly, the opportunity to practice the procedure beforehand gave me confidence that I could be safe and successful in doing something that had never been done before. Nearly 2 years after the surgery, the aneurysms no longer a threat and the patient's spleen is fully functioning.


referring To 3D model In OR

Figure 4: Referring to the 3D printed models in the OR during the surgical procedure to correct the splenic artery aneurysms.


In The OR

Figure 5: positioning a small catheter into the splenic artery via a needle puncture in the arm.


3D Printing Lessons Learned
This experience fundamentally changed my perception about the value of 3D printing in medicine. For safe, easy, and routine medical procedures, 3D printing will probably not have much of an impact in the foreseeable future. It's too time consuming and costly to make 3D printed models. For complicated or high risk procedures, however, it can be invaluable. No doctor wants to take unnecessary risks or have a bad outcome in surgery. Unfortunately, there are many, many unknowns in surgery, particularly with complex and unusual cases. 3D printing an anatomic model before surgery to study and practice reduces those unknown variables, making risky cases much safer. After my experience, I have no doubt that 3D printing will have a significant impact in improving patient care in all fields of medicine.


It is my belief in the potential of 3D printing to help doctors and patients that led me to the creation of this website, Embodi3D.com. Embodi3D is a place where 3D printing enthusiasts can help each other in all fields of biomedical sciences. Members can read medical 3D printing news, ask technical questions in the forums, and even download complete 3D printable medical models from the File Vault. There are several tutorials on how to start 3D printing medical models yourself. Everything on the website is free. I ask only that you give back to the community through comments, advice, and sharing of 3D models, if you are able.


Below are two 3D printable models used in actual testing. You can download the models yourself for free.


Download the FREE solid, splenic artery aneurysm lumen model. This is the solid model that shows the hollow space inside the artery (the lumen).


Download the FREE hollow splenic artery aneurysm model. This is the hollow model that the catheters and wires were tested in.


You can read the official peer-reviewed account of this 3D printing advance in the medical research journal Diagnostic and Interventional Radiology here.


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Other Free STL Downloads


Male skull from CT scan

A Collection of Free Downloadable STL Skulls for you to 3D print yourself.


3D printable human heart in stackable slices, shows amazing internal anatomy.


Lumbar spine

A Collection of Spine STL files to download and 3D print.

Dr. Mike


I have received several requests for spine STL files from CT scans and these files have been added to the file vault over time as more people are 3D printing vertebrae for medical moldeling. There was a really good response to my last article about the wonderful 3D printable skull models available for free download on the embodi3D.com website. So, I've decided to do another article about spine models.


Embodi3D.com contains a large collection of spine STL files within the Spine and Pelvis category of the Downloads area. These 3D printable files are available for download by registering an account. The vast majority of files are available for free download.


The spine is a very complicated anatomic structure. Some spinal bones, or vertebrae, are designed for flexibility, as in the cervical spine in the neck. Others are designed to support ribs, as in the thoracic spine in the chest. The lumbar spine, in the low back, has large, hearty vertebra that are designed to bear weight. The spine is the focus of many maladies, and a good anatomic understanding of the spine is needed before disease processes and their treatments can be fully understood.


I personally do many procedures on the spine. A few include lumbar punctures, epidural steroid injections, selective nerve root blocks, vertebroplasty, kyphoplasty, myelograms, lumbar drain placements, chemotherapy infusions, and biopsies of all kinds. Anatomy can be learned with books or pictures, but there is nothing quite like holding a 3D printed medical model in your hands to make that anatomy "click." 3D printed spine models can help teach spinal anatomy to all levels of students, from grade school to med school. To help others find the best medical models, I have put together a collection of the best 3D printable spine models available for free download on Embodi3D. I hope you find this collection useful and interesting.

Lumbar Spine STL Files from CT Scans

lumbar spine 1

Whole lumbar spine and sacrum


L3 Lumbar vertebra

Another L3 Lumbar vertebra


L4 Lumbar vertebra

Lumbar spine wedge compression fracture

Thoracic Spine STL Files For 3D Printing

T spine

Whole thoracic spine

Cervical Spine STL Files For Medical Models


Whole cervical spine

cspine with skull

Whole cervical spine with skull base


C1 (atlas) vertebra

Dr. Mike


A lot of great 3D printable anatomic files have been shared on Embodi3D in the past few years. One of the most popular categories is skulls. There are many files available, and they are organized under Skull and Head STLs in the file Downloads area of the site. You can download any of these files by registering an account and in most cases the files are free to download.


Below I created a list of my favorite skull files for your learning and enjoyment.

These 3D printable skull models are a fantastic resource for education and show both normal anatomy and disease and injury. Thanks to the generosity of our contributors, all of these models are available for free download and 3D printing.

This a diverse set of files ready for 3D bioprinting. These STL skull files come from CT scans and demonstrate some of the pathology physicians encounter. Several different cuts and individual bones make much of the anatomy easily accessible which is great for education.

I hope you enjoy this collection. If you are using these skull files for an interesting project, please share your experiences with the community by posting a comment.

skull 1

3D printable skull 1 - front tooth out, from Dr. Gobbato

Male skull from CT scan

3D printable skull 2 - Male skull

skull 3

3D printable skull 3 - from Dr. Marco Vettorello

Face fracture 1

Skull fracture 1 - fracture of frontal bone

Jaw fracture

Skull fracture 2 - fracture of mandible (jaw bone)

post craniotomy

Skull after craniotomy surgery (with surgical hole drilled into it)

half skull sagittal

Half skull (sagittal cut) great for education

skull base

skull base, showing foramina, for medical education

lace skulls

Full and half size "Lace" skulls. A unique item for your desk.

frontal bone

Frontal bone of skull (forehead bone)


Mandible (jaw bone)

Dr. Mike


Hello and welcome back. Once again, I am Dr. Mike, board-certified radiologist and 3D printing enthusiast. Today I'm going to show you how to correct severe mesh defects in a bone model generated from a CT scan. This will be in preparation for 3D printing. I'll be using the free software programs Blender and Meshmixer.

In my last medical 3d printing video tutorial, I showed you how to remove extraneous mesh within the medullary cavity of a bone. That technique is best used when mesh defects are limited. In instances where mesh defects in a bony model are severe and extensive, a different approach is needed. In this video, I'll show you how to correct extensive mesh errors in bony anatomical models using Blender and Meshmixer. This assumes that you know how to generate a basic STL file from a CT scan. There are a variety of commercial and freeware products that allow you to do this, on a variety of platforms. If you don't yet know how to do this, stay tuned, as I have a series of tutorials planned which will show you how to do this on a variety of operating systems and budgets.

If you wish to follow along with this tutorial, you can download the free tutorial file pack by clicking this link. This is highly recommended, as the files allow you to follow along with the tutorial, which will make learning easier. Included is the STL file used in this tutorial. Also, a powerful Blender script is included which will enable you to easily and efficiently prepare your own bone models for 3D printing. It's a real timesaver. If you haven't registered at Embodi3D.com, registration is free and only takes a moment.


You can watch the video tutorial for a quick overview, or read this article for a detailed description.

Initial analysis using Meshmixer

Let's take a look at an STL file of a talus fracture in the ankle. This 3D model is from a real patient who suffered a fracture of the talus. The talus is the bone in the ankle that the tibia, or shinbone, sits on. This STL file is included in the file pack. Let's open this file in Meshmixer (Figure 1). Meshmixer is free software published by Autodesk, a leading maker of engineering software. If you don't have Meshmixer, you can go to Meshmixer.com and download it for free.

Figure 01   ankle mesh errors

Figure 1

Once you have the file open in Meshmixer, click on the Analysis button and select Inspector. The inspector shows all the errors in this mesh. Blue parts represent holes in the mesh. Red parts show areas where the mesh is non-manifold. Magenta parts show disconnected components. As you can see, there are a lot of problems with this mesh, and it is not suitable for 3D printing in its current state (Figure 2).

Figure 02 ankle mesh errors displayed

Figure 2

Meshmixer has a feature to automatically repair these mesh defects. However, there are so many problems with this mesh that the auto repair function fails. Click on the Auto Repair All button. Meshmixer has tried to repair these mesh defects, and has successfully reduced the number of defects. However, it is also introduced gaping holes in the model. Entire bones are missing (Figure 3). This clearly isn't the desired outcome.

Figure 03 Meshmixer autorepair

Figure 3

Opening the STL file in Blender

The solution to this problem can be found with Blender. Blender is a free, open-source software package that is primarily designed for animation. It is so feature-rich however, that it can be used for a variety of different purposes, and increasingly is being used for tasks related to 3D printing. If you don't have Blender, you can download it from blender.org. At the time of this writing, the current version is 2.73 a.

Open up Blender. Go ahead and delete the default cube shown in the middle of the screen (Figure 4) by right clicking it and hitting the "X" key followed by the "D" key. If you are new to Blender, you'll soon learn that much of what you can do with Blender can be done with keyboard shortcuts. This can be daunting to learn for beginners, but makes use of Blender very efficient for heavy users.

Figure 04 Blender start screen

Figure 4

Next open the STL file in Blender. Go to the File menu in the upper left, select Import, and select "Stl (.stl)." Then, navigate to the folder for the tutorial files and select the "ankle - talus fracture.stl" file. You probably don't see anything, as is shown in Figure 5. To understand how this happens, you need to know a little bit about how Blender measures distances. Blender uses an arbitrary measure of distance called a "blender unit." One blender unit is equivalent to one of the little squares seen in the viewport. However, in real life distances are measured in real units, such as feet, inches, centimeters, and millimeters. Most STL files that are generated from medical imaging data have default unit of measurement of millimeters. When Blender imports the file it converts the millimeter units to blender units. Since our imported model is the size of human foot, measuring 240 mm or so, the model will be 240 blender units, or 240 of those little squares, in length. We can't see it because the model is too big! Our viewport is zoomed into much! Zoom out using the mouse wheel way, way back until you can see the model as shown in Figure 6.

Figure 05 where Is The model

Figure 5: Where is the model?

Figure  06 there It Is

Figure 6: There it is!

Correcting the Object Origin

You will notice that the origin of the ankle object, as shown by the red blue and green axes (Figure 6), is actually outside of object itself. Left uncorrected, this can be a really annoying issue. When you rotate or pan around the object, you will rotate or pan around these three axes, instead of the ankle object itself. Fortunately, correcting this takes only a moment. In the lower left-hand part of the window select the Object menu. Be sure that you have the ankle object selected first. Then choose Transform, Geometry to Origin. The ankle object is then moved to the red blue and green axes. With the object origin now in the center of the mesh, the mesh will be much easier to work with.

Figure 07   Geometry To origin

Figure 7: The ankle mesh and object origin are now aligned.

Inspect the ankle mesh

If you look closely at the ankle mesh you can see immediately that it has a lot of problems. In the solid shader mode, the bones look very faceted. The polygons are large, giving the bones a unnatural appearance (Figure 8). Don't worry, will fix this. If you turn on wireframe mode by hitting the "Z" key you can see that there is a lot of extraneous mesh within the bones that represents unwanted mesh from the medullary cavities of these bones (Figure 9). Furthermore, if you check for non-manifold mesh by holding control-shift-alt-M, you'll see that there are innumerable non-manifold mesh defects (Figure 10).

Figure 08 faceted bones

Figure 8: Note the very faceted appearance of the bones.

Figure 09 unwanted mesh

Figure 9: There is a significant amount of unneeded and extraneous mesh, particularly within the medullary cavities of the bones.

Figure 10 Non manifold defects

Figure 10: Non-manifold mesh defects.

If you are unfamiliar with the term "non-manifold," let me take a moment to explain. A mesh is simply a surface. It is infinitely thin. If the mesh is continuous and unbroken, and has a contained volume within it, then the mesh can be considered to represent something solid. In this case, the mesh surface represents the interface between the inside of the object and the outside of the object, such as the sphere shown in Figure 11. An object like this is considered to be "manifold," or watertight. It represents a solid that can really exist in the physical world, and can thus be 3D printed.

Figure 11 A sphere

Figure 11

If however, I cut a hole in the sphere, as shown in Figure 12, then there is a gap in the mesh. A 3D printer won't know what to do with this. Is this supposed to be solid like a ball, or hollow like a cup? If it is supposed to be like a cup, how thick are the walls supposed to be? The walls in this mesh are infinitesimally thin, so what is the correct thickness? This mesh is not watertight - that is, should water be placed in the structure it would leak out. The mesh is non-manifold. It cannot be 3D printed. If we use the control-shift-alt-M sequence to highlight non-manifold mesh, as shown in Figure 13, we can see that Blender correctly identifies the edge of the hole as having non-manifold mesh.

Figure 12 Non manifold sphere

Figure 12

Figure 13 Non manifold sphere errors shown

Figure 13

Closing major holes manually in Blender

In this particular mesh, there are many, many small mesh errors and two very large ones. The distal tibia and fibula bones have been cut off by the CT scanner, leaving gaping holes in the mesh as shown in Figure 14. Fixing these manually will only take a moment and make things easier down the road, so let's take care of that now. Enter Edit mode by hitting the Tab key, or clicking it in the Mode menu. If you hit control-shift-alt-M to select non-manifold edges, you can clearly see that these bone cuts are a problem as shown in Figure 15.

Figure 14 tibia And fibula defects

Figure 14

Figure 15 nonmanifold

Figure 15

Go to Vertex selection mode by clicking the vertex button or hitting control-tab-1 on the keyboard as shown in Figure 16. Select one of the vertices from the medullary portion of the tibia bone as shown in Figure 17. This mesh represents the medullary cavity of the tibia bone, and is not connected to the rest of the mesh. Hit control-L to select all contiguous vertices (Figure 18). All the unwanted medullary cavity mesh should now be highlighted. Delete this by hitting the "X" key followed by the "V" key, or by hitting the delete and selecting "vertices." There is another small bit of medullary cavity mesh at the edge of the tibia cut. Perform the same routine and delete this as well.

Figure 16 vertex selection mode

Figure 16

Figure 17

Figure 17

Figure 18

Figure 18

Next we will direct our attention to the unwanted medullary mesh of the thinner fibula bone. Click on a vertex in the fibula medullary mesh and hit control L. You will note that the entire mesh is highlighted as shown in Figure 19. This indicates that the medullary mesh is connected to the rest of the mesh in some way. We don't need to manually delete all of the medullary mesh. We just need to get it away from the edge where we will create a new face to close the bone edges. Go to Edge selection mode by hitting control-tab-2 or clicking the edge selection button as shown in Figure 20. Hit the "A" key to unselect everything. Then, click on a single edge along the unwanted medullary mesh, as shown in Figure 21.

Figure 19

Figure 19

Figure 20 edge selection mode

Figure 20

Figure 21

Figure 21

Next we will by holding down the alt key and right clicking on the edge again. Blender should select the loop around the entire edge as shown in Figure 22. We will now expand the selection by holding down the control tab and hitting the plus key on the number pad. Hit the plus key three times. Your selection should now look like that in Figure 23. Delete the highlighted mesh by hitting the "X" and "V" keys, or hitting the delete key and selecting vertices.

Figure 22

Figure 22

Figure 23

Figure 23

Next we are going to close the holes by holding down the alt key and right clicking along the edge of the cut line of the fibula. An entire loop should be selected as shown in Figure 24. Create a face by hitting the "F" key. Convert to triangles by hitting Control-T. The end of the fibula should be closed, as shown in Figure 25. Repeat the same for the open edge of the tibia bone. Afterwards the mesh should look as it does and Figure 26.

Figure 24

Figure 24

Figure 25

Figure 25

Figure 26

Figure 26

Creating a Shell of the model using the Shrinkwrap and Remesh modifiers in Blender

So how will it ever be possible to correct the hundreds and hundreds of mesh errors in the ankle model? This is the million-dollar question. A mesh of this complexity often cannot be fixed using automated mesh correction software, as we saw with Meshmixer. Correcting this many errors manually is a time-consuming and tedious process. I've spent hundreds of hours correcting mesh errors like this one by one. But, after years of creating 3D printable anatomical models, I've developed a technique to fix these mesh errors in only a few minutes.

The secret is this: You don't fix the mesh errors. Leave them alone. You create a new mesh to replace them!

Let's start by creating a sphere. If you are in Edit mode, exit that by hitting the Tab key. If you are still in wireframe viewport mode, hit the "Z" key to return to solid viewport shading. In the lower left-hand side of the window, hit the Add menu. Select Mesh, UV sphere and add a sphere. An "Add UV Sphere" panel will show up on the left side of your screen as shown in Figure 27. We want the sphere to have lots of detail. Under Segments enter 256. Under Rings, enter 128. The default size of the sphere is only one blender unit (1 mm) in size. This is too small, we want the thing to be huge. Enter 1000 for size. At this point you should have a very large sphere surrounding your entire scene. Believe it or not, this sphere will eventually be your new ankle object. Let's go ahead and rename it "Ankle skin" as shown in Figure 29.

Figure 27 Add UV sphere

Figure 27: Add a UV sphere

Figure 28 configure UV sphere

Figure 28: Configure the sphere. Segments 256, rings 128, size 1000

Figure 29 rename Ankle Skin

Figure 29: Rename the sphere to "Ankle skin"

Applying the Shrinkwrap Modifier

Select the "Ankle skin" object. Click on the Modifiers tab, it looks like a small wrench (Figure 30). From the Ad Modifier drop-down menu, select the Shrinkwrap item. Specify the Ankle object as "the target. Set off set to 0.5. Check the" Keep Above Surface" box. Your sphere will have shrunken down to envelop the ankle, as shown in Figure 30. Apply the modifier by hitting the "Apply" button. At this point you're thinking that your Ankle skin object hardly looks like an ankle, and you're right. If you try to apply the shrinkwrap modifier again, you won't get any change in the mesh. Blender has shrunken the sphere as best it can given the limited geometry of the sphere. To go further we need to change the geometry a bit, which is where the Remesh modifier comes in.

Figure 30 shrinkwrap modifier

Figure 30: The Shrinkwrap modifier

Applying the Remesh Modifier

Next go to Add Modifier again, and select Remesh. Set Mode to Smooth, Octree Depth = 8, and uncheck Remove Disconnected Pieces. By now you should have something that looks like Figure 31. Apply the modifier by clicking the Apply button.

Figure 31 remesh modifier

Figure 31: The Remesh modifier

Apply the Shrinkwrap Modifier again

Apply the shrinkwrap modifier again, using the same parameters as before. Your Ankle skin object should look like Figure 32. Now we are getting somewhere! There is still a long way to go, but the mesh somewhat resembles the bones of the foot. By repeatedly applying the Shrinkwrap and Remesh modifiers the Ankle skin object, which was originally a sphere, will slowly approximate the surface of the error-filled original ankle mesh. Because of the original skin was a sphere, and hence manifold, as it is shrink-wrapped around the ankle mesh it will preserve (for the most part) it's mesh integrity. There will be no unnecessary internal geometry. Any holes or other defects in the original mesh will be covered. Unfortunately, repeatedly applying the shrinkwrap and remesh modifier again and again is somewhat tedious (although not as tedious as manually correcting all the errors in the original mesh). Fortunately, we can automate this process using Python scripting. This allows us to create a new mesh in a matter of minutes.

Figure 32 shrinkwrap again

Figure 32

Automating the Shrinkwrap Process using Python Scripting

For those of you less familiar with Blender's more advanced features, you may be surprised to learn that it is fully scriptable. That means that you can program it to perform tasks repeatedly using a Python script. In this case we want to repeatedly execute shrinkwrap and remesh modifiers on our ankle skin object. With each iteration the skin will more closely approximate the surface of the original mesh. If you are familiar with Python scripting, you can write a script yourself to call the necessary modifiers and specify the necessary variables. To make things easier for you, I have written a Python script for you. It is included in the free tutorial file pack.

Change the bottom window to the text editor. View button in the bottom left-hand corner as shown in Figure 33. Select Text Editor. Click on the "Open" button and navigate to the folder with the tutorial file pack files as shown in Figure 34. Double-click on the "shrinkwrap loop.txt" file as shown in Figure 35.

Figure 33 select text editor

Figure 33: Select the text editor

Figure 34 open The script file

Figure 34: Click on the Open button

Figure 35 shrinkwrap loop

Figure 35: Open the "shrinkwrap loop.txt" file

The script file should now open in the text editor window. Adjust the target_object variable to be the target you want your skin wrapped around, in this case the "Ankle - Talus Fracture" object. Leave the shrinkwrap_offset variable at 0.5 for now. You can specify how many shrinkwrap-remesh iterations you want to run. For now leave it at 20. Click the "Run Script" button as shown in Figure 36. The script will now run, and it will apply the shrinkwrap-remesh modifiers 20 times. On my machine it takes about one minute for the script to execute.

Figure 36 configure The script

Figure 36

At this point you'll notice that the ankle skin object very closely approximates the original ankle object, as shown in Figure 37. Run the script again using the same settings. At this point the mesh is really looking pretty good. Let's run the script a final time with the smaller offset to more closely approximate the real bones. Set the shrinkwrap_offset variable to 0.3 and run the script again reducing iterations to 10. After completion the mesh should appear as it does in Figure 38. If you compare our new skin mesh as shown in Figure 39 (left) to the original ankle object in Figure 39 (right) you can see that our new skin is actually much more realistic than the original mesh. The highly faceted appearance of the original mesh has been replaced by a smoothed appearance of our shrink-wrapped skin. Furthermore, whereas the original mesh actually had separate bones that were disconnected, the new, shrink-wrapped mesh is a single interconnected object. From a 3D printing standpoint this is much better as the ankle bones will print together as a single unit

Figure 37

Figure 37

Figure 38

Figure 38

Figure 39

Figure 39: Comparison of original plus new shrink-wrapped mesh.

Finalizing the Ankle Model for 3D printing using Meshmixer.

Select the new ankle object. Export the object to the STL file format. From the file menu select Export and then "Stl (.stl)." Let's call the file "ankle corrected.STL." Open the new STL file in Meshmixer. You will notice that Meshmixer immediately identifies some mesh errors as shown in Figure 40. This is because the Remesh modifier in Blender occasionally introduces non-manifold mesh defects. You will note however that the number of defect is significantly less than our original model which was shown in Figure 1. With this smaller number of errors, Meshmixer can fix them automatically. Go to the Analysis button and select Inspector. Meshmixer will highlight the individual mesh defects, as shown in Figure 41. Click on the "Auto Repair All" button. Meshmixer will then automatically repair the mesh defects. The result is shown in Figure 42.

Figure 40

Figure 40

Figure 41 Meshmixer inspector.JPG

Figure 41: Meshmixer inspector

Figure 42.JPG

Figure 42: Corrected mesh

The mesh looks great, and is ready for 3D printing! Export the STL file by going to the File menu in Meshmixer and selecting Export. Save the file as "ankle final result.STL".

Please share with the community.

If you have found this tutorial helpful and are actively creating 3D printable anatomic models, please consider sharing your work with the Embodi3D community. You can share your models in the File Vault. If you have comments or advice, you can share your expertise in the Forums. If you are interested in blogging about your adventures in medical 3D printing, contact me or one of the administrators and we can set up blogging on your Embodi3D user account. If you wish to hire someone to help you with your anatomical 3D printing project, you can place an ad for free in the Services Needed Forum, If you are doing your own anatomical 3D printing and are willing to help others, list your services for free in the Services Offered Forum.

This is a community. We are all helping each other. Please consider giving back if you can.

Have fun 3D printing!

Dr. Mike


Summary: This is an advanced tutorial and assumes that you already know how to create STL files from CT scans. If you do not yet know how to do this, stay tuned, as a series of tutorials is planned on this website. Here we will use a free, open-source software package Blender to repair and correct a bony pelvis and lumbar spine model generated from a CT scan. If you would like to follow along with this tutorial, you can download the relevant Blender and STL files here, and follow along.


UPDATE: If you have very extensive mesh errors in your model, you can read my other medical 3D printing tutorial on how to repair mesh errors quickly using Blender.

You can watch the YouTube video for a high-yield introduction, but also read this page for additional details.


Background on the Problem

Before we dive in, let's take a moment to discuss what the medullary cavity of a bone is and why it's a problem if you're trying to 3D print bone models made from a CT scan. Bones are not solid, even though they may appear to be so. Most bones have a very hard, very dense outer layer comprised of cortical bone. This tough outer part of the bone is very hard and is what gives bones their strength. The inner core of most bones contains fatty bone marrow, and is made of much softer bone that is less dense, called spongy bone. On a CT scan you can see these two different types of bone. Take this CT scan of the pelvis, for example.

Figure 1

Figure 1

In the CT scan image shown in Figure 1, the hard, dense cortical bone is seen as a bright white outer surface of these pelvic bones. The white color indicates that it is very dense. The spongy bone, which is less dense and contains fatty bone marrow, can be seen in the center of the iliac bones and sacrum on this image. This type of bone is not white, but is a grayish color on a CT scan image. In some areas it is approaching black in color, which means is not very dense at all. Outside the bone we can see muscle represented by this light gray color, and intra-abdominal fat which is represented by this dark gray color.

Figure 2

Figure 2

If we measure the density of these bones in Hounsfield units, which is the unit of density that is measured on a CT scan, we can see that the dense cortical part of the iliac bone in this image measures 768 Hounsfield units, and is shown in the rightmost red circle (Figure 2). The less dense medullary bone within the sacrum measures 1.7 Hounsfield units, as shown within the red circle in the middle. If we measure the muscle in the gluteus maximus area, this measures 51 Hounsfield units, as shown in the red circle on the left. So in this case the medullary bone is actually less dense then muscle around it. How can bone be less dense than muscle? Because it is filled with fatty bone marrow. Remember, fat floats on water, and is thus less dense than water. (What also floats on water? A duck. But that is another story...) In Figure 2, the green circles represent the area of interest that is being measured. The text and red circles represent the measurements for the those areas of interest.

The fact that medullary bone and bone marrow is not dense causes a problem when we are trying to convert CT scan data into a digital model that is 3D printable. This is because algorithms designed to select the bone from all the other stuff in the body, such as fat, muscle, air, etc), use density as a means to identify the bones. Here's an example of the 3D model of the pelvis and lumbar spine created from the CT scan we were just looking at. If you look closely at Figure 3 you can see there's a lot of internal geometry within the bones that is not desired (red circles). This extra geometry can cause problems when the file is sent to 3D printer or 3D printing service. The model may be rejected because of characteristics of this internal medullary space, for example there may be thin walls and automated quality checkers may flag the model as unprintable. Furthermore, if you try to perform certain manipulations on the mesh, such as Boolean operators, this unwanted mesh may cause these operations to fail. If we want to 3D print our bone models, it is best to get rid of extraneous and unwanted mesh.

Figure 3

Figure 3

Getting started on cleaning your mesh in preparation for 3D printing.

1) Start by importing your STL file into Blender. If you don't have Blender, it is available for free at http://www.blender.org. Blender is available in Windows, Macintosh, and Linux versions. Be forewarned. Although Blender is powerful, it takes a little bit of time to get used to it. Be patient. Open Blender and select File -> Import -> Stl (stl) as shown in Figure 4. If you are following along with this tutorial using the tutorial files, select the "Pelvis and Lumbar spine, uncleaned.stl" file.

Figure 4

Figure 4

You will find that the mesh appears quite large. This is because Blender uses an arbitrary unit of measure for distance called a Blender Unit. The way that STL files are interpreted, one Blender unit is equivalent to 1 mm, thus the model appears quite large. Use the scroll wheel on your mouse to zoom out. If you want, you can re-size your mesh by hitting the S key.

You may also find that your mesh appears clipped, as shown in Figure 5. This is because by default Blender uses a clipping distance of 1000 by default for the view, clipping any objects in the scene too far from the camera. This is easily fixed. View the Properties bar by clicking the "+" in the upper right corner, as shown by the red circle in Figure 5. Or, you can type N to show the Properties panel. Then under View, type 100,000 in the Clip: End field, as shown in Figure 6.

Figure 5

Figure 5

Figure 6

Figure 6

2) To identify where you have extraneous mesh, you must first go to Edit mode. Before doing this, make sure you have selected your model by right clicking it. The model should be surrounded by a yellow halo, which indicates that it is selected, as shown in Figure 7.

Figure 7

Figure 7

Enter Edit mode by hitting the Tab key, or by selecting Edit mode from the Mode button, located on the bottom left toolbar, as shown in Figure 8. Use the Z key to toggle between types of viewport shading. You can also use the viewport shading button in the bottom toolbar as shown in Figure 9. Select Wireframe viewport shading.

Figure 8

Figure 8

Figure 9

Figure 9

3) Use the scroll wheel to zoom in and out, and the middle button to pan about. Zoom into the L3 vertebral body (3rd lumbar vertebral body. If you need a refresher on lumbar anatomy, check out Wikipedia). As was shown in Figure 3, there is excessive mesh in the medullary cavity of the bone that is persistent within the model. We want to remove it.

How this extra mesh got here has to do with the original CT scan and how the surface STL model is generated from CT scan data. If you look at the original CT scan of this vertebral body, as shown in Figure 10, you can see very small perforating holes within the posterior part of the vertebral body, as shown by the red arrows. These are nutrient foramina. They are tiny holes in the bone that allow arteries to penetrate through the thick outer cortex and into the medullary cavity, supplying blood to the bone marrow. When the surface generating algorithm creates the STL file from the CT scan, it finds its way from the surface into the nutrient foramina and maps the internal medullary cavity of the bone. Essentially, the algorithm determines that the bone is hollow, and has a connecting tunnel between the surface and the hollow interior, as shown in Figure 11. This is actually true, but for the purposes of 3D printing we are not interested in extremely complex geometries within the medullary cavities of the bone. For practical purposes of 3D printing we wish the bones to be solid, even though in nature they are not.

Figure 10

Figure 10

Figure 11

Figure 11

4) The easiest way to delete the medullary mesh is to identify where the mesh is connected to the surface via these nutrient foramina. To do this, inspect the mesh carefully using Wireframe viewport shading, which should give you an idea of where these connecting tunnels are located. Once you have identified the area, use the lasso tool by holding down the CTRL key and left clicking a loop around the area of interest, as shown in Figure 12. You must be in Wireframe viewport shading in order to make the selection. If you are in Solid viewport shading, you will only select the surface elements. Also, make sure you are in vertex selection mode. The three selection modes (Vertex, Edge, Face) are shown circled in red on the bottom toolbar in Figure 12.

Figure 12

Figure 12

5) Once you have selected the mesh elements of interest, you will hide the non-selected mesh elements. This simplifies your view and also reduces the processing time needed by the computer to display the image to you in real time. With large data sets, such as those collected by CT scans, even a powerful desktop system can become very sluggish when the entire mesh is displayed and manipulated at once during editing. Hiding temporarily unneeded mesh saves a lot of time.

6) With your mesh elements of interest selected in orange as shown in Figure 12, hold down the control key and hit the "I" button. This inverts the selection, as shown in Figure 13. Next, hide the selected mesh by hitting the "H" key. You should now have a very limited amount of mesh displayed, as shown in Figure 14.

Figure 13

Figure 13

Figure 14

Figure 14

Rotate the mesh to a different orientation and then select your target mesh, invert the selection, and hide the inverted selection again. At this point you should have a very small amount of mesh that you are focusing on, such as that shown in Figure 15.

Figure 15

Figure 15

7) Now that your visible mesh is small enough to work with, switch back to Solid viewport shading using the viewport shading box in the lower toolbar, or by hitting the "Z" key. Zoom in and identify where the nutrient foramina are present on the surface of the bone. Go to face selection mode using the face selection button on the bottom mouth bar or by hitting CTRL-TAB-3. Using the right mouse button to select a face near the opening of the nutrient foramen. Using the CTRL key and right mouse button, select a loop of face is completely around the foramen, as shown in Figure 16. Make sure you select an entire loop of faces around the hole. You want to complete cut it away from the surface.

Figure 16

Figure 16

Now delete this selection. Hit the delete key, and select Faces (or hit the delete key followed by the F key). You should now have a hole in your mesh, and the tunnel between the surface and the medullary mesh has been cut completely. Double check to make sure there are no stray edges or face still connecting the two parts.

8) Now we are going to close the hole. Go to Edge the selection mode using the button in the lower toolbar or by hitting CTRL-TAB-2. Holding down the ALT key, right-click on one of the edges abutting the hole. Blender should select the entire circumference of the hole, as shown in Figure 17. Next, fill in a face using the F key. A face should appear. Convert this face to triangles by hitting CTRL-T. if you want to smooth out the mesh, you can take an extra step and apply local smoothing by hitting W followed by O. Your hole should be filled in and smoothed, as shown in Figure 18.

Figure 17

Figure 17

Figure 18

Figure 18

Repeat steps 6 through 8 for each nutrient foramen tunnel connecting the surface to the medullary cavity.

9) When you have finished making all the edits to your viewable mesh, it is time to unhide the hidden mesh that comprises the bulk of your model. Hit Alt-H to unhide all the hidden mesh. Most of it will be selected. Hit the A key to unselect all. The A key toggles between select all and select none.

10) Once you have determined that all tunnels between the surface and medullary cavity have been deleted and filled, it is time to delete the entire block of medullary mesh in one operation. Make sure you are in edit mode, with wireframe viewport shading. Using the right mouse button, select a vertex from the medullary block mesh, as shown in Figure 19.

Figure 19

Figure 19

We are now going to select every vertex that is connected to this single vertex. Because the entire medullary mesh is disconnected from the rest of the model, the remainder of the model should not be selected. Hit the CTRL-L key to select all contiguous vertices. You should find that only the unwanted medullary mesh is selected, as shown in Figure 20. Hit the delete key, followed by "V" for vertices, and the entire block of unwanted medullary mesh will be deleted at once. Wow! That was gratifying! After all that work you have probably deleted several thousand unwanted vertices in one swoop.

Figure 20

Figure 20

Figure 21

Figure 21

Your target bone, in this case L3 -- the third lumbar vertebra -- should now be free of unwanted medullary cavity mesh. You can repeat this process for each medullary cavity in your model. In the particular model that accompanies this tutorial, that would be L4, the bilateral iliac boness, sacrum, and a few other places. It can be a time-consuming process, but with practice even a complex model with tens of thousands, or millions of faces can be cleaned in a few hours.

I hope you found this tutorial helpful. If you have questions, please leave a comment below. If you are making 3D anatomic models from medical scan data, please consider sharing your creations with the Embodi3D community. Embodi3d is a community of biomedical 3D printing enthusiasts. We are all trying to help each other, and by sharing your models you can contribute greatly to the community.

Here are a few examples of 3D printable anatomic models Embodi3D members have shared for free. Please share too!

Human heart

Human heart

Skull by Health Physics

Human male skull

023 small

Lace Skull

Tweet http://goo.gl/xuvTiv Post to FB http://goo.gl/Ns8MuI

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LinkedIn: https://www.linkedin.com/company/embodi3d

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Dr. Mike


3D printing is revolutionizing the treatment of aortic stenosis, as reported by researchers from St. Joseph's Hospital in Phoenix, Arizona and presented at the 2014 Radiological Society of North American (RSNA) meeting. Aortic stenosis is a deadly condition where the valve that connects the heart to the aorta does not open properly. The aortic valve, as it is called, is designed to open freely to allow blood pumped from the heart to move in a forward direction into the aorta, the main artery of the body. At the end of a heart contraction, the valve closes to prevent the blood from flowing backwards. In patients with aortic stenosis, the valve fails to open during contraction, thus preventing blood from flowing forward during cardiac contraction (systole). The heart compensates by squeezing harder and harder to maintain adequate forward flow. Eventually, the heart becomes too strained and a variety of severe complications can ensure, including heart attack, heart failure, syncope (fainting), and sudden death. In patients with severe aortic stenosis there is a 50% chance of dying within two years if untreated.

Traditional treatment of aortic stenosis involved open heart surgery to replace the valve. This is a major operation and involves sawing through the breast bone to open the chest and gain access to the heart. As one can imagine, the procedure is risky and recovery takes a long time. Many patients who are too ill or weak and are not eligible for the surgery.

Fortunately, there is a new procedure where a prosthetic aortic valve can be implanted by navigating a plastic tube, or catheter, to the heart through a puncture in the artery of the hip or sometimes via a direct puncture through the apex of the heart. This procedure, called a Transcatheter Aortic Valve Replacement, or TAVR, promises to make aortic valve replacement minimally invasive, that is doable through a small hole instead of requiring open surgery. Recovery time is significantly less and patients who are ineligible for conventional surgery can often get TAVR.

The major problem with TAVR is that it can be very difficult to accurately place the prosthetic valve through the catheter, and poor placement can result in devastating consequences. Unlike open surgery, where the surgeon has direct access to the diseased heart valve, with TAVR the physician must work through the catheter. The valve is loaded on a collapsed metal mesh called a stent. The stent is then inched forward through the catheter into the proper position. The position is checked with x-ray and then the stent is expanded -- hopefully in the correct position relative to the diseased aortic valve, pushing it aside and replacing it with the new prosthetic valve. Once the prosthetic valve is expanded it cannot be retrieved or repositioned, and millimeters matter. Valves come in different sizes. If the valve is the wrong size or malpositioned by even a few millimeters it can cover the coronary arteries and lead to heart attack, cause blood clots to form leading to stroke, or even come free and cause tearing of the aorta.


Different sized TAVR aortic valves

This is where 3D printing comes in. The Arizona researchers used contrast enhanced computed tomography (CT) scans to gather precise data on the anatomical structure of the heart, aorta, and aortic valve from three patients with severe aortic stenosis, and manufactured precise 3D printed replicas of the aortas. Then they tested various valve sizes and position to see what had the best anatomic fit. They then did CT scans of the prosthetic valves within the 3D models and compared those to postoperative CT scans of the actual patients after TAVR, and found that the pre-surgical test fitting in the 3D printed models accurately predicted how the valves would perform in real patients. Use of the 3D printed models helped the surgeons choose the correct size valve and positioning prior to the surgery, thus reducing the risk of he TAVR procedure.

digital aorta

Digital rendering of the aorta

deploying stent In aorta

Testing the implantable valve in the 3D printed model by deploying it through a catheter (blue)

I have personally used customized 3D printed models I designed to test wires and catheters prior to complex mesenteric artery aneurysm treatments (publication forthcoming), and I can tell you that knowing your wires and catheters will work before the procedure is far better than figuring it out with trial and error during the procedure. Presurgical testing with 3D printed models is here to stay.

If you are interested in learning more about applications of 3D printing in medicine or how to make your own 3D models, please register as a member (it's free and only takes a minute!) and join the community of medical professionals who are all trying to build the future of 3D printing in medicine. Ask a question, start a discussion, or download free 3D printable models to make on your own. I will put some links to a few of the free downloadable models related to this article below.


Heart and pulmonary artery tree


Heart and pulmonary arteries

Human heart


Human heart

Human heart #2


Human heart