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  2. yes , it is very easy in 3D slicer. after loading data as described above, go to1) volume rendering >select process 2) segmentation >export as> save>see for different format
  3. Dr. Mike, I followed this tutorial very closely but the exported .stl skin, when imported into MeshMixer (version 3.2.37) still showed about as many problems as the original mesh and "Auto Repair All" did not correct all those problems. I even exported just one iteration of the "skinwrap" modifier to the original mesh and that too showed lots of problems. I'm including screenshots of the MeshMixer Inspector for each case. Any ideas what might be going on here? Thanks much for any help you can provide. Gary
  4. Hello, I am new to the use of 3DSLICER Please can you advise if the SLICER program can be used to convert ultrasound DICOM files to a CAD (.STL) as is possible I see with CT scans etc? Thank you Peter
  5. 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. 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.
  6. Medical Three-dimensional (3D) printing has a variety of uses and is becoming an integral part of dentistry, oral surgery and dental lab workflows. 3D printing in dentistry is the natural progression from computer-aided design (CAD) and computer-aided manufacturing (CAM) technology which has been used for years by dental labs to create crowns, veneers, bridges and implants. Now, 3D printing is taking its place with 3D printing solutions for dental, orthodontic, and maxillofacial applications. Several 3D printer manufacturers, including Stratasys and EnvisionTEC, offer specialized materials and printers as part of their dental 3D printing solutions. Anyone can create 3D printed dental models and embodi3D has created a dental 3D printing tutorial which guides readers through the process of 3D printing teeth and mandible. What is Dental 3D Printing? Three-dimensional printing begins with a special scanner. The mouth of the patient can be scanned using contact or non-contact scanning technology. The device works by creating a super accurate, patient specific digital image of a dental surface that is then saved as a computer file. Using specialized software, the scan is translated into a 3D digital representation. The resulting digital model may be a tooth, several teeth or the jaw. This digital imaging is not only replacing CAD/CAM technology, but it is also replacing some of the old plaster impressions traditionally used. Once the scan is complete and a 3D image has been created, the specialized software will prepare it for physical model creation. There are two popular methods for creating a physical model from the digital representation. The first method involves using a technique called slicing. With the help of specialized computer software, the original three-dimensional image is divided into thin horizontal layers. These layers are then transmitted to the 3D printer. The physical model is then printed layer by layer until the physical 3D model is complete. The second method is CNC milling. In this case, the complete digital image is transferred to a milling machine. Rather than print a model layer by layer, the milling machine starts with a solid piece of material. The machine then carves the new 3D physical model out of that block of material. As techniques become more advanced, 3D models become more accurate and the technology becomes more readily available, the first method is used more often in dental diagnosis, treatment planning and construction of dental appliances such as dental implants, orthodontics, denture bases and bite guards. Advantages of 3D Printing Teeth, Crowns, Dentures and Other Dental Anatomy 3D imaging has been used in dentistry for many years, however, the traditional method of model creation involves dental plaster models. While these models are accurate, so are 3D printed oral models. In fact, dental 3D printing is not only accurate, it is quick and a lot less messy. Patients who have undergone fitting for a crown or other dental appliance generally do not remember the process fondly. Plaster is messy and it has been necessary for patients to be fitted with a temporary appliance only to return for a second visit. This is both inconvenient and time-consuming. 3D imaging and printing can alleviate this problem. In dental offices with the capability, the process is fast and patients can often be fitted with their permanent appliance in a single visit without the plaster mess. This makes the entire process far more convenient for patients. Dentists also benefit from 3D printing and imaging. Imaging files are far easier to store than bulky plaster casts. By going digital, dentists and maxillofacial surgeons can store patient information indefinitely. This makes it easier to refer to files time and again for comparison, planning and treatment. As the 3D printer technology becomes more accessible, the cost of use is going down. Patients can have these procedures performed at prices comparable to traditional methods, and these costs will continue to decrease as 3D printer prices decrease. Advances in 3D printing technology are constantly improving. Whereas manual creation of implants, crowns and prosthetics required a high degree of specialization, 3D printing can quickly and easily create highly accurate models. This provides better fitting, more personalized appliances improving both comfort and efficacy of prosthetics. 3D Printing in Maxillofacial and Oral Surgery Maxillofacial and oral surgery is an area where 3D printing is currently being utilized for a variety of reasons including cancer, birth defects, injury or receding bone. Corrective surgery is often needed in cases like these. A prosthesis, implant, dental mesh, surgical stent and more can be created through the 3D scanning and printing process to aid patients. In addition to creating the actual prosthetics, three-dimensional printing is also helpful as part of the planning process. Three-dimensional printing can be used to create prototypes of the planned devices prior to surgery. Having the ability to simulate devices prior to implantation can help surgeons work out complex reconstructions and ensure that devices fit well. This allows the entire surgical process to be safer and easier. 3D Printed Dental Implants As with maxillofacial surgery, 3D scanning and 3D printing improve the fit, comfort and ease of dental implant surgery. 3D scans of the patient’s teeth, gums and jaw allow dentists to have a high degree of accuracy and as a result 3D printed dental anatomy is patient specific. There are many advantages to using 3D printing for dental implant surgery including: Determine depth and width of bone Accurate sizing for implants Determine the location of sinuses and nerves Three dimensional printing creates accurate models that ensure a good fit. It is used to address issues such as location, angle and depth of the implant prior to surgery. This same technology allows dentists to create templates and surgical drill guides for permanent implants. Many dentists use these guides to improve surgical safety as they guide the surgeon’s hand, ensure correct placement and restrict the depth of the drill. How 3D Printing is Used for Crowns With 3D scanning and printing, dentists and patients can forgo the plaster dental mold and the need to rely on a lab for crown creation. With 3D technology, dentists can use a scanning camera and specialized software to create an exact three-dimensional image of the tooth that needs to be crowned if the tooth has not broken below the gum line. This image is then transmitted to a 3D printer or milling machine that carves a porcelain crown to exact specifications. The entire process can be completed in about an hour allowing patients to leave the dental office with a permanent crown on the same day. Three-dimensional imaging is one more tool in the dentists’ and oral surgeons’ arsenal to provide better oral health care. With three-dimensional imaging and printing, dentists can gain more complete information for diagnosis and treatment, ensure safer procedures and provide a more comfortable fit for oral devices.
  7. We had a file sharing contest in May of 2017, where those members who uploaded and shared a file were entered to win. We had many good entries and it was a tough choice, but we found a winner! Michael Platt is our winner! He submitted and shared two STL downloads; a thoracic vertebra and a renal cortex. We selected the renal cortex because the download contains two STL files: an intact renal cortex and another STL with the cortex sliced in half. Michael is a medical physicist with a passion for 3D printing and design. His research involves 3D printing and scanning in radiation oncology. He loves 3D printing and thinks that it has wonderful potential in medicine. We couldn't agree more! We are having a file review contest in June with a $50 prize. All that is required is to download a file and write a review. Each file you review in June 2017 will be an entry in our contest. There is no limit to the number of files you can review. To learn more and see complete rules please visit our contest page.
  8. 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 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 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 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 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.
  9. embodi3D May 2017 Newsletter

    Welcome to our May 2017 newsletter! Read on to learn how you can participate in our file sharing contest and win an Amazon gift certificate, what improvements we have made to democratiz3D, and where you can find source medical files for 3D printing. democratiz3D: New NRRD & STL Thumbnail Creation democratiz3D(TM), our online tool which converts a medical scan study to a 3D printable file, has had an exciting upgrade: it now automatically creates thumbnails for NRRD files. As a reminder, the NRRD files are created from the original DICOM files from CT scans. Thumbnails are now automatically generated for all newly uploaded files. Once you submit a file for processing the thumbnails images will be available almost immediately. Simply refresh your browser window to see the thumbnails. You can make thumbnails for your existing NRRD and STL files by clicking "Generate Thumbnails" on the file detail page. NRRD thumbnail generation takes a few seconds. Please note thumbnails are generated for STL files as well, but these take several minutes to process. A Collection of Medical Scan Files A new category called Medical Scan Files has been added to our Download area. This is a collection of NRRD source files uploaded and shared by members. Check it out, and please share your files so we can continue to grow our medical file library. May Medical 3D Printing File Sharing Contest Speaking of sharing, we are now running a contest for the best shared file with the winner receiving a $50 Amazon gift certificate. Share a file when you upload and you are automatically entered to win. The contest runs the month of May. April 3D Printable STL File Review Contest Winner Congratulations to Cris, who won our April file review contest! Cris is CEO and cofounder of Tenere Technology, a medical software development company, based in Madrid, Spain. Cris and her team are working to discover the world of 3D printing and excited about the amazing possibilities. She reviewed an anatomically accurate scapula STL file. She wrote a nice review including an image of the scapula she printed using a file contributed by member health_physics. In her review Cris also includes a picture of her 3D printer and helpful 3D printing details like wall thickness, print speed and type of material used. Meet Dr. Mike Dr. Mike will be speaking at FUSE 2017, Formlabs User Conference in Boston on June 6. If you are attending the conference, please seek out Dr. Mike. It is a unique opportunity to let him know how you use embodi3D and how we can improve. We Want Your Feedback We would like to thank our members who have provided feedback and thus contributed to the improvements we covered in this newsletter. Please keep sending us your feedback and making the experience better for everyone! Let's grow our community together! The Embodi3D Team
  10. 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. A Brief Overview of How CT and MRI Works For both CT (left) and MRI (right) scans you will lie on a moving table and be put into a circular machine that looks like a big doughnut. The table will move your body into the doughnut hole. The scan will then be performed. You may or may not get IV contrast through an IV. The machines look very similar but the scan pictures are totally different! CT and CAT Scans are the Same A CT scan, from Computed Tomography, and a CAT scan from Computed Axial Tomography are the same thing. CT scans are based on x-rays. A CT scanner is basically a rotating x-ray machine that takes sequential x-ray pictures of your body as it spins around. A computer then takes the data from the individual images, combines that with the known angle and position of the image at the time of exposure, and re-creates a three-dimensional representation of the body. Because CT scans are based on x-rays, bones are white and air is black on a CT scan just as it is on an x-ray as shown in Figure 1 below. Modern CT scanners are very fast, and usually the scan is performed in less than five minutes. Figure 1: A standard chest x-ray. Note that bones are white and air is black. Miscle and fat are shades of gray. CT scans are based on x-ray so body structures have the same color as they don on an x-ray. How does MRI Work? MRI uses a totally different mechanism to generate an image. MRI images are made using hydrogen atoms in your body and magnets. Yes, super strong magnets. Hydrogen is present in water, fat, protein, and most of the "soft tissue" structures of the body. The doughnut of an MRI does not house a rotating x-ray machine as it does in a CT scanner. Rather, it houses a superconducting electromagnet, basically a super strong magnet. The hydrogen atoms in your body line up with the magnetic field. Don't worry, this is perfectly safe and you won't feel anything. A radio transmitter, yes just like an FM radio station transmitter, will send some radio waves into your body, which will knock some of the hydrogen atoms out of alignment. As the hydrogen nuclei return back to their baseline position they emit a signal that can be measured and used to generate an image. MRI Pulse Sequences Differ Among Manufacturers The frequency, intensity, and timing of the radio waves used to excite the hydrogen atoms, called a "pulse sequence," can be modified so that only certain hydrogen atoms are excited and emit a signal. For example, when using a Short Tau Inversion Recovery (STIR) pulse sequence hydrogen atoms attached to fat molecules are turned off. When using a Fluid Attenuation Inversion Recovery (FLAIR) pulse sequence, hydrogen atoms attached to water molecules are turned off. Because there are so many variables that can be tweaked there are literally hundreds if not thousands of ways that pulse sequences can be constructed, each generating a slightly different type of image. To further complicate the matter, medical scanner manufacturers develop their own custom flavors of pulse sequences and give them specific brand names. So a balanced gradient echo pulse sequence is called True FISP on a Siemens scanner, FIESTA on a GE scanner, Balanced FFE on Philips, BASG on Hitachi, and True SSFP on Toshiba machines. Here is a list of pulse sequence names from various MRI manufacturers. This Radiographics article gives more detail about MRI physics if you want to get into the nitty-gritty. Figure 2: Examples of MRI images from the same patient. From left to right, T1, T2, FLAIR, and T1 post-contrast images of the brain in a patient with a right frontal lobe brain tumor. Note that tissue types (fat, water, blood vessels) can appear differently depending on the pulse sequence and presence of IV contrast. How to Tell the Difference Between a CT Scan and an MRI Scan? A Step by Step Guide Step 1: Read the Radiologist's Report The easiest way to tell what kind of a scan you had is to read the radiologist's report. All reports began with a formal title that will say what kind of scan you had, what body part was imaged, and whether IV contrast was used, for example "MRI brain with and without IV contrast," or "CT abdomen and pelvis without contrast." Step 2: Remember Your Experience in the MRI or CT (CAT) Scanner Were you on the scanner table for less than 10 minutes? If so you probably had a CT scan as MRIs take much longer. Did you have to wear earmuffs to protect your hearing from loud banging during the scan? If so, that was an MRI as the shifting magnetic fields cause the internal components of the machine to make noise. Did you have to drink lots of nasty flavored liquid a few hours before the scan? If so, this is oral contrast and is almost always for a CT. How to tell the difference between CT and MRI by looking at the pictures If you don't have access to the radiology report and don't remember the experience in the scanner because the scan was A) not done on you, or you were to drunk/high/sedated to remember, then you may have to figure out what kind of scan you had by looking at the pictures. This can be complicated, but don't fear I'll show you how to figure it out in this section. First, you need to get a copy of your scan. You can usually get this from the radiology or imaging department at the hospital or clinic where you had the scan performed. Typically these come on a CD or DVD. The disc may already have a program that will allow you to view the scan. If it doesn't, you'll have to download a program capable of reading DICOM files, such as 3D Slicer. Open your scan according to the instructions of your specific program. You may notice that your scan is composed of several sets of images, called series. Each series contains a stack of images. For CT scans these are usually images in different planes (axial, coronal, and sagittal) or before and after administration of IV contrast. For MRI each series is usually a different pulse sequence, which may also be before or after IV contrast. Step 3: Does the medical imaging software program tell you what kind of scan you have? Most imaging software programs will tell you what kind of scan you have under a field called "modality." The picture below shows a screen capture from 3D Slicer. Looking at the Modality column makes it pretty obvious that this is a CT scan. Figure 3: A screen capture from the 3D Slicer program shows the kind of scan under the modality column. Step 4: Can you see the CAT scan or MRI table the patient is laying on? If you can see the table that the patient is laying on or a brace that their head or other body part is secured in, you probably have a CT scan. MRI tables and braces are designed of materials that don't give off a signal in the MRI machine, so they are invisible. CT scan tables absorb some of the x-ray photons used to make the picture, so they are visible on the scan. Figure 4: A CT scan (left) and MRI (right) that show the patient table visible on the CT but not the MRI. Step 5: Is fat or water white? MRI usually shows fat and water as white. In MRI scans the fat underneath the skin or reservoirs of water in the body can be either white or dark in appearance, depending on the pulse sequence. For CT however, fat and water are almost never white. Look for fat just underneath the skin in almost any part of the body. Structures that contained mostly water include the cerebrospinal fluid around the spinal cord in the spinal canal and around the brain, the vitreous humor inside the eyeballs, bile within the gallbladder and biliary tree of the liver, urine within the bladder and collecting systems of the kidneys, and in some abnormal states such as pleural fluid in the thorax and ascites in the abdomen. It should be noted that water-containing structures can be made to look white on CT scans by intentional mixing of contrast in the structures in highly specialized scans, such as in a CT urogram or CT myelogram. But in general if either fat or fluid in the body looks white, you are dealing with an MRI. Step 6: Is the bone black? CT never shows bones as black. If you can see bony structures on your scan and they are black or dark gray in coloration, you are dealing with an MRI. On CT scans the bone is always white because the calcium blocks (attenuates) the x-ray photons. The calcium does not emit a signal in MRI scans, and thus appears dark. Bone marrow can be made to also appear dark on certain MRI pulse sequences, such as STIR sequences. If your scan shows dark bones and bone marrow, you are dealing with an MRI. A question I am often asked is "If bones are white on CT scans, if I see white bones can I assume it is a CT?" Unfortunately not. The calcium in bones does not emit signal on MRI and thus appears black. However, many bones also contain bone marrow which has a great deal of fat. Certain MRI sequences like T1 and T2 depict fat as bright white, and thus bone marrow-containing bone will look white on the scans. An expert can look carefully at the bone and discriminate between the calcium containing cortical bone and fat containing medullary bone, but this is beyond what a layperson will notice without specialized training. Self Test: Examples of CT and MRI Scans Here are some examples for you to test your newfound knowledge. 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.
  11. In April 2017, embodi3D held its first review writing contest. Many great reviews were posted and we selected a review by Cris as the winner. She is the recipient of the $25 Amazon gift certificate. Congratulations Cris! She reviewed an anatomically accurate scapula STL file. She wrote a nice review including an image of the scapula she printed using the file uploaded by health_physics. In her review Cris also includes a picture of her 3D printer and helpful 3D printing details like wall thickness, print speed and type of material used. We are having a file sharing contest in May and have increased the prize to $50. All that is required is to upload a file, share the file and write a brief description. Each shared file you upload in May 2017 will be an entry in our contest. There is no limit to the number of files you can upload and share. To learn more and see complete rules please visit our contest page.
  12. The Embodi3D website offers a large and ever-growing library of 3D printable files that are available for free to anyone who signs up for a free account. Images include files from normal anatomy to those related to paleontology to complex musculoskeletal tumors. This site was founded by a practicing interventional radiologist with a passion for 3D printing and perfecting an easier method for converting files into those that may be downloaded and printed—a medical 3D printing application called democratiz3D. Commercial Medical 3D Printing Software Three-dimensional printing has become a popular research and industrial interest in the orthopaedic surgery world. International companies such as Stryker ( and DePuy Synthes ( are now marketing designs in craniofacial reconstruction, arthroplasty, and spine deformity surgery that utilize 3D printing in order to individualize implants and surgical techniques. Specialized software for 3D printing in healthcare is sold by Materialise in an offering called Mimics. Vital Images, a medical imaging and informatics company, has partnered with Stratsys, a 3D printer manufacturer, to provide a segmentation and healthcare 3D printing solution. However, these technologies are costly, and may be cost-prohibitive for the average patient or surgeon. Three-Dimensional Printing for Patient Education and Surgical Planning Although most radiology departments currently have the capability to quickly convert a CT (computer tomography) scan to a three-dimensional image for better understanding of a patient’s anatomy, visualized anatomy cannot replace the ability to feel and manipulate a model. Three-dimensional printing can, however, bring these images to life. Printers have the capability to use differing materials, such as polymers, plastics, ceramics, metals, and biologics to create models. These models can be an excellent tool for patient and trainee education as well as surgical planning. In procedures such as complex tumors or difficult pelvic fractures, the surgeon could practice different techniques on an exact replica of the patient’s anatomy so that they have a better grasp of their approach to the patient. Furthermore, trainees currently learn and practice their surgical skills on cadaveric specimens, which can also be costly. Having access to a 3D printer that could create models could potentially decrease the utilization of cadavers. Free and Easy Medical Three-Dimensional Printing Creating files from CT scans that can be used in 3D printing is easy with the use of the Embodi3d website. Detailed instructions are available on the tutorial pages of the website, but a brief overview will be described here. CT scans may be obtained from the radiology department in DICOM format. Free software available online at can be used to review the DICOM imaging, isolate the area of interest and convert to an .nrrd file. This .nrrd file may then be loaded onto the democratiz3D application and formatted in a number of ways based on threshold as shown in the images below. Files may be opened through the application or dragged and dropped into the file area (Figure 1, Figure 2). Details of the file, such as the title, description of the anatomy or pathology, and keywords are placed beneath the upload (Figure 3). Different thresholds are available to be automatically placed on the uploaded file, including bone, detailed bone, muscle, and skin (Figure 4). These files as well as the final, processed, files may be shared or remain private, free or at a fee to download by the community. Figure 1. The link to the democratiz3D application is located at the top menu bar of the main page at Figure 2. Once on the democratiz3D application, you may upload the .nrrd file or drag and drop the .nrrd file into the uploading area. Figure 3. While the .nrrd file is processing, you may edit the details of the file, such as the title, tags, and description. Figure 4. The application allows for thresholding of bone, detailed bone, muscle, and skin from the uploaded CT scan. Once the file has been processed, you receive a notification and may view the file as well as automatically created screen shots (Figure 5). This is now an STL file that may be downloaded by clicking “Download this file”. If this is a file that you have downloaded, you may also edit the details of the file, move it to another category or upload a new version of the STL file directly onto the page (Figure 6). Although the democratiz3D application is a powerful and quick tool to convert .nrrd files to STL files, it is limited by the quality of the CT scan. Therefore, users may wish to clean up the model using free software such as Meshmixer or Blender. Once the files have been edited, they are maintained as an STL file that may be directly uploaded onto the page as a new version (Figure 7). These may then be placed in a category that is most descriptive of the file (Figure 8). Figure 5. After about 5-20 minutes of processing (depending on the size of the file), you will get a notification and e-mail that the file has processed. The democrati3D application has converted the file into an STL file is now available for downloading and use in 3D printing. Figure 6. If you would like to change the details, or upload new files or screen shots, you may choose from the drop-down menu. Figure 7. In order to upload a new version of the file, such as after it is edited in the free software Meshmixer or Blender, you may choose from the drop-down menu and drag and drop a new STL file. Figure 8. Because Embodi3D has created a library divided into different categories, you may move your file into the appropriate category to allow for ease of sharing with the community. Alternatively, files that have been downloaded and edited may be uploaded as new files using the “Create” selection on the top menu (Figure 9). Once you have chosen the most accurate category (Figure 10), you can upload the new file by selecting the file or drag and drop into the proper area (Figure 11). This will then take you to similar section as outlined above in order to edit the details and sharing options for your file. Figure 9. Upload an STL file by selecting the “Create” menu at the top of the webpage. Figure 10. Select the category under which the file most accurately fits. Figure 11. Upload the STL file by dragging and dropping or selecting the file. As you can see, creating STL files from individual CT scans is an easy, 15-20 minute process that is reasonable for the busy orthopaedic surgeon to utilize in their practice. For educational purposes, however, not every trainee, surgeon, or radiologist has access to patients with such a wide array of pathologies. The Embodi3D community provides an ever-growing diverse library of normal anatomy and pathology that may be downloaded for free and used for 3D printing. The files are divided into categories including: Bones, Muscles, Cardiac and Vascular, Brain and nervous system, Organs of the Body, Veterinary, Paleontology, Anthropology, Research and Miscellaneous. In order to access these files, click “Download” from the top menu (Figure 12), which will take you to the main Downloads page (Figure 13). The categories available are listed on the right side of the page, and will bring you to each category page. There, the number of files available within each category is listed. Once the desired file is selected, the file may be downloaded as described above. Figure 12. In order to access the library of files, click “Download” from the top menu on the main page. Figure 13. The Downloads page has a listing of the available categories to browse and explore for the desired files. Creating and printing 3D models of CT scans will be useful in the future of medicine and the era of individualized medicine. The free library of medical 3D printing files available at as well as the free conversion application democratiz3D will be an invaluable resource for education as well as for the private orthopaedic surgeon with limited resources. Furthermore, because healthcare costs are a main focus in the United States, having the ability to download and create models for a much lower price than through commercial 3D printing companies will be useful to decrease the cost of individualized care. For more information about 3D printing in orthopaedic surgery, please see the following references: Cai H. Application of 3D printing in orthopedics: status quo and opportunities in China. Ann Transl Med. 2015;3(Suppl 1):S12. Eltorai AEM, Nguyen E, Daniels AH. Three-Dimensional Printing in Orthopedic Surgery. Orthopedics. 2015;38(11):684-687. Mulford JS, Babazadeh S, Mackay N. Three-dimensional printing in orthopaedic surgery: review of current and future applications. ANZ J Surg. 2016;86(9):648-653. Tack P, Victor J, Gemmel P, Annemans L. 3D-printing techniques in a medical setting: a systematic literature review. Biomed Eng Online. 2016;15(1):115.
  13. Segmentation of a foot MRI scan

    Thresholding is also my least favorite method of segmenting. I work in a radiation oncology department with access to some fantastic contouring software (MIM, Raystation, Eclipse, Pinnacle). Unfortunately, none of them have simple volume export functions. We've written a simple script which takes a Dicom structure file and outputs a simple CSV file with the contour point cloud. Using these tools along with 3DSlicer we generate volumes from these contours that seem to be much more accurate, have less noise, and are produced much faster than with the tools in 3DSlicer. Hopefully the contouring tools found in those softwares will make their way to 3DSlicer someday.
  14. Welcome to our April 2017 newsletter! Read on to learn how you can participate in our review writing contest and win an Amazon gift certificate, what improvements we have made to democratiz3D, and what our medical device development service offers. 3D Printable File Review Writing Contest Download a file, post a review and you are automatically entered to win a $25 Amazon gift certificate. We will award the prize to the writer of the best review. The contest runs the month of April. democratiz3D: Medical 3D Printing for All democratiz3D(TM), our online tool which converts a medical scan study to a 3D printable file, has had an upgrade that allows for improved processing of dental, and face bone models. Lung CT scans with hard (sharpened) reconstruction kernels also have improved performance. Additionally, there are new materials that are shown in thumbnail renders for muscle and skin files. Going forward, thumbnails are now three colors white (bone), redish-brown (muscle) and gray (skin). Check it out, and let us know how you like it. Custom 3D Printing for Medical Device Development Embodi3D creates customized and highly detailed 3D printed medical models from real patient medical scans. You are assured the anatomy is realistic because it comes from a real patient. We can create sets of models, meeting your specifications for age/gender/pathology, thus giving you the most accurate picture of anatomic variability in your target patient population. A Collection of Medical Scan Files Prior to model creation we perform a consultation to understand your needs in detail, so that the models are precisely tailored to test your device. Reply to this email for more information. We Want Your Feedback We would like to thank our members who have provided feedback and thus contributed to the improvements we covered in this newsletter. Please keep sending us your feedback and making the experience better for everyone! Let's grow our community together! The Embodi3D Team
  15. Excellent comment Our firm currently its working on this type of application through FDM 3D printing and use of different methods and materials such as Carbon fiber molding etc.
  16. Segmentation of a foot MRI scan

    Great post Mike. Thank you.
  17. Segmentation of a foot MRI scan

    Thanks for sharing Mike!
  18. So I have seen some questions here on embodi3D asking how to work with MRI data. I believe the main issue to be with attempting to segment the data using a threshold method. The democratiz3D feature of the website simplifies the segmentation process but as far as I can tell relies on thresholding which can work somewhat well for CT scans but for MRI is almost certain to fail. Using 3DSlicer I show the advantage of using a region growing method (FastGrowCut) vs threshold. The scan I am using is of a middle aged woman's foot available here The scan was optimized for segmenting bone and was performed on a 1.5T scanner. While a patient doesn't really have control of scan settings if you are a physician or researcher who does; picking the right settings is critical. Some of these different settings can be found on one of Dr. Mike's blog entries. For comparison purposes I first showed the kind of results achievable when segmenting an MRI using thresholds. With the goal of separating the bones out the result is obviously pretty worthless. To get the bones out of that resultant clump would take a ridiculous amount of effort in blender or similar software: If you read a previous blog entry of mine on using a region growing method I really don't like using thresholding for segmenting anatomy. So once again using a region growing method (FastGrowCut in this case) allows decent results even from an MRI scan. Now this was a relatively quick and rough segmentation of just the hindfoot but already it is much closer to having bones that could be printed. A further step of label map smoothing can further improve the rough results. The above shows just the calcaneous volume smoothed with its associated surface generated. Now I had done a more proper segmentation of this foot in the past where I spent more time to get the below result If the volume above is smoothed (in my case I used some of my matlab code) I can get the below result. Which looks much better. Segmenting a CT scan will still give better results for bone as the cortical bone doesn't show up well in MRI's (why the metatarsals and phalanges get a bit skinny), but CT scans are not always an option. So if you have been trying to segment an MRI scan and only get a messy clump I would encourage you to try a method a bit more modern than thresholding. However, keep in mind there are limits to what can be done with bad data. If the image is really noisy, has large voxels, or is optimized for the wrong type of anatomy there may be no way to get the results you want.
  19. 3D Printed Wrist Brace

    What is often done is to open a whole half of the brace and attach it with velcro in several points for each segment
  20. 3D printing technologies have opened up the capabilities for customization in a wide variety of applications in the medical field. Using bio-compatible and drug-contact materials, medical devices can be produced that are perfectly suited for a particular individual. Another trend enabled by 3D printing is mass customization, in that multiple individualized items can be produced simultaneously, saving time and energy while improving manufacturing efficiency. 3D printers are used to manufacture a variety of medical devices, including those with complex geometry or features that match a patient’s unique anatomy. Some devices are printed from a standard design to make multiple identical copies of the same device. Other devices, called patient-matched or patient-specific devices, are created from a specific patient’s imaging data. Commercially available 3D printed medical devices include: Instrumentation (e.g., guides to assist with proper surgical placement of a device) Implants (e.g., cranial plates or hip joints) External prostheses (e.g., hands) Prescription Glasses Hearing Aids In summary, the 3D Printing medical device market looks exciting and promising, Various Reports and surveys suggest the unexpected growth and demand for 3D Printing in medical device industry and it is expected to blossom more but a number of existing application areas for 3D printing in healthcare sector require specialized materials that meet rigid and stringent bio-compatibility standards, Future 3D printing applications for the medical device field will certainly emerge with the development of suitable additional materials for diagnostic and therapeutic use that meet CE and FDA guidelines.
  21. 3D Printed Wrist Brace

    Great work Mike!
  22. 3D Printed Wrist Brace

    Well for my particular case its hard to say as I don't wear it 24/7. I swap between it and the cloth type. With tendonitis the printed brace is rigid and restrictive. Important for a broken bone but not so much for a soft tissue injury where it is important to have just limited mobility. I may tweak the design some more to give a bit more comfort and flexibility. Yes the early designs were far from usable/comfortable took some trial and error to get it right.
  23. Atlas and Axis, 3D PDF

    I used a 3d pdf generator (pdf3d reportgen) and it has an option to convert several models (I used obj) into a document with a model tree.
  24. Very few infectious diseases in recent years have commanded the kind of attention and concern that Zika Virus has. Although Zika outbreaks have been reported in Africa, Southeast Asia and other parts of the world since the 1952, recent announcement by the Center for Disease Control and Prevention (CDC) confirming its link with microcephaly has forced everyone to sit up and take notice. The CDC estimates that the current pandemic is widespread with at least 50 countries reporting active Zika transmissions at this time. Most people with Zika virus infection will not have any symptoms though some may experience mild fever, conjunctivitis, muscle and joint pain, and headaches. The virus is primarily transmitted by the Aedes mosquito. However, pregnant women may pass the infection to their babies, which may lead to microcephaly, a neurological condition associated with an abnormally small brain in the infant. The condition can lead to birth defects ranging from hearing loss to poor vision and impaired growth. Prompt diagnosis and treatment of Zika virus infections in pregnant women can, nonetheless, lower the risk of microcephaly to a great extent. Researchers have, therefore, put in a lot of time, money and effort to find a solution, and as always, three-dimensional (3D) medical printing and bioprinting technologies are leading the way. Understanding the Disease To begin with, 3D printing has played a crucial role in conclusively establishing the link between Zika virus and microcephaly. Researchers at John Hopkins Medicine used 3D bioprinting technology to develop realistic models of brain that revealed how the virus infects specialized stem cells in the outer layers of the organ, also known as the cortex. The bioprinted models allowed researchers to study the effects of Zika exposure on fetal brain during different stages of pregnancy. The models are also helping the scientists with drug testing, which is the obvious next stage of their research. Zika Test Kit Engineers at Penn’s School of Engineering and Applied Science, under the leadership of Professor Changchun Liu and Professor Haim Bau, have developed a simple genetic testing device that helps detect Zika virus in saliva samples. It consists of an embedded genetic assay chip that identifies the virus and turns the color of the paper in the 3D printed lid of the device to blue. This can prompt healthcare professionals to send the patient for further testing and to initiate treatment. Unlike other Zika testing techniques, this screening method does not require complex lab equipment. Each device costs about $2, making Zika screening accessible to pregnant women from the poorest parts of the world. Treating Microcephaly The scientists at the Autonomous University of the State of Morelos (UAEM) in Mexico are relying on the additive printing technology to create a microvalve that may help treat microcephaly in infants. The valve reduces the impact of the neurological disease and slows its progression by draining out excessive cerebrospinal fluid associated with this disorder. It can be inserted into the infant brain through a small incision to relieve fluid pressure and provide space for normal development. Researchers estimate the device will be available for patient use by 2017. These examples clearly demonstrate the impact of 3D printing on every aspect of the fight against Zika virus from diagnosing the disease to treating it. The results have been extremely promising, and both researchers and healthcare professionals are immensely hopeful that additive printing technology will help them overcome the infection quickly and effectively.
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