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Found 13 results

  1. I received this inquiry from a member. I am going to post the response here so that it can help others with the same question: QUESTION: "I am printing out a spine model.... Why are there so many defects in the rendering? I can't print this out on a 3d printer, half of the vertebrae are hollow. I get these from a 3d CT and on a computer monitor, the vertebrae are whole. Just take a look at the thumbnails and you'll know what I'm talking about. I don't have the expertise or time to fill all of the defects. Is there a paid service somewhere that could do this for me? I'm just surprised the STL file wouldn't look like the 3d CT since they use the same dicom imagery?" ANSWER: If you are creating bony models and are finding that the bones have holes or other large defects in them (see above), this is probably an issue with the Threshold value used during the conversion. Threshold is the number of Hounsfield units to use to create the surface of the model. Anything above the threshold value is considered bone and is included. Anything below is not considered bone and is excluded. Normal cortical bone is very dense, greater than 300 Hounsfield units, so the default threshold of 150 is more than enough to catch it. The inside of the bone (medullary, or marrow cavity) is filled with fatty bone marrow and is a much lower Hounsfield value. If the patient has osteoporosis or very thin cortical bones they may not register as bone if the default threshold of 150 is used. You can decrease this to a lower threshold value (maybe 100 or so) and you will be more likely to capture this thin, deossified bone. If you go too low though (60 or so) you will start to capture non-bony structures like muscle. Another thing that may help get the highest quality models is using premium operations such as Very Detailed Bone and Ultra quality level. These operations are time-consuming however. To save on time, you can run your scan through democratiz3D using free operations such as Detailed Bone and medium or high quality until you find the threshold you like. Once you find the threshold value you like, you can run you scan through a final time using the highest quality (and slowest) operation settings, such as Very Detailed Bone and Ultra quality. Hope this helps! Dr. Mike
  2. A member recently asked me the following question. I am posting the answer here so that everyone can benefit. QUESTION: I am a neurosurgeon and have made 3D brain models from architectural software (Form Z). Some of these models are on my web site which I did more than 5 years ago (________). I am starting to update my web site (for patient information, noncommercial). I have not tried your software as yet. Tutorials imply bone, vascular, muscle, skin, etc. I plan to try this for spine. I did see a brain in your gallery. Do I use the same technique as in your tutorial to make a brain? Will it show any intraparenchymal lesions? ANSWER: Thank you for the question. Brain are particularly difficult to segment for 3D printing because they have to come from MRIs, and MRI data is highly variable, unlike CT data. Not only are there many differing kinds of MRI basic pulse sequences (T1, T2, FLAIR, MPRAGE, STIR, etc), but they are acquired in different planes (axial, sagittal, coronal) and differing slice thicknesses. Furthermore, the protocols are different between venders. For example a T2 fat-sat sequence from GE will be different than those from Philips, Siemens, Toshiba, etc. All of this makes it very difficult to automate the segmentation. At this time if you want to segment a brain, you'll probably need to do it manually. This is a time-consuming process, but can be done with a variety of software packages, such as 3D Slicer, for example. You'll have to segment out any intraparenchymal lesions separately as well. There are many tutorials on this site to get you started. Hope this helps. Dr. Mike
  3. I user recently sent me the following question. I am posting the answer in the hopes it will help others. "We are trying to convert a CBCT of a denture that was scanned into an STL for a custom try. I already converted the dicom to NRRD file, but when we go to convert the NRRD file to the stl, The stl being produced is not of the denture, it is only of the alignment markers that was placed on the denture. Am I doing something wrong within the settings possibly? Answer: I was able to process your NRRD file using our premium dental operation and manually adjusting the threshold. Normally the dental operation sets the threshold to 300 (Hounsfield units). However, this doesn't work well because the denture material is less dense than normal jaw bone. By lowering the threshold value to 100, it targets the denture material. A good looking STL file is created using the premium dental operation, with ultra quality and threshold set to 100. Remember that you can always adjust the threshold level to suite your specific needs. You don't have to stick with the defaults. Hope this helps. Dr. Mike
  4. AFTER OPENING MY DICOR FILES IN 3D SLICER AND SAVING THEM INTO JUST ONE NRRD FILE , THE FILE IS OVER 500 MB SIZE SO DEMCRATIZ3D CAN T WORK WITH THE FILE BECAUSE IT IS TOO BIG....WHAT CAN I DO ?
  5. If you are planning on using the democratiz3D service to automatically convert a medical scan to a 3D printable STL model, or you just happen to be working with medical scans for another reason, it is important to know if you are working with a CT (Computed Tomography or CAT) or MRI (Magnetic Resonance Imaging) scan. In this tutorial I'll show you how to quickly and easily tell the difference between a CT and MRI. I am a board-certified radiologist, and spent years mastering the subtleties of radiology physics for my board examinations and clinical practice. My goal here is not to bore you with unnecessary detail, although I am capable of that, but rather to give you a quick, easy, and practical way to understand the difference between CT and MRI if you are a non-medical person. Interested in Medical 3D Printing? Here are some resources: Free downloads of hundreds of 3D printable medical models. Automatically generate your own 3D printable medical models from CT scans. Have a question? Post a question or comment in the medical imaging forum. A Brief Overview of How CT and MRI Works For both CT (left) and MRI (right) scans you will lie on a moving table and be put into a circular machine that looks like a big doughnut. The table will move your body into the doughnut hole. The scan will then be performed. You may or may not get IV contrast through an IV. The machines look very similar but the scan pictures are totally different! CT and CAT Scans are the Same A CT scan, from Computed Tomography, and a CAT scan from Computed Axial Tomography are the same thing. CT scans are based on x-rays. A CT scanner is basically a rotating x-ray machine that takes sequential x-ray pictures of your body as it spins around. A computer then takes the data from the individual images, combines that with the known angle and position of the image at the time of exposure, and re-creates a three-dimensional representation of the body. Because CT scans are based on x-rays, bones are white and air is black on a CT scan just as it is on an x-ray as shown in Figure 1 below. Modern CT scanners are very fast, and usually the scan is performed in less than five minutes. Figure 1: A standard chest x-ray. Note that bones are white and air is black. Miscle and fat are shades of gray. CT scans are based on x-ray so body structures have the same color as they don on an x-ray. How does MRI Work? MRI uses a totally different mechanism to generate an image. MRI images are made using hydrogen atoms in your body and magnets. Yes, super strong magnets. Hydrogen is present in water, fat, protein, and most of the "soft tissue" structures of the body. The doughnut of an MRI does not house a rotating x-ray machine as it does in a CT scanner. Rather, it houses a superconducting electromagnet, basically a super strong magnet. The hydrogen atoms in your body line up with the magnetic field. Don't worry, this is perfectly safe and you won't feel anything. A radio transmitter, yes just like an FM radio station transmitter, will send some radio waves into your body, which will knock some of the hydrogen atoms out of alignment. As the hydrogen nuclei return back to their baseline position they emit a signal that can be measured and used to generate an image. MRI Pulse Sequences Differ Among Manufacturers The frequency, intensity, and timing of the radio waves used to excite the hydrogen atoms, called a "pulse sequence," can be modified so that only certain hydrogen atoms are excited and emit a signal. For example, when using a Short Tau Inversion Recovery (STIR) pulse sequence hydrogen atoms attached to fat molecules are turned off. When using a Fluid Attenuation Inversion Recovery (FLAIR) pulse sequence, hydrogen atoms attached to water molecules are turned off. Because there are so many variables that can be tweaked there are literally hundreds if not thousands of ways that pulse sequences can be constructed, each generating a slightly different type of image. To further complicate the matter, medical scanner manufacturers develop their own custom flavors of pulse sequences and give them specific brand names. So a balanced gradient echo pulse sequence is called True FISP on a Siemens scanner, FIESTA on a GE scanner, Balanced FFE on Philips, BASG on Hitachi, and True SSFP on Toshiba machines. Here is a list of pulse sequence names from various MRI manufacturers. This Radiographics article gives more detail about MRI physics if you want to get into the nitty-gritty. Figure 2: Examples of MRI images from the same patient. From left to right, T1, T2, FLAIR, and T1 post-contrast images of the brain in a patient with a right frontal lobe brain tumor. Note that tissue types (fat, water, blood vessels) can appear differently depending on the pulse sequence and presence of IV contrast. How to Tell the Difference Between a CT Scan and an MRI Scan? A Step by Step Guide Step 1: Read the Radiologist's Report The easiest way to tell what kind of a scan you had is to read the radiologist's report. All reports began with a formal title that will say what kind of scan you had, what body part was imaged, and whether IV contrast was used, for example "MRI brain with and without IV contrast," or "CT abdomen and pelvis without contrast." Step 2: Remember Your Experience in the MRI or CT (CAT) Scanner Were you on the scanner table for less than 10 minutes? If so you probably had a CT scan as MRIs take much longer. Did you have to wear earmuffs to protect your hearing from loud banging during the scan? If so, that was an MRI as the shifting magnetic fields cause the internal components of the machine to make noise. Did you have to drink lots of nasty flavored liquid a few hours before the scan? If so, this is oral contrast and is almost always for a CT. How to tell the difference between CT and MRI by looking at the pictures If you don't have access to the radiology report and don't remember the experience in the scanner because the scan was A) not done on you, or you were to drunk/high/sedated to remember, then you may have to figure out what kind of scan you had by looking at the pictures. This can be complicated, but don't fear I'll show you how to figure it out in this section. First, you need to get a copy of your scan. You can usually get this from the radiology or imaging department at the hospital or clinic where you had the scan performed. Typically these come on a CD or DVD. The disc may already have a program that will allow you to view the scan. If it doesn't, you'll have to download a program capable of reading DICOM files, such as 3D Slicer. Open your scan according to the instructions of your specific program. You may notice that your scan is composed of several sets of images, called series. Each series contains a stack of images. For CT scans these are usually images in different planes (axial, coronal, and sagittal) or before and after administration of IV contrast. For MRI each series is usually a different pulse sequence, which may also be before or after IV contrast. Step 3: Does the medical imaging software program tell you what kind of scan you have? Most imaging software programs will tell you what kind of scan you have under a field called "modality." The picture below shows a screen capture from 3D Slicer. Looking at the Modality column makes it pretty obvious that this is a CT scan. Figure 3: A screen capture from the 3D Slicer program shows the kind of scan under the modality column. Step 4: Can you see the CAT scan or MRI table the patient is laying on? If you can see the table that the patient is laying on or a brace that their head or other body part is secured in, you probably have a CT scan. MRI tables and braces are designed of materials that don't give off a signal in the MRI machine, so they are invisible. CT scan tables absorb some of the x-ray photons used to make the picture, so they are visible on the scan. Figure 4: A CT scan (left) and MRI (right) that show the patient table visible on the CT but not the MRI. Step 5: Is fat or water white? MRI usually shows fat and water as white. In MRI scans the fat underneath the skin or reservoirs of water in the body can be either white or dark in appearance, depending on the pulse sequence. For CT however, fat and water are almost never white. Look for fat just underneath the skin in almost any part of the body. Structures that contained mostly water include the cerebrospinal fluid around the spinal cord in the spinal canal and around the brain, the vitreous humor inside the eyeballs, bile within the gallbladder and biliary tree of the liver, urine within the bladder and collecting systems of the kidneys, and in some abnormal states such as pleural fluid in the thorax and ascites in the abdomen. It should be noted that water-containing structures can be made to look white on CT scans by intentional mixing of contrast in the structures in highly specialized scans, such as in a CT urogram or CT myelogram. But in general if either fat or fluid in the body looks white, you are dealing with an MRI. Step 6: Is the bone black? CT never shows bones as black. If you can see bony structures on your scan and they are black or dark gray in coloration, you are dealing with an MRI. On CT scans the bone is always white because the calcium blocks (attenuates) the x-ray photons. The calcium does not emit a signal in MRI scans, and thus appears dark. Bone marrow can be made to also appear dark on certain MRI pulse sequences, such as STIR sequences. If your scan shows dark bones and bone marrow, you are dealing with an MRI. A question I am often asked is "If bones are white on CT scans, if I see white bones can I assume it is a CT?" Unfortunately not. The calcium in bones does not emit signal on MRI and thus appears black. However, many bones also contain bone marrow which has a great deal of fat. Certain MRI sequences like T1 and T2 depict fat as bright white, and thus bone marrow-containing bone will look white on the scans. An expert can look carefully at the bone and discriminate between the calcium containing cortical bone and fat containing medullary bone, but this is beyond what a layperson will notice without specialized training. Self Test: Examples of CT and MRI Scans Here are some examples for you to test your newfound knowledge. 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.
  6. The free democratiz3D 3D printing service 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.
  7. Version 1.0.0

    206 downloads

    These are the DICOM CT scan files for the instructables tutorial for creating a 3D printable model. Download the zipped folder and unzip it. You will add the entire directory to Slicer to start the process. Also included is the intermediary NRRD file for use with the democratiz3D file conversion service. You must be logged into your free embodi3d account to download. To register, click here.

    Free

  8. Occasionally files uploaded to the democratiz3D service for conversion to STL will not process correctly. What should you do if this happens? Usually these failure are due to one of two items: 1) There is some problem with the uploaded file, or 2) The uploaded file is simply massive (i.e. head to toe thin cut CT). If you encounter a problem with processing of your file, the first thing to do it check the quality of your input file. See my earlier tutorial, Choosing the Best Medical Imaging Scan to Create a 3D Printed Medical Model, if you want more details. 1) Check the modality. Did you upload an MRI when the operation calls for a CT? 2) Check for artifacts. This will often cause the model to have obvious deformities. The most common is beam hardening from dental fillings, as shown below. Normal teeth without fillings are on the left, and teeth with metal dental fillings are shown on the right. Unfortunately, you can't make an STL file from data that isn't there. If you scan has lots of artifact, you can either choose another scan or go through the laborious process of fixing the artifacts manually after the model is created. 3) Reconstruction kernel. This refers to the edge enhancement or sharpening algorithm that was applied to the scan images after they were acquired on the scanner. These are often done on dedicated bone or lung CT scans to enhance the contrast as make it easier for the radiologist to see subtle findings, like hairline fractures. Which the edge enhancement algorithm (or sharp kernel) as shown on the left below makes the edges easier to see, it also results in a speckled or noisy appearance of the tissue. This can confuse the algorithm because some very high intensity spots may look like bone. If your file is failing and you are using a sharp kernel series from you scan, consider using a different series that has a smooth kernel, such as shown on the right below. If you must stick with the sharp kernel, increase the threshold level to reduce the amount of "sand" in your output file and increase the changes of a successful processing job. Hope this helps, Dr. Mike
  9. 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.
  10. Please 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. >>> DOWNLOAD THE TUTORIAL FILE PACK <<< 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!
  11. Please note the democratiz3D service was previously named "Imag3D" In this tutorial you will learn how to quickly and easily make 3D printable bone models from medical CT scans using the free online service democratiz3D®. The method described here requires no prior knowledge of medical imaging or 3D printing software. Creation of your first model can be completed in as little as 10 minutes. You can download the files used in this tutorial by clicking on this link. You must have a free Embodi3D member account to do so. If you don't have an account, registration is free and takes a minute. It is worth the time to register so you can follow along with the tutorial and use the democratiz3D service. >> DOWNLOAD TUTORIAL FILES AND FOLLOW ALONG << Both video and written tutorials are included in this page. Before we start you'll need to have a copy of a CT scan. If you are interested in 3D printing your own CT scan, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figures 1 and 2 show the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available. Figure 1: The radiology department window at my hospital. Figure 2: An example of what a DVD containing a CT scan looks like. This looks like a standard CD or DVD. Step 1: Register for an Embodi3D account If you haven't already done so, you'll need to register for an embodi3d account. Registration is free and only takes a minute. Once you are registered you'll receive a confirmatory email that verifies you are the owner of the registered email account. Click the link in the email to activate your account. The democratiz3D service will use this email account to send you notifications when your files are ready for download. Step 2: Create an NRRD file with Slicer If you haven't already done so, go to slicer.org and download Slicer for your operating system. Slicer is a free software program for medical imaging research. It also has the ability to save medical imaging scans in a variety of formats, which is what we will use it for in this tutorial. Next, launch Slicer. Insert your CD or DVD containing the CT scan into your computer and open the CD with File Explorer or equivalent file browsing application for your operating system. You should find a folder that contains numerous DICOM files in it, as shown in Figure 3. Drag-and-drop the entire DICOM folder onto the Slicer welcome page, as shown in Figure 4. Click OK when asked to load the study into the DICOM database. Click Copy when asked if you want to copy the images into the local database directory. Figure 3: A typical DICOM data set contains numerous individual DICOM files. Figure 4: Dragging and dropping the DICOM folder onto the Slicer application. This will load the CT scan. Once Slicer has finished loading the study, click the save icon in the upper left-hand corner as shown in Figure 5. One of the files in the list will be of type NRRD. make sure that this file is checked and all other files are unchecked. click on the directory button for the NRRD file and select an appropriate directory to save the file. then click Save, as shown in Figure 6. Figure 5: The Save button Figure 6: The Save File box The NRRD file is much better for uploading then DICOM. Instead of having multiple files in a DICOM data set, the NRRD file encapsulates the entire study in a single file. Also, identifiable patient information is removed from the NRRD file. The file is thus anonymized. This is important when sending information over the Internet because we do not want identifiable patient information transmitted. Step 3: Upload the NRRD file to Embodi3D Now go to www.embodi3d.com, click on the democratiz3D navigation menu and select Launch App, as shown in Figure 7. Drag and drop your NRRD file where indicated. While NRRD file is uploading, fill in the "File Name" and "About This File" fields, as shown in Figure 8. Figure 7: Launching the democratiz3D application Figure 8: Uploading the NRRD file and entering basic information 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!
  12. Version 1.0.0

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    A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes which allows you to follow along with the tutorial. Included is an anonymized chest abdomen pelvis CT in both DICOM and NRRD formats.

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  13. Dear Embodi3D Members, We are excited today to announce democratiz3D -- the world's first one-click CT scan-to-medical model creation service. No longer will you have to struggle with expensive or difficult to use software to make 3D printable models. With democratiz3D, just upload your CT scan, fill out a few basic parameters, and click Submit. Within 10 or 15 minutes or so you should receive an email that your model is finished and ready to download. Your model will be manifold (error free) and ready for 3D printing. If you want to share your model with the community, you can do so with a click. democratiz3D is free for Embodi3D members. Right now only the bone making module is active. Look for tutorials and additional information in the coming weeks. democratiz3D takes medical 3D printing from something that was difficult, expensive, and time consuming and makes it quick, easy, and free. Click here to get started. Thank you for supporting us as we try to bring medical 3D printing to the masses! Sincerely, Dr. Mike and the Embodi3D team