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  1. A Foot 3D Model and Other Anatomical Models of the Lower Extremities Food 3D Model | embodi3D® This week we want to share some of the best representations of how embodi3D® members are using democratiz3D® conversions to create a foot 3D model and other skin, tissue, and skeletal features of the lower extremities. Successful 3D (three-dimensional) printing from radiologic images is multidisciplinary; accurate models that represent patient anatomy and pathologic processes require close interaction between radiologists and referring physicians. Preoperative 3D printing of bone structures has expanded planning and navigation of orthopedic procedures. Recently, the American Journal of Roentgenology published a research article on how a 3D printing was used to plan a femoracetabular impingement surgery. 3D printing is also contributing to novel surgical approaches for osteotomies, fracture fixation, and arthroplasties. Three-dimensional printing is an essential tool in the design and testing of complicated or innovative reconstructive surgeries. If you are Interested in lower limb 3D Printing here are some resources: Free downloads of hundreds of 3D printable lower limb models. Automatically generate your own 3D printable lower limb models from CT or CBCT scans. Have a question? Post a question or comment in the forum. Dr. Mike has also put together a tutorial on how convert CT scans to 3D-printable bone STL files (in minutes), as well as creating multiple bone model STL files from a single CT scan. Be sure to check these out. We look forward to your uploads! 1. A CT DICOM Dataset Conversion Showing the Bones of the Feet An excellent example of lower extremity 3D model of bony anatomy and skin surface of the L and R feet, as extracted from a CT DICOM dataset (0.5 mm slice thickness x 250 slices). 2. An Anatomically Precise 3D-Printed Talus Bone (Available for Free in STL Format) A 3D model human talus bone was generated from real CT scan data and is thus anatomically accurate as it comes from a real person. It shows the detailed anatomy of the talus bone -- a critical component of the ankle. In the attached thumbnails, the talus is shown in white with the rest of the foot bones in clear glass. 3. An Incredible 3D-Printed Leg model Showing Femur and Shaft Coxa vara describes a deformity of the hip where the angle formed between the head and neck of the femur and its shaft (Mikulicz angle) is decreased, usually defined as less than 120 degrees. Pathology It can be congenital or acquired. The common mechanism in congenital cases is a failure of medial growth of the physeal plate Classification One of the very early classifications proposed by Fairbank in 1928, is often considered most useful from a radiologic point of view. A slight modifcation of this system includes: idiopathic: congenital: mild or severe coxa vara, with associated congenital anomalies: see associations developmental: progressive, usually appearing between the ages of two and six years, with characteristic roentgenologic features rachitic: usually associated with active rickets adolescent: secondary to slipped capital femoral epiphysis traumatic: usually following fracture of the femoral neck (rare in children) inflammatory: secondary to tuberculosis or other infection secondary to other underlying bone diseases such as: osteogenesis imperfecta cretinism dyschondroplasia(s) Paget's disease osteoporosis capital coxa vara: occasionally seen in severe osteoarthritis and Legg-Perthes' disease 4. Use This STL File to 3D-Print an Ankle Bone This whole ankle was generated from real CT scan data and is thus anatomically accurate as it comes from a real person. It shows the detailed anatomy of the ankle bones. 5. View the Intricate Bones of the Calcaneus (Heel Bone) with this CT-Converted STL File This left calcaneus was generated from real CT scan data and is thus anatomically accurate as it comes from a real person. It shows the heel and articular surfaces of the calcaneus in great detail. 6. 3D-Print a Left Knee Joint Model with this Excellent STL Upload (Converted from CT Scan) A 3D model of left knee, we can see that is formed by three bones: the femur, the tibia and the patella. the knee joint is the largest synovial joint and provides the flexion and extension movements of the leg as well as relative medial and lateral rotations while in relative flexion. 7. Colorized STL Files of the Uploader's Own Lower Leg This is an excellent 3D model of the segmented bones from a partial weight bearing CT scan of a healthy 25 year old male. There is also a model of the outer foot surface (skin) to have the full foot volume. All bones are separate as well as combined as a single file. Shoe size 10.5 for reference. 8. A 3D-Printable Distal Tibia Bone (Generated from CT Scan Data) This 3D printable distal tibia bone from the left leg was generated from real CT scan data and is thus anatomically accurate as it comes from a real person. It shows the detailed anatomy of how the tibia articulates with the talus and distal fibula to form the ankle joint. In the thumbnails, the tibia is shown in white and the rest of the ankle bones in glass. 9. A CT-Converted Scan of the Feet, Showing the Intricate Bone Structure User mikefazz makes another appearance in our list with this CT scan of a 25-year-old healthy male (himself a few years back) partial weight bearing. 0.9766mm in plane and 0.5mm out of plane resolution. 10. Osteochondroma Detailed in a 3D-Printed Model of the Hip Bone A 3D model of a large osteochondroma on the posterior surface of the proximal femur. The popliteal artery is in close proximity to the osteochondroma. Osteochondroma, the most common benign bone lesion (representing about 45% of all benign bone tumors and 12% of all bone tumors) , is a cartilage- capped bony projection on the external surface of a bone. Usually diagnosed before the third decade, it most commonly involves the metaphyses of long bones, particularly around the knee and the proximal humerus. In general, the lower extremities are more often affected than the upper extremities. Malignant transformation to chondrosarcoma very rare, occurring in less than 1% of solitary lesions. Pain (in the absence of a fracture, bursitis, or pressure on nerves) and a growth spurt or continued growth of the lesion beyond skeletal maturity are highly suspicious for this complication. Variants of osteochondroma include subungual exostosis, turret exostosis, traction exostosis, bizarre parosteal osteochondromatous proliferation (BPOP), florid reactive periostitis, and dysplasia epiphysealis hemimelica (also known as intraarticular osteochondroma). References 1. Differential diagnosis of tumors and tumor-like lesions of bones and joints/Adam Greenspan and Wolfgang Remagen. 2007. 2. Marro, A., Bandukwala, T., & Mak, W. (2016). Three-dimensional printing and medical imaging: a review of the methods and applications. Current problems in diagnostic radiology, 45(1), 2-9. 3. Mitsouras, D., Liacouras, P., Imanzadeh, A., Giannopoulos, A. A., Cai, T., Kumamaru, K. K., ... & Ho, V. B. (2015). Medical 3D printing for the radiologist. Radiographics, 35(7), 1965-1988.
  2. DICOM to STL Files and Other Medical Scans Uploaded to embodi3D® 3D printing is a technology that is constantly evolving, especially among medical professionals who are converting medical CT scans into 3D-printed anatomical models. Patient-specific models with anatomical fidelity created from imaging dataset have the potential to significantly improve the knowledge and skills of a new generation of surgeons. In terms of research and education, 3D-printed anatomical models have proven to be a major benefit in helping students and researchers gain first-hand knowledge of specific conditions and the human anatomy. In a recent University of Pennsylvania research article ("From medical imaging data to 3D printed anatomical models") there merits of DICOM to STL conversions are highlighted and this is a medical technology that will continue to grow in the coming years. As a manufacturing process, 3D printing is well suited for the generation of biomedical phantoms, which is essentially a low-volume process for patient-specific models. The relatively high tooling costs for alternative processes—such as lost-wax investment casting—make 3D printing a cost-effective choice. This week we want to share the top ten downloads of medical scans. 3D prnting technology can be aligned with the predefined educational need, as listed below. Teaching anatomy, patient education: To teach the anatomy and explain pathology, models constructed of hard materials are often sufficient. The low cost and most accessible method FDM is most certainly the best choice if there is no need for fine printing definition and if the size of the model is large, otherwise we would recommend SLA. Models obtained by SLA present more detail thus would be better for small printing models (eg, coronary arteries). However, in the case of the thoracic aortic model with root aneurysm we put the emphasis on the realism of the geometry by representing as much as details as possible which is why we needed to use one of the most accurate 3D printing method: PJ. It also allowed us to change easily the colours of the 3D printed model if desired. Surgical planning and review of procedure: Surgical planning and review of procedure do not necessarily require materials to have the same mechanical properties of the biological tissues. Hard material model can be well representative of the anatomical structure and once again, FDM and SLA might be your best options. Preprocedural planning: preprocedural planning models are more complicated to fabricate since they require materials mechanically representative to the biological tissues. Discussions on the matter are provided in the following section where all printing methods are eventually used. To see more CT scans, check out the embodi3D® Medical CT Scan Files library. Remember: to get the most out of embodi3D® you need to register on the embodi3D® website. It's completely free and will take only a few minutes of your time. Plus, you will gain access to many of our cutting-edge conversion tools and algorithms! 1. A Whole-Body CT Scan in DICOM and NRRD File Formats First place: 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. Take a look to this CT model of whole body. 2. An Incredible CT Scan of an Open Bite CT is indicated for implant site assessment in anatomically difficult cases or when extensive implant treatment is planned. In addition, bone quantity and quality, in the implantation area are evaluated in the CT scans. Classifications are based upon jaw shape (degree of resorption), bone quality (amount of compact bone) and bone density. Information about the location of vital structures, such as mandibular canal, mental foramen, incisive foramen, maxillary sinuses and nasal cavity can be evaluated. 3. Head and Neck CT Scan — Great Addition to our Top 10 Medical CT Scans! A source Head and Neck CT scan in NRRD file format for the Radiological Society of North America (RSNA) Annual Meeting 2017 course on Open-Source and Freeware Medical 3D Printing, RCA12 and RCA21, November 26 and 27, 2017. Be sure to view the full tutorial that uses this file here. https://meeting.rsna.org/program/index.cfm Search for "3D Printing Hands-on with Open Source Software: Introduction (Hands-on)" CT angiography of the cerebral arteries is a noninvasive technique allows visualization of the internal and external carotid arteries and vertebral arteries and can include just the intracranial compartment or also extend down to the arch of the aorta. By using multidetector CT (MDCT) after intravenous contrast administration, the vessels become enhanced with contrast allow them to be differentiated from adjacent tissues. Following image acquisition, post-processing techniques are applied for better 3D visualization of the vessels and their abnormalities. 4. A Contrast-Enhanced CT Scan Showing a Chest Wall Tumor Tumors of the chest wall are varied, some of which are found most often in this region. They can be divided into benign and malignant tumors and into those which arise in the ribcage and those of soft tissue density. - Benign: soft tissue , haemangioma: common, lymphangioma: common, lipoma: chest wall lipoma, schwannoma, neurofibroma, ganglioneuroma paraganglioma, skeletal (ribcage), fibrous dysplasia: common, aneurysmal bone cyst (ABC): common, giant cell tumour (GCT), ossifying fibromyxoid tumour, chondromyxoid fibroma, osteochondroma, mesenchymal hamartoma of chest wall: sometimes even considered a developmental anomaly - Malignant: The most common malignant lesions are metastases. Lesions include: rhabdomyosarcoma: common, Ewing sarcoma: including Askin tumour (or pPNET), ganglioneuroblastoma, neuroblastoma, angiosarcoma, leiomyosarcoma, malignant fibrous histiocytoma (MFH), malignant peripheral nerve sheath tumour, dermatofibrosarcoma protuberans, skeletal (ribcage), chest wall metastases: common, myeloma, chondrosarcoma osteosarcoma, 5. CT Scan of the Brain and Structures (Without Contrast) This upload shows a CT scan of the human brain and related structures. This scan has not been contrast-enhanced. window: W:2800 L:600 Review the bones. This should always be performed, even when a bony algorithm hasn't been provided or where slice thickness is suboptimal. Note that if there is a history of trauma, then dedicated thin bony images are required to detect undisplaced fractures. Review the skull vault for any fractures or destructive lesions. Spend some time checking the base of the skull as the increased complexity of this region can make identification of abnormalities more difficult. Don't forget to ensure that both TMJs are normally aligned. Review the paranasal sinuses for evidence of fluid that may represent acute sinusitis or, in the correct setting, fractures. 6. Whole-Body NRRD File Showing the Chest, Abdomen, and Pelvis A whole body NRRD file converted from CT Scan for Medical 3D Printing includes the chest, abdomen and pelvis. It includes a skin, bone and muscle 3D model. 7. Jawbone Implant as Shown in a 3D Model A 3D model of mandible implant with exquisite detail from a CT scan from planning. Current 3D-printers are easy to use and represent a promising solution for medical prototyping. The 3D printing will quickly become undeniable because of its advantages: information sharing, simulation, surgical guides, pedagogy. They allow for better preoperative planning and training for the procedures and for pre-shaping of plates. Occlusal splints and surgical guides are intended for the smooth transfer of planning to the operating room. 8. The Whole Body of a Female — Available in a 3D Printer-Ready Format A 3D model of female's whole body (with bone, muscle and skin 3D printing) 9. Head and Neck Scan from the Cancer Imaging Archives 62yo male skull from the Head-Neck Cetuximab collection of The Cancer Imaging Archives. 10. Contrast-Enhanced CT Scan of the Skull and Brain A brain CT scan with contrast showing all the structures of the skull and brain. References 1. Lekholm U, Zarb G. Patient selection and preparation. In: Brånemark P-I, Zarb G, Albrektsson T, editors. Tissue-integrated prostheses. Osseointegration in clinical dentistry. Chicago: Quintessence; 1985 p. 199 – 209. 2. Wood MR, Vermilyea SG. A review of selected dental literature on evidence-based treatment planning for dental implants: report of the Committee on Research in Fixed Prosthodontics of the Academy of Fixed Prosthodontics. J Prosthet Dent 2004; 92: 447 – 62. 3. Lindh C, Petersson A, Klinge B. Measurements of distances related to the mandibular canal in radiographs. Clin Oral Impl Res 1995; 6: 96 – 103. 4. Garcia, J., Yang, Z., Mongrain, R., Leask, R. L., & Lachapelle, K. (2018). 3D printing materials and their use in medical education: a review of current technology and trends for the future. BMJ Simulation and Technology Enhanced Learning, 4(1), 27-40.
  3. I wanted to know that, is there any size difference between the .stl file generated form CT scan and the actual size of the skull of the patient. at the conversion, is there any dimensional change could be happen in the software.
  4. There are many challenging cases, in which the single segmentation is not enough. The paranasal sinuses and the congenital heart defects are notable examples. My usual workflow was to segment whatever I can as good as it's possible, to clean the unnecessary structures and the artefacts, to export the segmentation as stl 3d model and then to "CAD my way around". This is solid philosophy for simple, uncomplicated models, but for complex structures with a lot of small details and requirement from the client for the highest quality possible, this is just not good enough, especially for a professional anatomist like myself. Then I started to exploit the simple fact, that you're actually able to export the model as stl, to model it with your CAD software and then to reimport it back and convert it into label map again. I called this "back and forth technique". You can model the finest details on your model and then you can continue the segmentation right where you need it, catching even the slightest details of the morphology of the targeted structure. This technique, combined with my expertise, gives me the ability to produce the best possible details on some of the most challenging cases, including nasal cavity, heart valves, brain models etc. etc.To use this technique, just import the stl file, convert it into a label map (for 3D slicer - segmentation module/ export/import models and label maps). The main advantages of this technique are:1. You can combine the segmentation with the most advanced CAD functions of your favorite software. Two highly specialized programs are better than one "Jack of all trades" (cough cough Mimics cough cough)2. Advanced artefact removing.3. Advanced small detail segmentation and modelling.4. Combined with several markers (separate segmentations, several voxels in size) on the nearby anthropometric points, this technique increases the accuracy of the final product significantly. Without points of origin, the geometry of your model will go to hell, if you're not especially careful (yes, I'm talking about the 3D brushes in Slicer).5. You can easily compare the label map with the 3d model, converted back. Every deviation, produced during the CAD operations will be visible like a big, shining dot, which you can easily see and correct. This is one of the strongest quality control techniques.6. You can create advanced masks with all the geometrical forms you can possibly imagine, which you can use for advanced detail segmentation. Those masks will be linked with the spatial coordinates of the targeted structures - the stl file preserves the exact coordinates of every voxel, which was segmented.7. You can go back and forth multiple times, as many as you like.8. This technique is more powerful than the best AI, developed by now. It combines the best from the digital technologies with the prowess of the human visual cortex (the best video card up to date).The main disadvantages are:1. It's time consuming.2. It produces A LOT of junk files.3. Advanced expertise is needed for this technique. This is not some "prank modelling", but an actual morphological work. A specialized education and practical experience in the human anatomy, pathology and radiology will give you the best results, which this technique can offer. 4. You need highly developed visual cortex for this technique (dominant visual sense). This technique is not for the linguistic, spatial-motor, olphactory etc. types of brains. Recent studies confirms, that a part of the population have genetically determined bigger, more advanced visual cortex (The human connectome project, Prof. David Van Essen, Washington University in Saint Louis). Such individuals become really successful cinematographers, designers, photographers and medical imaging specialists. The same is true for all the other senses, but right now we're talking about visual modality and 3D intellect (I'm sorry, dear linguists, musicians, craftsmen and tasters). It's not a coincidence that I have so many visual artists in my family (which makes me the medical black sheep). But if you don't have this kind of brain, you can still use the technique for quality control and precise mask generation. Just let the treshould module or the AI to do the job for you in the coordinates, in which you want (You should really start using the Segment Editor module in Slicer 3D).5. You really need to love your work, if you're using this technique. For the usual 3D modelling you don't need so many details in your model and to "CAD your way around" is enough for the task.6. You should use only stl files. For some reason, the obj format can't preserve the spatial geometry as good as the stl format. Maybe because the stl is just a simple map of vertex coordinates and the obj contains much more sophisticated data. The simple, the better.On the picture - comparison of the semilunar valves, made by treshould segmentation at 250-450 Hounsfield units (in green) and modelled and reimported model (in red).
  5. Version 1.0.0

    978 downloads

    This Brain model was created from a high resolution MRI scan. The model includes the cerebrum. The cerebellum and brain stem are not depicted. The model has been made hollow, with 4 mm wall thickness to save on material when 3D printing. The model is full-size. It has been successfully printed at full size on an Ultimaker 3 Extended printer, and at 95% size on a Formlabs Form 2 printer. Technical parameters: Vertices: 350725 Triangles: 701950 Size: 17.9 x 13.4 x 11.5 cm

    Free

  6. 0 downloads

    This is a 3D model of lumbar vertebrae ready for print., spine, bone, stl, 3dmodel, print, column,

    $1.99

  7. 1,025 downloads

    This full-size skull with web-like texture was created from a real CT scan. The beautiful lace-like structure not only makes the piece aesthetically interesting and strong, but also reduces material cost when 3D printing. The file is in STL format. This is the full-size version. A half-size version is also available here. Please share your 3D printable creations in the File Vault as I have shared mine with you. Feel free to print this model for your own personal use but please do not use this file for commercial purposes.

    Free

  8. 159 downloads

    Half skull, full size, STL format This full size, half skull model shows detailed skull anatomy, including the cervical spine, skull base foramina, paranasal sinuses, and orbit. Perfect for teaching and as a discussion piece. Available for download in full and half size, STL and COLLADA formats. Please download and modify! Share your new creation by uploading to Embodi3D!

    Free

  9. Version 1.0.0

    47 downloads

    mandible - stl file processed This file was created with democratiz3D. Automatically create 3D printable models from CT scans. Learn more. mandible, stl, 3d, model, angle, body, symphisis, dental, arch, dentistry, coronoid, process, bone

    Free

  10. A member asked us the following question: "I uploaded a NRRD file and was hoping to be able to download it as an STL - any advice?" You can use our democratiz3D service to automatically convert an NRRD into a 3D printable bone STL model. You can find more about democratiz3D here. There are many tutorials available here. Hope this helps.
  11. 71 downloads

    This 3D printable STL file of a hip with coxa vara was generated from real CT scan data and is thus anatomically accurate as it comes from a real person. It shows coxa vara, which is a deformity of the hip due to an abnormal angle of the femoral head relative to the shaft. Download is free for registered members. This file was originally created by Dr. Bruno Gobbato, who has graciously given permission to share it here on Embodi3D. Modifications were made by Dr. Mike to make it suitable for 3D printing. The file(s) are distributed under the Creative Commons Attribution-NonCommercial-ShareAlike license. It can't be used for commercial purposes. If you would like to use it for commercial purposes, please contact the authors. Technical specs: File format: STL Manifold mesh: Yes Triangles: 217408

    Free

  12. 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!
  13. Version 1.0.0

    455 downloads

    This 3D printable model of a human heart was generated from a contrast enhanced CT scan. This model is an improvement over a prior version (here). It shows the heart with slices cut in the anatomical transverse plane. If you are interested in a heart with short-axis slices, check out my short-axis stackable slice model here. Notches have been added to ensure the slices fit together and do not slide against each other. The model demonstrates the detailed anatomy of the human heart in exquisite detail. Each slice stacks on top of the prior slice to form a complete human heart. Individual slices show the detailed cardiac anatomy of the right and left ventricles, and right and left atria, and outflow tracts. Perfect for educational purposes. It has been validated as printable on an Ultimaker 3 Extended printer. Technical parameters: manifold STL (watertight) vertices: 462576 triangles: 925800 dimensions: 15.1 x 15.2 x 10.5 cm

    $19.99

  14. Version 1.0.0

    5 downloads

    Dog Legs to convert, whole, body, ct, scan, without, contrast, .stl, axial, dicom, muscles, pectoral, shoulder, bone, cervical, dorsal, lumbar, sacrum, tail, trachea, esophagus, lung, heart, cardiac, mediastinum, ribs, scapula, frontleg, foreleg, k9, canine, dog, pelvis, femur, head, neck, skull,

    Free

  15. Version 1.0.0

    61 downloads

    GNGuir - stl file processed This file was created with democratiz3D. Automatically create 3D printable models from CT scans. Learn more. lower, limb, stl, 3d, model, bone, knee, fibula, tibia, patella, Lateral femoral epicondyle, Medial femoral epicondyle, Lateral femoral condyle, Medial femoral condyle, Lateral tibial condyle, Medial tibial condyle, Medial and lateral tubercles of the intercondylar eminence, printable

    $9.99

  16. 313 downloads

    This anatomically accurate L3 vertebra was extracted from a DICOM CT dataset (0.5 mm slice thickness x 95 slices). The model may be useful for medical education and shows shows the vertebral body, spinous process, facets, transverse processes and spinal canal. The file is in STL format and compressed with ZIP. Printed on a Makerbot Replicator 1. Thank you to Dr Mike for the excellent renders. Find us at www.healthphysics.com.au

    Free

  17. 888 downloads

    This half-size skull with web-like texture was created from a real CT scan. The beautiful lace-like structure not only makes the piece aesthetically interesting and strong, but also reduces material cost when 3D printing. The file is in STL format. This is the half-size version. A full-size version is also available here. Please share your 3D printable creations in the File Vault as I have shared mine with you. Feel free to print this model for your own personal use but please do not use this file for commercial purposes.

    Free

  18. UPDATED TUTORIAL: A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes Hello, it's Dr. Mike here again with another tutorial and video on medical 3D printing. In this tutorial we're going to learn how to take a DICOM-based medical imaging scan, such as a CT scan, and convert into an STL file in preparation for 3D printing. We will use the free, open-source software program Osirix to do this. Once the file is converted into STL format, we will use the free software packages Blender and Meshmixer to prepare the file for 3D bioprinting. If mastered, this material should easily allow you to make a high-quality 3D printed medical model in less than 30 minutes using free software. Expensive, proprietary software is not needed. This tutorial is designed primarily for Macintosh users since Osirix is a Macintosh-only program. If you use Windows or Linux, please stay tuned for my upcoming tutorial on using free, open-source 3D Slicer to create medical and anatomic models. If you haven't already done so, please see my tutorial on selecting the best medical scan to create a 3D printed model. If you start your 3D printed model project with the wrong kind of scan, your model will not turn out well. Selecting the right kind of scan is critically important and will save you a lot of frustration. Take a few minutes to look over this brief tutorial. It will be well worth your time. Before you start, DOWNLOAD THE FILE PACK that accompanies this video so you can follow along on your own computer. When you finish the tutorial, you will have your very own 3D printable skull STL file. Download is free for members, and registration for membership is also free and only takes a minute. Video 1: The video version of this tutorial. It takes you from start to finish in 30 minutes. The written version here has more detail though. A Few Brief Definitions What is Osirix? Osirix is a Macintosh-only software package for reading medical imaging scans (Figure 1). There are several versions. There is an FDA-approved version designed for doctors reading scans in clinics and hospitals, a 64-bit version for research and other nonclinical activities, and a free, 32-bit version. The main difference between the free 32-bit version and the paid 64-bit version is the 64-bit version can open very large imaging studies, such as MRI exams with thousands of images. The 32-bit version is limited to about 500 images. Additionally, there is a performance boost with the paid versions. If you are just getting into 3D bioprinting, the free, 32-bit version is a great place to start. It can be downloaded at the Osirix website here. Figure 1: An example of Osirix being used to read a CT scan. What is DICOM? DICOM stands for Digital Imaging and Communications in Medicine. It is the standard file format for most medical imaging scans, such as Computed Tomography (CT), Magnetic Residence Imaging (MRI), ultrasound, and x-ray imaging studies. What is STL? STL, or STereoLithography format , is an engineering file format created by 3D Systems for use with Computer Aided Design software (CAD). The file format is primarily used in engineering, and has become the standard file format for 3D printing. The Problem with 3D Printing Anatomic Structures The major problem with trying to 3D print anatomic structures from medical scans is that the medical scan data is in DICOM format and 3D printers require files in STL format. The two formats are incompatible. There are very expensive, proprietary software packages that can perform the conversion between DICOM and STL. A little-known secret is that this can also be done using free, open-source software. Osirix is the best solution for Macintosh. 3D Slicer is the best solution for Windows and Linux. I will discuss 3D Slicer in an upcoming tutorial. If you haven't already, please download the DICOM data set we will be using in this tutorial. This data set is from a high quality CT scan of the brain and skull. It has been anonymized and has been put in the public domain for research by the US National Cancer Institute. Also included with the download packet are other files we will use for this tutorial, including the final STL file of the skull. The download is free for members, and registration for membership is also free and only takes a minute. From the Macintosh Finder navigate to the folder with the downloaded tutorial file pack and double-click on the file TCGA-06-5410 sharp.zip. Opening the CT scan with Osirix Open Osirix. From the File menu, click Import, Import Files. Click Open. (Figure 2) Figure 2: Importing the CT scan into Osirix Navigate to the folder that contains your DICOM data set. Click the Open button. Osirix will ask you if you want to copy the DICOM files into the Osirix database, or only copy the links to these files. Click "Copy Files." Osirix will begin to copy the files into the database. A progress bar will be shown on the lower left-hand corner. When the data is imported you'll see a small orange circle with a "+" in it. This orange circle will eventually go away when Osirix is finished analyzing the study, but you can open the study and work with it while Osirix does some cleanup postprocessing. Left click on the study. You will see an icon with a label "FIDUCIALS 1.0 SPO cor, 216 Images." This is a CT scan of the head with coronal slices at 1 mm intervals. Double-click on this icon, Figure 3. Figure 3: The study when opened Osirix will remind you that you're not supposed to be using it for diagnostic scan reading on real patients unless you are using the more expensive FDA approved version, Osirix MD we're just using it to create a 3D model, so click "I agree." At this point, the study will load. Use the mouse wheel or the bar on the top of the screen to scroll. You can see that this is a pretty decent CT scan of the head for 3D printing. There is not much artifact from metallic dental implants because the maxilla and mandible have been cut off. Segmenting the bony skull and creating a new series We can measure the density of the bony structures using the Region Of Interest or ROI tool. This measures the Hounsfield density, or CT density, of the target area. Select the oval tool from the drop-down menu, Figure 4. Figure 4: The ROI tool. Choose a region of bone using the oval tool. You will see that information about this region is displayed. What we are interested in is the mean density, which in this case is 1753.194, Figure 5. Figure 5: Density measurement using ROI tool. The mean density is 1753.194, as shown in maroon field. Use the ROI tool to select another region in the brain. You will see that the mean attenuation, or density, is much less, in this case 1059.137, Figure 6. Figure 6: Density measurement of the brain tissue. Finally, use the oval tool to choose an area in the air adjacent to the head. You can see that the mean attenuation of this region is 38.514, Figure 7. Figure 7: Density measurement of air. In this scan the Hounsfield attenuation numbers have been shifted. In a typical scan, air measures about -1000, soft tissue between 30 and 70, and bone typically greater than 300. In this scan those numbers have been increased by 1000. Since we were thorough enough to check the Hounsfield attenuation before moving on, we can easily correct for this shift. Under ROI menu select Grow Region 2D/3D Segmentation, Figure 8. Figure 8: The Grow Region tool In the Segmentation Parameters window that pops up, set the following: Lower Threshold 1150 Upper Threshold 3000. Generate a new series with: Inside pixels 1000 Outside pixels 0 Be sure to check the checkbox next to the Set Inside Pixels, and Set Outside Pixels fields, Figure 9. Figure 9: Setting up the Segmentation Parameters window. Next, make sure you select a starting point for the algorithm. Left click on one of the skull bones. Green crosshairs will show. All of the bone that is contiguous with point you clicked will now be highlighted in green, Figure 10. Figure 10: Setting the starting point for segmentation. The target region turns green. Click the Compute button Osirix will generate a new series with the bones being a single white color with a value of 1000, and everything else being a black color with a value of zero, Figure 11. Creating a separate series just for 3D printing purposes is the secret to getting good 3D models from Osirix. Trying to generate a 3D surface model directly from the 3D Surface Rendering function underneath the 3D Viewer menu is tempting to use, however it will not work well for generating STL files. This is not obvious, and the source of much frustration for beginners trying to use Osirix for 3D printing. Figure 11: The new bitmapped series shown on right of screen. This series has only two colors, black and white. It is idea for conversion to and STL surface model. Generating an STL file from the new bitmapped series Now we are ready to create our 3D surface model. Make sure that your new bitmapped series is highlighted. Click on the 3D viewer menu and select 3D Surface Rendering, Figure 12. Leave the settings set to their default values. Click OK as shown in Figure 13. Figure 12: Selecting 3D Surface Rendering Figure 13: Setting 3D surface rendering settings Osirix will then think for a few moments as it prepares the surface. You can see that a relatively good approximation of the skull has been generated. Use of the left mouse button to rotate the 3D model. Next were going to export the 3D surface model to an STL file. Click Export 3D-SR and choose Export as STL as show in Figure 14. Type the file name "skull file." Click Save. Figure 14: Exporting model to STL file format. Cleaning up the 3D model in Blender You can see from the 3D rendering that there are many small islands of material that have been included with the STL file. Also, the skull has a very pixelated appearance. It does not have the smooth surface that would be expected on a real skull. In order to fix these problems, we're going to do a little postprocessing in Blender, a free open-source 3D software program. If you don't already have Blender on your computer, you can download it free from blender.org. Blender is available for Windows, Macintosh, and Linux. Select your operating system, preferred installation method, and download mirror. Once Blender is installed on your computer, open it. In the default scene there will be a cube. We don't need this. Right click on the cube to select it. Then delete it using the delete key on a full keyboard or the X key on a laptop keyboard. Blender will ask you to confirm you want to delete the object. Click Delete as shown in Figure 15. Figure 15: Deleting the default cube. Next, we are going to import the skull STL file. From the File menu select Import, STL, as shown in Figure 16. Navigate to the skull STL file you saved from Osirix, and double-click it. Blender will think for a few seconds and then return to what appears to be an empty scene, as shown in Figure 17. Where is your skull? To find your skull, use the mouse scroll wheel to zoom out. If you zoom out far enough you will see the skull. The skull appears to be gigantic, as shown in Figure 18. This is because the default unit of measurement in the skull is 1 mm. In Blender, an arbitrary unit of measurement called a "blender unit" is used. When the skull was imported, 1 mm of real size was translated into 1 blender unit. Thus the skull appears to be hundreds of blender units large, and appears very big. Figure 16: Importing the STL file into Blender Figure 17: The "empty" scene. Where is the skull? Figure 18: Zoom out and the skull appears! The skull is also offset from the origin. We are going to correct that. Make sure that the skull is still selected by right clicking on it. If it is selected it will have a orange halo. In the lower left corner of the window click on the Object menu. Select Transform, Geometry to Origin as shown in Figure 19. The skull is now centered on the middle of the scene. Figure 19: Centering the skull in the scene. Deleting Unwanted Mesh Islands First, let's get rid of the extra mesh islands. There is a menu in the lower left-hand corner of the window that says Object Mode. Click on this and go to Edit Mode, as shown in Figure 20. Figure 20: Entering Edit mode in Blender. Now we are in Edit Mode. In this mode we can edit individual edges and vertices of the model. Right now the entire model is selected because everything is orange. In edit mode you can select vertices, edges, or faces. This is controlled by the small panel of buttons on the bottom toolbar. Make sure that the leftmost or vertex selection mode is highlighted and then right click on a single vertex on the model, as shown in Figure 21. That vertex should become orange and everything else should become gray, because only that single vertex is now selected, Figure 22. Figure 21: Vertex selection mode Figure 22: Select a single vertex by right clicking on it. Under the Select menu, click Linked, as shown in Figure 23. Alternatively, you can hit Control-L. This selects every vertex that is connected to the initial vertex you selected. All the parts of the model that are contiguous with that first selection are now highlighted in orange. You can see that the many mesh islands we wish to get rid of are not selected. Figure 23: Selecting all linked vertices. We are next going to invert the selection. Do this by again clicking on the Select menu and choosing Inverse, Figure 24. Alternatively, you can hit Control-I. Now, instead of the skull being selected, all of the unwanted mesh islands are selected, as shown in Figure 25. Now we can delete them. Hit the delete key, or alternatively the X key. Blender asks you what you want to delete. Click Vertices, Figure 26. Now all of those unwanted mesh islands have been deleted. Figure 24: Inverting the selection. Figure 25: The result after inverting the selection. Only the unwanted mesh islands are selected! Figure 26: Deleting the unwanted mesh islands. Repairing Open Mesh Holes We can see that on the top of the skull there is a large hole where the skull was cut off by the scanner. Because the bone surface was cut off, Osirix left a gaping defect, Figure 27. Before 3D printing, this will have to be corrected. This is what is called a manifold mesh defect. It is an area where the surface of the model is not intact. A 3D printer will not know what to do with this, such as whether it should be filled in or left hollow. Fortunately, it is relatively easy to correct. Figure 27: A large open mesh hole at the top of the skull. Using the Select menu in the lower left-hand corner, click on Non-Manifold. This will select all of the non-manifold mesh defects in your model. You can see that the edge of our large hole at the top of the skull has been selected and turned orange. This confirms that this defect has to be fixed. Unselect by hitting the A key. Then, go to Edge select mode by clicking on the Edge Select button along the lower toolbar. Holding down the Alt key, right-click on one of the edges of the target defect, in this case the top of the skull. That familiar orange ring has formed. Your selection should look like Figure 28. Let's fill in this hole by creating a new face. Hit the F key. This creates a new face to close this hole, Figure 29. Figure 28: The edge of the hole is selected, as indicated by the orange color. Figure 29: The hole when filled with a new face. Due to the innumerable polygons along the edges, the face is actually quite a complex polygon itself. Let's convert it to a simpler geometry. With the face still selected hit Control T. You can alternatively go to the Mesh menu and select Faces, Triangulate Faces as shown in Figure 30. This will convert the complicated face into simpler triangles. As you can see, some of these triangles are quite large relative to the other triangles along the skull surface. These large triangles may become apparent when smoothing algorithms are applied or 3D printing is performed. Let's reduce their size. Hit the W key and then select Subdivide Smooth, as shown in Figure 31. The triangles are now subdivided. Let's repeat that operation again so that they are even smaller. Hit the W key and again select Subdivide Smooth. Figure 30: Converting all faces into triangles. ] Figure 31: Subdividing and smoothing the selected faces. Smoothing the Model Surface Next let's get rid of that pixelated appearance of the model surface. First, we need to convert all of the polygons in the model to triangles. The smoothing algorithms just work better with triangles. Staying in Edit mode, hit the A key. The A key toggles between selecting all and unselecting all. If you need to, hit the A key a second time until the entire model is orange, thus indicating that it is selected. Hit Control-T, or alternatively use the Mesh menu, Faces, Trangulate Faces. This will convert any remaining complex polygons to triangles. Go back to Object mode by hitting the tab button or selecting Object Mode from the bottom toolbar. We are now going to apply a smoothing function, called a modifier, to the skull. Along the right of the screen you'll see a series of icons, one of which is a wrench, as shown in Figure 32. Click on that. This brings up the modifier panel, a series of tools that Blender uses to manipulate digital objects. Click on the Add Modifier button and select the Smooth modifier. Do not select the Laplacian Smooth modifier. That is different. We just want the regular Smooth modifier, as shown in Figure 33. Leaving the Factor value at 0.5, increase the Repeat factor until you are satisfied with the surface appearance of your model. For me, a factor of 20 seemed to work, Figure 34. At this point the modifier is only temporary, and has not been applied to the model. Click on the Apply button. Now the smoothing function has been applied to the model. Figure 32: The Modifiers toolbar on the right. Figure 33: The Smooth modifier Figure 34: Setting the Smooth modifier to repeat 20 times. Rotating and Adjusting the Model Orientation When the model was originally exported from Osirix and opened in Blender, it was at a strange orientation. We can correct to this easily. Click on the View menu from the left portion of the lower now bar and select Front. This orients the model from the frontal view, and you can see that in this orientation we are looking at the top of the skull. To correct this, we will rotate the model along the X axis. First, make sure that the cursor is inside the model window. Then, Hit the R key and then the X key, and type "180." This will rotate the model on the X axis by 180°. Hit the return key to confirm the modification. Don't worry if the skull isn't facing the correct way right now, we will fix that later. Now we are ready to export our cleaned up skull model. Go to the File menu, click Export, STL. Navigate to your desired folder and save your STL file. Since I corrected several defects in this mesh file, I called the file "skull file corrected.stl" Performing a Final Inspection Using Meshmixer If you haven't already done so, go to the Autodesk Meshmixer website at http://www.meshmixer.com/download.html and download and install Meshmixer. The software is free. Once installed open the program and select Import. Navigate to your STL file and double-click it. Meshmixer has a variety of nice features, and one of them is a mesh correction function. Once your file is open click on the Analysis button along the left nav bar. Click on Inspector as shown in Figure 35. Meshmixer will now analyze the STL file for obvious mesh defects. Anything that is detected will be highlighted by red, pink, or blue lines. You can see that our skull model appears to be defect free. Click on the done button and quit Meshmixer. Figure 35: Running the inspector tool in MeshMixer Your STL file of the skull is now ready for 3D printing! Conclusion In this tutorial you have learned how to take a DICOM data set from a CT scan and use it to create a 3D printable STL file using free software. First we used the Osirix to segment a CT scan and convert it to an STL file. Then we performed cleanup operations on the STL file using the Blender and Meshmixer, both free programs. For additional information on how to select an appropriate CT or MRI scan for 3D printing please see my previous tutorial. If you want to learn more about using Blender to fix more extensive defects in bone models, you can view to other tutorials I have created: 3D Printing of Bones from CT Scans: A Tutorial on Quickly Correcting Extensive Mesh Errors using Blender and MeshMixer Preparing CT Scans for 3D Printing. Cleaning and Repairing STL Files from Bones using Blender, an advanced tutorial A variety of useful tutorials for 3D printing is available on the Tutorials page. If you are planning on attending the 2015 Radiological Society of North America (RSNA) meeting in Chicago this November, look for my hands-on course "3D Printing and 3D Modeling with Free and Open-Source Software." I will give more tips and tricks for creating great 3D printed medical models using freeware. I hope you find this tutorial helpful in creating your own medical and anatomic models for 3D printing. Please stay tuned for my next tutorial on using the free, open-source program 3D Slicer to create medical 3D models on Windows and Linux platforms. If you are creating your own 3D printed medical models, please share your models with the Embodi3D community in the File Vault. If you have questions or comments, please leave a comment below or start a discussion thread in the Forums. Sample free downloads A Collection of Free Downloadable STL Skulls for you to 3D print yourself. 3D printable human heart in stackable slices, shows amazing internal anatomy. A Collection of Spine STL files to download and 3D print. Follow Embodi3D on social media Twitter | Facebook | LinkedIn | YouTube | Google+
  19. UPDATED TUTORIAL: A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes Hello and welcome back. I hope you enjoyed my last tutorial on creating 3D printable medical models using free software on Macintosh computers. In this brief video tutorial I'll show you how to create a 3D printable skull STL file from a CT scan in FIVE minutes using only free and open source software. In the video I use a program called 3D Slicer, which is available from slicer.org. 3D Slicer works on Windows, Macintosh, and Linux operating systems. Also, I use Blender, which is available from blender.org, to perform some mesh cleanup. Finally, I check my model prior to 3D printing using Meshmixer from Autodesk. This is available at meshmixer.com. All software programs are free. If you like this, view my complete tutorial where I go through each step shown here in detail. I hope you enjoy the video.
  20. 187 downloads

    This 3D printable STL file of the cervical spine was generated from real CT scan data and is thus anatomically accurate as it comes from a real person. It shows the relationship between the skull base and the C1 and C2 vertebrae, as well as the alignment and position of the cervical vertebrae. Perfect for education. Download is free for registered members. This file was originally created by Dr. Bruno Gobbato, who has graciously given permission to share it here on Embodi3D. Modifications were made by Dr. Mike to make it suitable for 3D printing. The file(s) are distributed under the Creative Commons Attribution-NonCommercial-ShareAlike license. It can't be used for commercial purposes. If you would like to use it for commercial purposes, please contact the authors. Technical specs: File format: STL Manifold mesh: Yes Triangles: 352794

    Free

  21. Version 1.0.0

    24 downloads

    This is my latest version of my paranasal sinuses model with emphasis on the nasal cavity. Every cavity is connected and can be reached with endoscope as an otorhynolaryngological training model. The wall thickness is 0,6mm. For best results, use transparent material with water or oil soluble support. paranasal, sinuses, osteology, ethmoid, sinus, paranasal, septum, nasal, maxillary, turbinate, otorhynolaryngology, 3d, model, stl, frontal, sphenoid, facial

    $25.00

  22. Version 1.0.0

    7 downloads

    Find a best way of rander, .stl, bone, axial, ct, scan, frontal, temporal, parietal, occipital, petrous, ridge, mastoid, cells, paranasal, sinuses, maxillary, sphenoid, ethmoid, clinoid, apophysis, atlas, axis, cervical, spine, neck, nasal, septum, maxilla, mandible, upper, lower, incisor, molar, premolar, incisor, molar, premolar, canine, hard, palate,

    Free

  23. Version 1.0.0

    3 downloads

    STL testing, .stl, testing, maxilla, bone, 3d, model, .stl, printable, teeth, angle, body, edentula, partial, incisor, molar, premolar, canine

    Free

  24. Version 1.0.0

    135 downloads

    from cat scan, bone, stl, dicom, 3dmodel, lumbar, spine, vertebrae,

    Free

  25. Version 1.0.0

    24 downloads

    CT HAND - stl file processed hand, wrist, bone, 3dmodel, stl, upper, limb, print

    Free

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