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  1. Here is another tutorial on hollowing meshes, specifically head meshes to obtain a face shell, but I use this method to hollow out bones as well. Dr. Mike recently posted a great video tutorial on hollowing a head using Meshmixer: https://www.embodi3d.com/blogs/entry/359-how-to-create-a-hollow-shell-from-a-medical-stl-file-using-meshmixer/. I tend to go back and forth between Meshmixer and Meshlab for different functions to prep a print, but I like to use Meshlab for hollowing because it's quick and you can easily control how much "external" surface is selected, which is especially handy for models that have highly complex internal structures. Note that this workflow is also useful if you simply want a 3D model (for viewing/interacting in software, Sketchfab) of a smaller file size where you don't need the internal structures and/or you don't want to decimate the model to achieve a smaller file size. Here are the steps to hollow a head model in Meshlab. I will post screeshots below which you can also find in the Gallery, https://www.embodi3d.com/gallery/album/73-hollowing-skin-model-with-meshlab/. Step 1: Import a model into Meshlab. Go to Filters --> Color Creation and Processing --> Ambient Occlusion per Vertex. When the new box opens, check the box to select "Use GPU Acceleration" and click "Apply." The default settings are fine for a first step. Once you become comfortable with the workflow, you can play around with applying the light from different axes: "Lighting Direction" and "Directional Bias". Step 2: You will notice that your model is now colorized from light to dark, with "deeper" areas shaded darker. On the main toolbar, select the "transparent wireframe" view. You can now see the internal structures that are shaded completely black. Step 3: We can now use the shading values to select the areas we want to remove. Go to Filters --> Selection --> Select Faces by Vertex Quality. The shading values are stored in the Vertex Quality field of your 3D model, with values from 0 (black) to 1 (white), so we can use these values to select the dark (internal or deep) areas we want to remove. Step 4: When the Selection box opens up, slide the "Min Quality" value all the way to 0 (to the left). Check the "Preview" box so that you can see which areas are selected in red. Adjust the "Max Quality" slider left and right until you see that no external surfaces are selected in red. In the image below, you can see that the bottom edges of the eyelids are still red and some skin below the nostrils is also red. When you find a good value, click "Apply" and Close. **Depending on the model, it may be difficult to adjust the Max slider to a value that doesn't include parts of the eyelids or nose, but I will explain in Step 6 how you can recover these features. Instead of deleting the selection in Step 5, skip to Step 6. Step 5: Once you are happy with your selection from Step 4, you can delete everything selected in red by clicking the button shown in the image below. You can see that the model is now hollow, although there may be some disconnected pieces which we will remove in multiple cleaning steps. Step 6: If you think you may have selected some external features in Step 4 that you don't want deleted, instead of deleting (Step 5), you can move the selected (red) areas to another layer. Sometimes with overhanging eyelids or very deeply set eyes, these areas might have the same shading values as some internal structures and can't be excluded from the red. Go to Filters --> Mesh Layer --> Move selected faces to another layer (if your layer dialog is already open, you can right-click on the model name to access the Mesh Layer menu as well). The layer dialog will open up on the right and you will see the name of your original model as well as the new layer. Use the eye icons to toggle visibility. The Meshlab selection tools can be used to select the areas from the red you want to keep, then move them to another layer. Right-clicking on a mesh name will open the Mesh Layer menu, from which you can "Flatten Visible Layers"--the layers you want to keep can be kept visible and merged into a new mesh. Step 7: This image shows the view from the bottom. The head is empty except for that big flat piece at the top of the head. Step 8: As an initial cleaning step to remove small pieces, go to Filters --> Cleaning and Repairing --> Remove Isolated pieces (wrt Diameter). The default size works well, but you can adjust it up to 40% or so to remove larger pieces. This is a deletion function, so the floating pieces will be removed and gone forever! Try to not to adjust the size too high--we'll remove large pieces in step 9. Step 9: Step 8 will usually not remove large pieces, especially if you're being cautious and only remove small pieces. To remove larger pieces, go to Filters --> Mesh Layer --> Split in Connected Components. The pieces will drop into separate layers in the layer dialog box on the right, and they will be named CC 0, CC 1, etc. You don't want to apply this filter until you've removed small pieces, or you might end up crashing the program because there are too many pieces separating out! As mentioned above, the Mesh Layer menu can also be accessed by right-clicking on the mesh name in the right-hand layer dialog box. Step 10: The largest layer is usually CC 0. Toggle visibility to figure out which layer is the one you want. Left-click on it to highlight it in yellow and then export using File --> Export Mesh as... I prefer to fill holes (Inspector) and create internal walls (Extrude or Offset) in Meshmixer, so you can now import the hollowed model to Meshmixer to fix it up for printing if needed. You can also use the plane cut tool in Meshmixer to remove the flattened edge at the top of the skin model, or apply Ambient Occlusion again in only the z-direction (see Step 1--"Lighting Direction"). This can be an interative process depending on the complexity of the model you're trying to hollow, but it can save on printing time as well as $$ if you're only interested in the external surface. Play around with lighting directions to select the surfaces you want and as always, SAVE meshes along the way in case the program crashes or you make a mistake!
  2. Version 1.0.0

    2 downloads

    CTA head for video tutorial ct scan tutorial ct with contrast brain, stl, axial, dicom, Head basic, head, skull, ct, scan, with, contrast, axial, dicom, .stl, hemisphere, lobes, frontal, parietal, temporal, brainstem corpus, callosum, cisures, muscles, neck, paranasal, sinuses, atlas, axis, tongue, parotid, gland, carotid, space, nasal, septum, deviation, pterygoid, mastoid, cells, petrous, ridge, mandible, maxilla, upper, teeth, incisor, canine, molar, premolar, dens, 3d, model, lobes, printable

    Free

  3. Version 1.0.0

    144 downloads

    This is an anonymized CT scan DICOM dataset to be used for teaching on how to create a 3D printable models.

    Free

  4. Version 1.0.0

    589 downloads

    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. Serratus anterior muscle, Right lung, Latissimus dorsi muscle, Liver (right lobe), Diaphragm (lumbar part) Suprarenal gland, Rib, Right kidney, Psoas major muscle, . Spinal canal with cauda equina, Transversospinales muscles, . Superior articular process (zygapophysis), Inferior articular process (zygapophysis), Iliac crest, . Dorsal sacroiliac ligaments, Ilium (ala), Gluteus maximus muscle Piriformis muscle, . Left lung, External intercostal muscle, Thoracic aorta, Diaphragm, Stomach, Spleen, Thoracic vertebra (T12), Left kidney, Descending colon, Transversus abdominis muscle, Internal abdominal oblique muscle, External abdominal oblique muscle, Quadratus lumborum muscle, Iliocostalis muscle, Ligamenta flava, Gluteus medius muscle, Vertebral arch (lamina of L5), Sacroiliac joint, Sacrum, Rectum,

    Free

  5. 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.
  6. Version

    3,440 downloads

    UPDATE: There is an improved tutorial that shows you how to create 3D printable bone models even more easily and for free on any operating system. Click here to learn more. This file pack contains files to accompany the tutorial "Creating 3D Printable Models from Medical Scans in 30 Minutes Using Free Software: Osirix, Blender, and Meshmixer." Download the files to follow along with the tutorial and create a 3D printed model yourself! If you haven't registered, please do so. Registration is free and only takes a minute. Included files: TCGA-06-5410 sharp.zip - contains the DICOM files with an anonymized research CT scan used to create the skull model skull file.zip - Contains the uncorrected, raw STL file generated from Osirix. skull file corrected.zip - Contains the skull STL file after correcting mesh errors in Blender. skull file corrected preform.zip - Contains the .form file of the corrected STL. This is the file format used with the Formlabs Form1+ printer. If you have this type of printer, download this file and print yourself. All files are compressed with zip.

    Free

  7. Version 1.0.0

    5 downloads

    CTA head for video tutorial ct scan, ct with contrast, stl, head, neck, dicom

    Free

  8. In this tutorial we will learn how to use the free medical imaging conversion service on embodi3D.com to create detailed anatomic muscle and skin 3D printable models in STL file format from medical CT scans. Muscle models show the detailed musculature by subtracting away the skin and fat. Even when created from a scan of an obese person, the model looks like it comes from a bodybuilder, Figure 1A. Skin models show an exact replica of the skin surface. The finest details are captured, including wrinkles and veins underneath the skin. Hair however is not captured in a CT scan and thus the model does not have any hair, Figure 1B. Figure 1A (left): A muscle 3D printable model. Figure 1B (right): A skin 3D printable model These models can be used for a variety of purposes such as medical and scientific education and research. Additionally, the skin models can be used to re-create a person's likeness in 3D from a medical scan. If you have had a CT scan of the head, you can create a lifelike replica of your head. You can create replicas of your friends, family, or even pets if they have had a medical CT scan. Alternatively, if you have a loved one who passed away but had a CT scan prior to death, you can use the scan to re-create an exact replica of their face. Even scans that are years old can be used for this purpose. Some people may consider this to be a little creepy, so if you are considering doing this think carefully first. Before proceeding please register for an embodi3D.com account if you haven't already. You will need an account to use the service. It is highly recommended that you download the associated file pack for this tutorial so that you can follow along with the exact same files that are used in this tutorial. >> DOWNLOAD THE FREE FILE PACK BY CLICKING HERE << If you are interested in learning how to use the free embodi3D.com service, see my prior tutorials on creating bone models, processing multiple models simultaneously, and sharing and selling your models on the embodi3D.com website. If you are interested in converting your own CT scan or that of a friend or family member, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figure 2 shows the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available. If you have downloaded the file pack for this tutorial, example CT scans are included Figure 2A, the Image Management (radiology) department at my hospital, where you can pick up a DVD of your CT scan as shown in Figure 2B (right). My hospital does this for free, but some may charge a trivial fee. PART 1: Creating a Muscle STL model from NRRD File Before we begin please bear in mind that this process only works for CT scan images. It will not work for MRI images. Before proceeding please check that the scan you wish to convert is a CT (CAT) scan! Step 1: Convert Your CT scan to an Anonymized NRRD File with 3D Slicer Open 3D Slicer. If you don't have the software program you can download it for free from slicer.org. Once Slicer has opened, take the folder from the download pack that is called STS_004. This folder contains anonymized DICOM images from a CT scan of the legs of a 24-year-old woman who had a muscle tumor. Drag and drop the entire folder onto the Slicer window, as shown in Figure 3. Slicer will ask you if you want to load the images into the DICOM database. Click OK. Slicer will also ask you if it should copy the images into the database, click Copy. Slicer will take about one minute to load the scanned. Figure 3: Drag-and-drop the STS_004 DICOM folder from the file pack onto the Slicer window Next, load the scan into the active wor king area in slicer. If the DICOM browser is not open, click on the Show DICOM browser button, as shown in Figure 4. Click on the STS_004 patient and series, and click the Load button, as shown in Figure 4. The leg CT scan will now load into the active seen within Slicer, as shown in Figure 5. Figure 4: Open the DICOM browser and load the study into the active seen Figure 5: The leg CT scan is shown in the active seen Step 2: Trim the Scan so that only the Right Thigh is included. Click on the Volume Rendering module from the Modules drop-down menu as shown in Figure 6. Turn on volume rendering by clicking on the eyeball button, as shown in Figure 7. Then, center the model in the 3D pane by clicking on the crosshairs button, Figure 7. If you don't have the same window layout as shown in Figure 7, you can correct this by clicking on the Four-Up window layout from the window layout drop-down menu, as shown in Figure 8. Figure 6: Turn on the volume rendering module Figure 7: Center the rendered volume. Figure 8: Make sure you are in the Four-Up window layout Next we are going to crop the volume so that we exclude everything other than the right knee and thigh. From the modules menu, select All Modules, Crop Volume, as shown in Figure 9. Turn on ROI visibility by clicking on the eyeball button, as shown in Figure 10. Then, move the region of interest box so that it only encapsulates the right thigh, as shown in Figure 10. You can adjust the size of the box by grabbing on the colored circular handles and moving the sides of the box as needed. Figure 9: The Crop Volume module. Figure 10: Turning on and adjusting the crop volume ROI (Region Of Interest) Once the crop volume ROI is adjusted to the area that you want, perform the crop by clicking on the Crop button, Figure 11. Figure 11: the Crop button. The new, smaller volume that encompasses the right fight and knee has been assigned a cryptic name. The entire scan had a name of "2: CT IMAGES – RESEARCH," and the new thigh volume has a name "2: CT IMAGES-RESEARCH-subvolume-scale_1." That's a mouthful and I want to rename it to something more descriptive. I'm going to select the Volumes module, and then select the "2: CT IMAGES-RESEARCH-subvolume-scale_1" from the Active Volume drop-down menu. Then, from the same drop-down menu I'm going to select "Rename Current Volume". Type in whatever name you want. In this case I'm choosing "right thigh." Figure 12: Renaming the newly cropped volume. Step 3: Save the right thigh volume as an anonymized NRRD file. Click on the Save button in the upper left-hand corner. The save window is then shown. All the checkboxes on the left except for the one that corresponds to the right by. Make sure the file format for this line says NRRD (.nrrd). Make sure you specify the proper directory you want the file to be saved as. When you are satisfied click on save. This is demonstrated in Figure 13. In the specified directory you should see a called right thigh.nrrd. Figure 13: The save file options. Step 4: Upload the NRRD file to embodi3D.com Make sure you are logged into your embodi3D.com account. Click on Imag3D from the nav bar, Launch App. Then drag-and-drop your NRRD file onto the upload pain, as shown in Figure 14. Figure 14: Uploading the NRRD file to embodi3D.com. While the file is uploading, fill in the required fields, including the name of the uploaded file, a brief description, file privacy, and license type. Except the terms of use. next, turn on Imag3D processing. Under operation, select "CT NRRD to Muscle STL." Leave the threshold value unchanged. Under quality, select medium or high. Specify your privacy preference for your output STL file. If you are going to share this file, you can choose to share it for free or sell it. Please see my separate tutorial on how to share and sell your files on the embodi3D.com website for additional details. When you're happy with your choices, save the file, as shown in Figure 15: Figure 15: File processing options. Step 5: Download your new STL file after processing is completed. In about 5 to 15 minutes you should receive an email that says your file has finished processing and is ready to download. Follow the link in the email or access the new file via your profile on the embodi3D.com website. Your newly created STL file should have several rendered thumbnails associated with it on its download page. If you want to download the file click on the Download button, as shown in Figure 16. Figure 16: the download page for your new muscle STL file I opened the file in AutoDesk MeshMixer to have another look at it, and it looks terrific, as shown in Figure 17. This file is ready to 3D print! Figure 17: The final 3D printable muscle model. PART 2: Creating a Skin Model STL File Ready for 3D Printing Creating a skin model is essentially identical to creating the muscle model, except instead of choosing the CT NRRD to Muscle STL on the embodi3D.com service, we choose CT NRRD to Skin STL. Step 1: Load DICOM image set into Slicer Launch Slicer. From the tutorial file pack drag and drop the MANIX folder onto the Slicer window to load this head and neck CT scan data set. This is shown in Figure 18. Figure 18: Loading the head and neck CT scan into Slicer. It may take a minute or two to load. From the DICOM browser, click on the ANGIO CT series as shown in Figure 19. Figure 19: Loading the ANGIO CT series from the MANIX data set Step 2: Skip the trimming and crop volume operations In this case we don't need to trim and crop a volume as we did with the muscle file above. We can skip Step 2. Step 3: Save the CT scan in NRRD format. Just as with the muscle file above, save the volume in NRRD format. Click on the save button, make sure that the checkbox for the nrrd file is selected and all other checkboxes are deselected. Specify the correct directory you want the file to be saved in, and click Save. Step 4: Upload your NRRD file of the head to the embodi3D website. Just as with the muscle file process as shown above, upload the head NRRD file to the embodi3D.com website. Enter in the required fields. In this case, however, under Operation choose the CT NRRD to Skin STL operation, as shown in Figure 20. Figure 20: Selecting the CT NRRD to Skin STL file operation Step 5: Download your new Skin STL file After about 5 to 15 minutes, you should receive an email that says your file processing has been completed. Follow the link in the email or look for your file in the list the files you own in your profile. You should see that your skin STL file has been completed, with several rendered images, as shown in Figure 21. Go ahead and download your file. You can then check the quality of your file in Meshmixer as shown in Figure 22. In this instance everything looks great and the file is error free and ready for 3D printing. Figure 21: The download page for your newly created 3D printable skin STL file. Figure 22: Opening the file in Meshmixer for quality control checks. The file is error free and incredibly lifelike. It is ready for 3D printing. Thank you very much! I hope you enjoyed this tutorial. If you use this service to create 3D printable models, please consider sharing your models with the embodi3D community. Here is a detailed tutorial that I wrote on exactly how to do this. This community is built on medical 3D makers helping each other. Please share the models that you create!
  9. Dr. Mike

    Tutorial file pack

    Version

    461 downloads

    File pack to accompany the tutorial: "3D Printing of Bones from CT Scans: A Tutorial on Quickly Correcting Extensive Mesh Errors using Blender and MeshMixer"

    Free

  10. Version 1.0.0

    122 downloads

    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)"

    Free

  11. Hello everybody it's Dr. Mike here again with another medical 3D printing tutorial. In this tutorial we are going to be going over freeware and open-source software options for medical 3D printing. This tutorial is based on a workshop I am giving at the 2017 Radiological Society of North America (RSNA) Annual Meeting in Chicago Illinois, November 2017. In this tutorial we will be going over desktop software that can be used to create 3D printable anatomic models from medical scans, as well as a free online automated conversion service. At the end of this tutorial you should be able to make high-quality 3D printable models from a medical imaging scan using free software or services. Do I need to use FDA-approved software for Medical 3D Printing? Before I dive into the tutorial I'd like to take a minute to talk to learners from the United States about the US Food and Drug Administration (FDA) and how this federal agency impacts medical 3D printing. Many healthcare professionals are confused and concerned about the ability to use non-FDA-approved software for medical 3D printing. Software vendors sell software that has been FDA-approved, but the software is usually quite expensive, to the tune of many thousands of dollars per year in license fees. There has been a lot of confusion about whether non-FDA-approved free software can be used for medical applications. In August 2017 a meeting was held at the main FDA campus between FDA staff and representatives from RSNA. During this meeting the FDA clarified its stance on the issue (Figure 1). Basically the FDA indicated that if a doctor needs a 3D printed model for patient care, the doctor does NOT need to use FDA-approved software, as this is a medical decision and the FDA does not regulate the practice of medicine. FDA-approved software is not required even if the doctor is using the model for diagnostic use (Figure 2). If a company or other organization is marketing or designing software for diagnostic use, then that company or organization is required to seek FDA approval for that product. Basically if you are a physician or working on behalf of the physician and require a model, FDA-approved software is not required as long as you are not running a commercial service or company. Despite this leeway granted by the FDA's interpretation, I encourage anyone considering using freeware to create models for diagnostic use to use common sense and double check your findings before making any critical decision that could impact patient care. I also encourage you to look at the slides from the FDA presentation directly at the link below. Of course, none of this applies if you are not creating models for medical use. https://www.fda.gov/downloads/MedicalDevices/NewsEvents/WorkshopsConferences/UCM575723.pdf Figure 1: Title slide from the FDA presentation Figure 2: The relevant slide from the FDA presentation. Doctors creating 3D printable models for clinical and diagnostic use do not need to use FDA-approved software as this is considered practice of medicine, which the FDA does not regulate. Medical 3D Printing Overview In this tutorial we're going to go over two different ways to use free and open-source software to convert a medical imaging scan to a 3D printable model. This can be done using free desktop software or a free online service. The desktop software requires more steps and more of a learning curve, but also allows more control for customized models. The online service is fast, easy, and automated. However, if you want to design customized elements into your model, you'll not be able to. The overall workflow of the session is shown in Figure 3. Figure 3: Workflow overview Part 1: Free online service – embodi3D.com Step 1: Download the scan Please download the scan for this tutorial from the embodi3D.com website at the link below. You have to have a free embodi3D.com account in order to download. If you don't have an account go ahead and register by clicking on the "Sign Up" button on the upper right-hand portion of the page. Registration is easy and only takes about one minute. You will have to confirm your email address before your account is active, so make sure you have access to your email. Step 2: Inspect the scan If you don't already have it, download and install the desktop software program 3D Slicer from slicer.org (http://www.slicer.org/). Slicer is a free medical image viewing and research software application. We are going to use Slicer to view our scan. Once Slicer is installed, open the application. Drag-and-drop the file "CTA Head.nrrd" onto the Slicer window. Slicer will ask if you want to add the file, click OK. The scan should now show in Figure 4. If your window doesn't look this then select the Four Up layout from the Layouts drop-down menu. Figure 4: The 4 panel view and Slicer You can navigate and manipulate the images with Slicer using the various mouse buttons. Your left mouse button to adjust the window/level settings as shown in Figure 5. Figure 5: Use the left mouse button to adjust window/level. The right mouse button allows you to zoom into a specific panel, as shown in Figure 6. Figure 6: The right mouse button controls zoom. The scroll wheel allows you to move through the various slices of the scan, as shown in Figure 7. Figure 7: The mouse wheel controls scrolling Step 3: Upload the scan to embodi3D.com Now that we have an idea about what's in the scan, you can upload it to embodi3D.com for automatic processing into a 3D printable model. Go to https://www.embodi3d.com/. If you don't yet have a free embodi3D.com user account, you will need one now. Go ahead and register. The process only takes a minute. Under the democratiz3D menu, click Launch App, as shown in Figure 8. Figure 8: Launching the democratiz3D medical scan to 3D printable model automated conversion service. Drag and drop the file "CTA Head.nrrd" onto the upload panel, as shown in Figure 9. The NRRD file format is an anonymized file format so this transfer is HIPAA compliant. If you want to know more about how to create an NRRD file from a DICOM data set, please see my tutorial on the topic here. Figure 9: Drag-and-drop the scan file "CTA Head.nrrd" onto the highlighted upload panel A submission form will open up. The first part of the form will ask you questions about the source file you're uploading. The second part will ask about the new model being generated. Start with the first part of the form, as shown in Figure 10, and fill in information about your uploaded scan file, including a filename, short description, any tags you wish to use to help people identify your file, whether you wish to share the file with the community or keep it private, and whether you want to make the file free for download or for sale. Obviously if you keep the file private this last setting doesn't matter as nobody will be able to see the file except you. Figure 10: The first part of the form relates to information about your uploaded scan file. Make sure you fill in at least the required elements. In the second part of the form fill in information about your model file that will be generated, as shown in Figure 11. First of all, make sure democratized processing is turned on. The slider should be green in color, as shown in Figure 11. This is very important because if processing is turned off, you will not generate an output model file! Specify what operation you would like to perform on the scan, and whether you would like to generate a bone, muscle, or skin model. Also, specify the desired quality of the output model (low, medium, high, etc.) and whether you want the output model to be shared with the community (recommended) or private. If your file is going to be shared, choose a Creative Commons license that people can use it under. When you're satisfied with your parameters, click the Submit button. Figure 11: The second part of the form relates to information about your 3D printable model to be generated. Choose an operation, quality level, as well as privacy settings. Step 4: Download your finished 3D printable model. After anywhere between 5 to 20 minutes you should receive an email saying that your model processing is complete. The exact time depends on a variety of factors including the complexity of your model, the quality that you've chosen, as well as server load. Once you receive the email follow the link to the model download page. Alternatively you can find the model by clicking on your username at the upper right-hand corner of any embodi3D.com webpage and selecting My Files. Once you find your model page you can inspect the thumbnails to make sure the model meets your criteria, as shown in Figure 12. When you are ready click the download button, agree to the terms, and your model STL file will download to your computer. Figure 12: Download your file after processing is complete. That's it! Your 3D printable model is ready to send to a printer. The process takes about 2 to 3 minutes to enter the data, plus 5 to 15 minutes to wait for the processing to be done. The embodi3D.com service is batchable, so it is possible for you to upload multiple files simultaneously. The service will crank out models as fast as you can upload them. Part 2: Free desktop software – 3D Slicer and Meshmixer You can use the free software program 3D slicer and Meshmixer to generate 3D printable models. The benefit of using desktop software is that you have more control over the appearance of the model and which structures you want included and excluded. The downside of using desktop software is that software is complicated and somewhat time-consuming to learn. If you haven't already download 3D Slicer and Meshmixer from the links below. Be sure to choose the appropriate operating system for your computer. http://www.slicer.org/ http://meshmixer.com/ Step 1: Download the tutorial scan file and load into Slicer as described above in Part 1 Steps 1 and 2. Step 2: Create a surface model from the scan data. From within Slicer, open the Grayscale Model Maker module. In the Modules menu at the top now bar, select All Modules and choose the Grayscale Model Maker item, as shown in Figure 13. Figure 13: Selecting the Grayscale Model Maker module. You will now be taken to the Grayscale Model Maker module, which will convert the volumetric data in the CT scan to a surface model that can be used to create a STL file for 3D printing. In the parameters panel on the left side of the screen, make sure that the parameter set value is set to "Grayscale Model Maker", and the Input Volume is set to "CTA Head." Under Output Geometry, choose Create a New Model, since we wish to create a new output model. These parameters are shown in Figure 14. Figure 14: Input parameters for the Grayscale Model Maker module Set the Threshold value to 150 Hounsfield units. Also, set the Decimate value to 0.8 and make sure the Split Normals checkbox is unchecked. These are shown in Figure 15. When you're happy with your parameters, check Apply, and the grayscale model maker will work for a minute or so to create your surface model. Figure 15: Additional input parameters for the Grayscale Model Maker module Step 3: Save the surface model to an STL file. Now that you have generated a surface model, you are ready to export it to an STL file. Click on the Save button on the upper left-hand corner of the 3D Slicer window. A Save dialog box will pop up, as shown in Figure 16. Find the row that contains the item "Output Geometry.vtk." Make sure that the checkbox next to this item is checked. All other rows should be unchecked. In the File Format column, make sure that the file shows as STL. Finally, make sure that the directory specified in the third column is the one you wish to save the file to. When everything is correct go ahead and click Save. Your surface model will now be exported and STL file saved in the directory specified. Figure 16: The Save dialog box Step 4: Repair the model in Meshmixer The model is in STL format, but it has multiple errors in it which need to be corrected prior to 3D printing. We will do this in the freeware software program Meshmixer. Open Meshmixer, and drag-and-drop the just-created STL file "Output Geometry.stl" onto the Meshmixer window. The model will now open in Meshmixer. You will notice that the model is quite large, having about 300,000 polygons, as shown in Figure 17. Figure 17: Open the model in Meshmixer Navigating in Meshmixer is quite intuitive. The left mouse button uses tools and selects structures. The right mouse button is used to rotate the model. The scroll wheel is used to zoom in and out, as shown in Figure 18. Figure 18: Navigating in Meshmixer Run an initial repair on the model using the Inspector tool We will be able to get rid of most (but not all) errors using the automated Inspector tool. Click on the Analysis button on the left navigation pane and choose the Inspector tool. Inspector will run and highlight all of the problems with the model, as shown in Figure 19. As you can see there are many hundreds of errors. Click on the Auto Repair All button to automatically attempt to fix these. At least one error will remain after the end of the process, but don't worry we will fix that later. Click on the Done button. Figure 19: The Inspector tool shows errors in the mesh Remesh the model The Remesh operation recalculates all the polygons in the model, adjusting their size, and giving the model in more natural and less faceted look. Remesh and can also help to fix lingering mesh errors. First, select all the polygons in the model by hitting control-A. The entire model should turn orange, as shown in Figure 20. Figure 20: Selecting all the polygons in the model. Next, run the Remesh operation. Hit the R key, or choose Select-> Edit-> Remesh. The Remesh operation will now run, and will take approximately 1.5 to 2 minutes, depending on the power of your computer. This is shown in Figure 21. Figure 21: The Remesh operation. At the end of the Remesh operation, your model should have a much smoother and more natural appearance. You can adjust some of the Remesh parameters in the visualized pane, and the operation will recalculate. When you're happy with the result, click on the Accept button. This is shown in Figure 22. Figure 22: The model after the Remesh operation. Repeat the Inspector tool operation Now that we have re-mashed the model, we can rerun the Inspector tool to clean up any residual errors. Click on Analysis and then the Inspector menu item. Click Auto Repair All, and inspector should repair any problems that still remain. When you're finished, click the Done button, as shown in Figure 23. Figure 23: Running the Inspector tool a second time Expose the cerebral vessels. We are now going to take an extra step and make a cut through the crowd of the skull to expose the cerebral vessels. This can be easily achieved in about one minute. First, make sure to select all the vertices in the model by hitting control-A or using the menus Select-> Modify-> Select all, as shown in Figure 24. The entire model should turn orange to indicate that it is selected. Figure 24: Selecting all the polygons in the model prior to performing a cut. Next, start a plane cut by choosing Select-> Edit-> Plane cut. The plane cut will show on the screen. The portion of the model that is transparent will be cut off. The portion of the model that is opaque will be left behind. Move the plane by using the purple and green arrow handles. Rotate the plane by using the red arc handle, as shown in Figure 25. Figure 25: Move and rotate the plane cut using the arrow and arc handles. In this case we wish to move the plane cut to the four head, and rotated 180° so that the transparent portion of the cut is at the top of the head, and the opaque portion encompasses the face, jaw, and lower part of the skull. After you have finished positioning the plane, your model should look similar to Figure 26. When you're happy with position, click Accept. Figure 26: The best position of the plane cut tool The crown of the skull will now be cut off, exposing the cerebral vessels within the brain. This includes the anterior, posterior, and middle cerebral arteries as well as the venous structures such as the straight sinus and sigmoid sinuses, as shown in Figure 27. As you can see, this is a highly detailed model and excellent for educational purposes and teaching neurovascular anatomy. Figure 27: The final model Conclusion In this tutorial we learn how to create a 3D printable skull and vascular model utilizing the free online service from embodi3D.com, as well as free desktop software 3D Slicer and Meshmixer. Both methods have their advantages and disadvantages. Embodi3D.com has a very fast and easy to use service. The desktop software is more difficult to use and learn, but gives more flexibility in terms of customization. Alternatively, you can use a combination of the two techniques, for example generating your model on the embodi3D.com website and then performing custom modifications, such as the plane cut we did in this tutorial, utilizing Meshmixer. I hope you found this tutorial helpful and entertaining. Please give the tutorial a like. If you are engaged in medical 3D printing, please consider sharing your work on the embodi3D.com website. Thank you very much and happy 3D printing!
  12. NRRD is a file format for storing and visualizing medical image data. Its main benefit over DICOM, the standard file format for medical imaging, is that NRRD files are anonymized and contain no sensitive patient information. Furthermore NRRD files can store a medical scan in a single file, whereas DICOM data sets are usually comprised of a directory or directories that contain dozens if not hundreds of individual files. NRRD is thus a good file for transferring medical scan data while protecting patient privacy. This tutorial will teach you how to create an NRRD file from a DICOM data set generated from a medical scan, such as a CT, MRI, ultrasound, or x-rays. To complete this tutorial you will need a CD or DVD with your medical imaging scan, or a downloaded DICOM data set from one of many online repositories. If you had a medical scan at a hospital or clinic you can usually obtain a CD or DVD from the radiology department after signing a waiver and paying a small copying fee. Step 1: Download Slicer Slicer is a free software program for medical imaging. It can be downloaded from the www.slicer.org. Once on the Slicer homepage, click on the Download link as shown in Figure 1. Figure 1 Slicer is available for Windows, Mac, and Linux. Choose your operating system and download the latest stable release as shown in Figure 2. Figure 2: Download Slicer Step 2: Copy the DICOM files into Slicer. Insert your CD or DVD containing your medical scan data into your CD or DVD drive, or open the folder containing your DICOM files if you have a downloaded data set. If you navigate into the folder directory, you will notice that there are usually multiple DICOM files in one or more directories, as shown in Figure 3. Navigate to the highest level folder containing all the DICOM files. Figure 3: There are many DICOM files in a study Open Slicer. The welcome screen will show, as demonstrated in Figure 4. Left click on the folder that contains the DICOM files and drop it onto the Welcome panel in Slicer. Slicer will ask you if you want to load the DICOM files into the DICOM database, as shown in Figure 5. Click OK Slicer will then ask you if you want to copy the files or merely add links. Click Copy as shown in Figure 6. Figure 4: Drag and drop the DICOM folder onto the Slicer Welcome window. Figures 5 and 6 After working for a minute or two, Slicer will tell you that the DICOM import was successful, as shown in Figure 7. Click OK Figure 7 Step 3: Open the Medical Scan in Slicer. At this point you should see a window called the DICOM Browser, as shown in Figure 8. The browser has three panels, which show the patient information, study information, and the individual series within each study. If you close the DICOM Browser and need to open it again, you can do so under the Modules menu, as shown in Figure 9. Figure 8: DICOM Browser Figure 9: Finding the DICOM browser Each series in a medical imaging scan is comprised of a stack of images that together make a volume. This volume can be used to make the NRRD file. Modern CT and MRI scans typically have multiple series and different orientations that were collected using different techniques. These multiple views of the same structures allow the doctors reading the scan to have the best chance of making the correct diagnosis. A detailed explanation of the different types of CT and MRI series is beyond the scope of this article, but will be covered in a future tutorial. Click on the single patient, study, and a series of interest. Click the Load button as shown in Figure 8. The series will then begin to load as shown in Figure 10. Figure 10: The study is loading Step 4: Save the Imaging Data in NRRD Format Once the series loads you will see the imaging data displayed in the Slicer windows. Click the Save button on the upper left-hand corner, as shown in Figure 11. Figure 11: Click the Save button The Save Scene dialog box will then appear. Two or more rows may be shown. Put a checkmark next to the row that has a name that ends in ".nrrd". Uncheck all other rows. Click the directory button for the nrrd file and specify the directory to save the file into. Then click the save button, as shown in Figure 12. Figure 12: Check the NRRD file and specify save directory. The NRRD file will now be saved in the directory you specified!
  13. Version 1.0.0

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    File pack to accompany the tutorial listed above. Download this file pack to follow along with the tutorial. View the full tutorial here.

    Free

  14. 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!
  15. Version 1.0.0

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    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

  16. Note: This tutorial accompanies a workshop I presented at the 2016 Radiological Society of North America (RSNA) meeting. The workflow and techniques presented in this tutorial and the conference workshop are identical. In this tutorial we will be using two different ways to create a 3-D printable medical model of a head and neck which will be derived from a real contrast-enhanced CT scan. The model will show detailed anatomy of the bones, as well as the veins and arteries. We will independently create this model using two separate methods. First, we will automatically generate the model using the free online service embodi3D.com. Next, we will create the same file using free desktop software programs 3D Slicer and Meshmixer. If you haven't already, please download the associated file pack which contains the files you'll need to follow along with this tutorial. Following along with the actual files used here will make learning these techniques much easier. The file pack is free. You need to be logged into your embodi3D account to download, but registration is also free and only takes a minute. Also, you'll need an embodi3D.com account in order to use the online service. Registration is worth it, so if you haven't already go ahead and register now. >> DOWNLOAD THE FILE PACK NOW << Online Service: embodi3D.com Step 1: Go to the embodi3D.com website and click on the democratiz3D menu item in the naw bar. Click on the "Launch democratizD" link, as shown in Figure 1. Figure 1: Opening the free online 3D model making service service democratiz3D. Step 2: Now you have to upload your imaging file. Drag and drop the file MANIX Angio CT.nrrd from the File Pack, as shown in Figure 2. This contains the CT scan of the head and neck in NRRD file format. If you are using a file other NRRD that provided by the file pack, please be aware the file must contain a CT scan (NOT MRI!) and the file must be in NRRD format. If you don't know how to create an NRRD file, here is a simple tutorial that explains how. Figure 2: Dragging and dropping the NRRD file to start uploading. Step 3: Type in basic information on the file being uploaded, including File name, file description, and whether you want to share the file or keep it private. Bear in mind that this information pertains to the uploaded file, not the file that will be generated by the service. Step 4: Type in basic parameters for file processing. Turn on the processing slider. Here you will enter in basic information about how you would like the file to be processed. Under Operation, select CT NRRD to Bone STL Detailed, as shown in Figure 3. This will convert a CT scan in NRRD format to a bone STL with high detail. You also have the option to create muscle and skin STL files. The standard operation, CT NRRD to Bone STL sacrifices some detail for a smoother output model. Leave the default threshold at 150. Figure 3: Selecting an operation for file conversion. Next, choose the quality of your output file. Low-quality files process quickly and are appropriate for structures with simple geometry. High quality files take longer to process and are appropriate for very complex geometry. The geometry of our model will be quite complex, so choose high quality. This may take a long time to process however, sometimes up to 40 minutes. If you don't wish to wait so long, you can choose medium quality, as shown in Figure 4, and have a pretty decent output file in about 12 minutes or so. Figure 4: Choosing a quality setting. Finally, specify whether you want your processed file to be shared with the community (encouraged) or private and accessible only to you. If you do decide to share you will need to fill out a few items, such as which CreativeCommons license to share under. If you're not sure, the defaults are appropriate for most people. If you do decide to share thanks very much! The 3D printing community thanks you! Click on the submit button and your file will be submitted for processing! Now all you have to do is wait. The service will do all the work for you! Step 5: Download your file. In 5 to 40 minutes you should receive an email indicating that your file is done and is ready for download. Follow the link in the email message or, if you are already on the embodi3D.com website, click on your profile to view your latest activity, including files belonging to you. Open the download page for your file and click on the "Download this file" button to download your newly created STL file! Figure 5: Downloading your newly completed STL file. Desktop software If you haven't already, download 3D Slicer and Meshmixer. Both of these programs are available on Macintosh and Windows platforms. Step 1: Create an STL file with 3D Slicer. Open 3D Slicer. Drag and drop the file MANIX Angio CT.nrrd from the file pack onto the 3D Slicer window. This should load the file into 3D Slicer, as shown in Figure 6. When Slicer asks you to confirm whether you want to add the file, click OK. Figure 6: Opening the NRRD file in 3D Slicer using drag-and-drop. Step 2: Convert the CT scan into an STL file. From within Slicer, open the Modules menu item and choose All Modules, Grayscale Model Maker, as shown in Figure 7. Figure 7: Opening the Grayscale Model Maker module. Next, enter the conversion parameters for Grayscale Model Maker in the parameters window on the left. Under Input Volume select MANIX Angio CT. Under Output Geometry choose "Create new model." Slicer will create a new model with the default name such as "Output Geometry. If you wish to rename this to something more descriptive, choose Rename current model under the same menu. For this tutorial I am calling the model "RSNA model." For Threshold, set the value to 150. Under Decimate, set the value to 0.75. Double check your settings to make sure everything is correct. When everything is filled in correctly click the Apply button, as shown in Figure 8. Slicer will process for about a minute. Figure 8: Filling in the Grayscale Model Maker parameters. Step 3: Save the new model to STL file format. Now it is time to create an STL file from our digital model. Click on the Save button on the upper left-hand corner of the Slicer window. The Save Scene pop-up window is now shown. Find the row that corresponds to the model name you have given the model. In my case it is called "RSNA model." Make sure that the checkbox next to this row is checked, and all other rows are unchecked. Next, under the File Format column make sure to specify STL. Finally, specify the directory that the new STL file is to be saved into. Double check everything. When you are ready, click Saved. This is all shown in Figure 9. Now that you've created an STL file, we need to postprocessing in Meshmixer. Figure 9: Saving your file to STL format. Step 4: Open Meshmixer, and drag-and-drop the newly created STL file onto the Meshmixer window to open it. Once the model opens, you will notice that there are many red dots scattered throughout the model. These represent errors in the mesh and need to be corrected, as shown in Figure 10. Figure 10: Errors in the mesh as shown in Meshmixer. Each red dot corresponds to an error. Step 5: Remove disconnected elements from the mesh. There are many disconnected elements in this model that we do not want in our final model. An example of unwanted mesh are the flat plates on either side of the head from the pillow that was used to secure the head during the CT scan. Let's get rid of this unwanted mesh. First use the select tool and place the cursor over the four head of the model and left click. The area under the cursor should turn orange, indicating that those polygons have been selected, as shown in Figure 11. Figure 11: Selecting a small zone on the forehead. Next, we are going to expand the selection to encompass all geometry that is attached to the area that we currently have selected. Go to the Modify menu item and select Expand to Connected. Alternatively, you can use the keyboard shortcut and select the E key. This operation is shown in Figure 12. Figure 12: Expanding the selection to all connected parts. You will notice that the right clavicle and right scapula have not been selected. This is because these parts are not directly connected to the rest of the skeleton, as shown in Figure 13. We wish to include these in our model, so using the select tool left click on each of these parts to highlight a small area. Then expand the selection to connected again by hitting the E key. Figure 13: The right clavicle and right scapula are not included in the selection because they are not connected to the rest of the skeleton. Individually select these parts and expand the selection again to include them. At this point you should have all the geometry we want included in the model selected in orange, as shown in Figure 14. Figure 14: All the desired geometry is selected in orange Next we are going to delete all the unwanted geometry that is currently unselected. To start this we will first invert the selection. Under the modify menu, select Invert. Alternatively, you can use the keyboard shortcut I, as shown in Figure 15. Figure 15: Inverting the selection. At this point only the undesired geometry should be highlighted in orange, as shown in Figure 16. This unwanted geometry cannot be deleted by going to the Edit menu and selecting Discard. Alternatively you can use the keyboard shortcut X. Figure 16: Only the unwanted geometry is highlighted in orange. This is ready to delete. Step 6: Correcting mesh errors using the Inspector tool. Meshmixer has a nice tool that will automatically fix many mesh errors. Click on the Analysis button and choose Inspector. Meshmixer will now identify all of the errors currently in the mesh. These are indicated by red, blue, and pink balls with lines pointing to the location of the error. As you can see from Figure 17, there are hundreds of errors still within our mesh. We can attempt to auto repair them by clicking on the Auto Repair All button. At the end of the operation most of the errors have been fixed, but if you remain. This can be seen in Figure 18. Figure 17: Errors in the mesh. Most of these can be corrected using the Inspector tool. Figure 18: Only a few errors remain after auto correction with the Inspector tool. Step 7: Correcting the remaining errors using the Remesh tool. Click on the select button to turn on the select tool. Expand the selection to connected parts by choosing Modify, Expand to Connected. The entire model should now be highlighted and origin color. Next under the edit menu choose Remesh, or use the R keyboard shortcut, as shown in Figure 19. This operation will take some time, six or eight minutes depending on the speed of your computer. What remesh does is it recalculates the surface topography of the model and replaces each of the surface triangles with new triangles that are more regular and uniform in appearance. Since our model has a considerable amount of surface area and polygons, the remesh operation takes some time. Remesh also has the ability to eliminate some geometric problems that can prevent all errors from being automatically fixed in Inspector. Figure 19: Using the Remesh tool. Step 8: Fixing the remaining errors using the Inspector tool. Once the remesh operation is completed we will go back and repeat Step 6 and run the Inspector tool again. Click on Analysis and choose Inspector. Inspector will highlight the errors. Currently there are only two, as shown in Figure 20. These two remaining errors can be easily auto repair using the Auto Repair All button. Go ahead and click on this. Figure 20: running the Inspector tool again. At this point the model is now completed and ready for 3D printing as shown in Figure 21. The mesh is error-free and ready to go! Congratulations! Figure 21: The final, error-free model ready for 3D printing. Conclusion Complex bone and vascular models, such as the head and neck model we created in this tutorial, can be created using either the free online service at embodi3D.com or using free desktop software. Each approach has its benefits. The online service is easier to use, faster, and produces high quality models with minimal user input. Additionally, multiple models can be processed simultaneously so it is possible to batch process multiple files at once. The desktop approach using 3D Slicer and Meshmixer requires more user input and thus more time, however the user has greater control over individual design decisions about the model. Both methods are viable for creating high quality 3D printable medical models. Thank you very much for reading this tutorial. Please share your medical 3D printing designs on the embodi3D.com website. Happy 3D printing!
  17. In this brief tutorial we will go over how to use Meshmixer to create a hollow shell from a medical 3D printable STL file. Hollowing out the shell, as shown in the pictures below, can allow you to 3D print the model using much less material that printing a solid piece. The print will take less time and cost less money. For this tutorial we will use a head that we created from a real medical CT scan in a prior tutorial, " Easily Create 3D Printable Muscle and Skin STL Files from Medical CT Scans" If you haven't seen the prior tutorial, please check it out. To follow along with the tutorial, please download the accompanying file. This will enable you to replicate the process exactly as it is shown in the tutorial. >> DOWNLOAD THE TUTORIAL FILE NOW <<
  18. Version 1.0.0

    61 downloads

    This file accompanies the tutorial "How to Create a Hollow Shell from a Medical STL Model using MeshMixer." Download the file to follow along with the tutorial.

    Free

  19. 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+
  20. Version 1.0.0

    211 downloads

    This file pack accompanies the tutorial on Creating 3D printable muscle and skin STL files from medical CT scans. You must register for a free account to download. Read the full tutorial https://www.youtube.com/watch?v=3qPgmVSdSkg

    Free

  21. Getting from DICOM to 3D printable STL file in 3D Slicer is totally doable...but it is important to learn some fundamental skills in Slicer first if you are not familiar with the program. This tutorial introduces the user to some basic concepts in 3D Slicer and demonstrates how to crop DICOM data in anticipation of segmentation and 3D model creation. (Segmentation and STL file creation are explored in a companion tutorial ) This tutorial is downloadable as a PDF file, 3D Slicer Tutorial.pdf or can be looked through in image/slide format here in the blog 3D Slicer Tutorial.pdf
  22. Version

    119 downloads

    These are Blender and STL files to accompany the tutorial Preparing CT scans for 3D printing. Cleaning and repairing STL file mesh from bones using Blender, an advanced tutorial. Files are in ZIP format. Download and follow along.

    Free

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