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  1. 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!
  2. 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.
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