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  1. 6 points
    I was recently contacted by another doctor who asked if I could help him to create a 3D printed replicate of his spine to visualize pinched nerves in his low back and aid with planning a future back surgery. In order to work this doctor has to stand for long hours while performing surgical procedures. Excruciating low back pain had limited his ability to stand to only 30 minutes. As you can imagine, this means he couldn't work. Things only got worse after he had low back surgery. A CT scan of his lumbar spine (the low back portion of the spine) was performed. It showed that his fifth lumbar vertebra was partially sacralized. This means it looked more like a sacral vertebra than a lumbar vertebra. Was this causing his problem? On the image slices of the CT scan it was difficult to tell. How the Spine is Organized First, a word about the different vertebrae (bones) in the spine. There are four main sections of spinal bones. The seven cervical vertebrae are in the neck and support the head. They are generally small but flexible, and allow rotation of the head. The 12 thoracic vertebrae are in the chest. Their most distinctive characteristic is they all have associated ribs, which make up the rib cage. The five lumbar vertebrae are in the low back. These are large and strong, and designed for supporting lots of weight. They do not have associated ribs. The five sacral vertebrae are in the pelvis. In adults, they are fused together and effectively form a single bone, the sacrum. The coccyx, or tailbone, which is a tiny bone at the bottom end of the vertebral column, can be considered a fifth spinal section. This is the bone that is often injured when you fallen your behind. Figure 1 shows the different sections of the vertebral column. Figure 1. Sections of the vertebral column. Source:aimisspine.com Although the bones of the individual sections of the spine usually have their own unique features, it is not uncommon for vertebrae in one section to have features typically associated with an adjacent section. This is particularly true of the vertebrae that are immediately adjacent to a neighboring section. These hybrids are a mix between both sections, are called transitional vertebrae. Do you recall that only thoracic vertebrae have associated ribs? Occasionally the highest lumbar vertebra, L1, will have tiny ribs attached to it. This is a normal variant and is usually harmless. Radiologists who are interpreting medical scans need to be careful to not confuse an L1 vertebra which may have tiny ribs for the adjacent T12 vertebra which normally has ribs. Similarly, the lowest lumbar vertebra, L5, which is normally unfused, can exhibit fusion. As you recall, fusion is a characteristic of sacral vertebrae. A Congenital Spine Abnormality This was the situation with our physician. His lowest lumbar vertebra, L5, has partially fused with S1, the highest sacral vertebra. This condition is congenital. He has had it all his life. The fusion can have the side effect of creating a very narrow bony canal through which the L5 nerve roots can exit the spine. Normally, these nerve roots would have much more space as a large gap would exist between the normally unfused L5 and S1 vertebrae. Was this the problem? The CT scan showed the sacralization of L5, but it was difficult to get a sense for how tight the holes through which the nerves exit, the neural foramina, were. See Figures 2 and 3. Figure 2: Coronal CT image through the L5 and S1 vertebral bodies. Is this the cause of the problem? It is very difficult to get an intuitive sense of what is going on with these flat image slices. Figure 3: Image from Figure 2 with the neural foramina marked. Seeking help through Embodi3D The doctor contacted me through the Embodi3D website and asked if I could create a 3D model design and 3D print of his lumbar spine to help him and his team of spinal specialists understand his unique anatomy better. Of course, I was happy to help. The CT scan was of high quality and allowed me to extract the bones and metallic spinal fusion implants with little trouble. The individual nerves, however, were very difficult to see even on a high quality CT scan. I had to manually segment them one image at a time, which was a very tedious and time-consuming process. After fusing everything together, I had a very good digital model of the lumbar spine. I created some photorealistic 3D renders to illustrate the key findings. Figures 4 and 5 show the very tight L5-S1 bony neural foramina. The inter-vertebral disc sits within the gap between the two vertebral bodies, and you can see how a lateral bulge from this disc would significantly pinch these exiting nerve roots. Figure 4: Right L5 nerve root (yellow) exiting the tight neural foramen caused by the fused L5 and S1 lateral processes. Figure 5: Left L5 nerve root (yellow) exiting the tight neural foramen caused by the fused L5 and S1 lateral processes. Additionally, I showed that a bone screw that had been placed during the last surgery had partially exited the L4 vertebral body and was in very close proximity, and probably touching, the adjacent nerve root. Ouch! This can be seen in Figure 6. This may explain why the pain seem to get worse after the last surgery. Figure 6: Transpedicular orthopedic screw which has partially exited the L4 vertebral body and is in very close proximity or in contact with the right L3 nerve root. The Final 3D Printed Spine Model The doctor wanted his spine 3D printed in transparent material, so I used a stereolithographic printer with transparent resin. I printed the spine in two separate parts that could be separated and fit together. When separated, the nerves exiting through the neural foramina can be inspected from inside the spinal canal, which gives an added degree of understanding. Final pictures of the transparent 3D printed model are shown below. I just recently shipped the model to this doctor and don't yet know how his back problems will be resolved. With this 3D printed model in hand however, he will be able to have much more meaningful discussions with his spinal surgeons about the best way to definitively fix his low back problems. I hope that the 3D printed spine model will literally help to get this good doctor back on his feet again.
  2. 5 points
    valchanov

    Postprocessing 3D prints

    Every Slicer software have automatic support function. Just click it and it will generate the right amount of support you need. For bone models the important question is - are your fellow surgeons planning to cut the model or not. It will be a shame, if they break their instruments into your model... For metal implant premodelling prior the operation, you need smooth bones with high resolution details. In my experience, 0,150mm layer thickness, with 4 perimeters (1,7mm shell thickness with 0,4mm nozzle), 15% gyroid or cuboid infill, a bit colder extrusion temperature (200C for PLA) is perfect. Your fellow surgeons can bend the metalic osteosynthesis implants on the model into their optimal shape, can sterilise them and this whole operation will decrease the surgery time with 1 hour. This is a big difference for the outcome of the operation, the recovery time, the complications ect. ect. If you want to print fracture fragments, make them in different colors. Then you can make 3D visualization with the corresponding colors. The model will look marvelous and you'll become the surgeon's best buddy. They will love you, they will cheer you and they will give you a lot of money for that. If you need specific information, please tell us - printer model, slicer software, material on choice. I can give you more specific information, if you do that.
  3. 5 points

    580 downloads

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

    Free

  4. 4 points
    Hello and welcome back. Once again, I am Dr. Mike, board-certified radiologist and 3D printing enthusiast. Today I'm going to show you how to correct severe mesh defects in a bone model generated from a CT scan. This will be in preparation for 3D printing. I'll be using the free software programs Blender and Meshmixer. In my last medical 3d printing video tutorial, I showed you how to remove extraneous mesh within the medullary cavity of a bone. That technique is best used when mesh defects are limited. In instances where mesh defects in a bony model are severe and extensive, a different approach is needed. In this video, I'll show you how to correct extensive mesh errors in bony anatomical models using Blender and Meshmixer. This assumes that you know how to generate a basic STL file from a CT scan. There are a variety of commercial and freeware products that allow you to do this, on a variety of platforms. If you don't yet know how to do this, stay tuned, as I have a series of tutorials planned which will show you how to do this on a variety of operating systems and budgets. If you wish to follow along with this tutorial, you can download the free tutorial file pack by clicking this link. This is highly recommended, as the files allow you to follow along with the tutorial, which will make learning easier. Included is the STL file used in this tutorial. Also, a powerful Blender script is included which will enable you to easily and efficiently prepare your own bone models for 3D printing. It's a real timesaver. If you haven't registered at Embodi3D.com, registration is free and only takes a moment. DOWNLOAD THE ACCOMPANYING FILE PACK. CLICK HERE. You can watch the video tutorial for a quick overview, or read this article for a detailed description. Initial analysis using Meshmixer Let's take a look at an STL file of a talus fracture in the ankle. This 3D model is from a real patient who suffered a fracture of the talus. The talus is the bone in the ankle that the tibia, or shinbone, sits on. This STL file is included in the file pack. Let's open this file in Meshmixer (Figure 1). Meshmixer is free software published by Autodesk, a leading maker of engineering software. If you don't have Meshmixer, you can go to Meshmixer.com and download it for free. Figure 1 Once you have the file open in Meshmixer, click on the Analysis button and select Inspector. The inspector shows all the errors in this mesh. Blue parts represent holes in the mesh. Red parts show areas where the mesh is non-manifold. Magenta parts show disconnected components. As you can see, there are a lot of problems with this mesh, and it is not suitable for 3D printing in its current state (Figure 2). Figure 2 Meshmixer has a feature to automatically repair these mesh defects. However, there are so many problems with this mesh that the auto repair function fails. Click on the Auto Repair All button. Meshmixer has tried to repair these mesh defects, and has successfully reduced the number of defects. However, it is also introduced gaping holes in the model. Entire bones are missing (Figure 3). This clearly isn't the desired outcome. Figure 3 Opening the STL file in Blender The solution to this problem can be found with Blender. Blender is a free, open-source software package that is primarily designed for animation. It is so feature-rich however, that it can be used for a variety of different purposes, and increasingly is being used for tasks related to 3D printing. If you don't have Blender, you can download it from blender.org. At the time of this writing, the current version is 2.73 a. Open up Blender. Go ahead and delete the default cube shown in the middle of the screen (Figure 4) by right clicking it and hitting the "X" key followed by the "D" key. If you are new to Blender, you'll soon learn that much of what you can do with Blender can be done with keyboard shortcuts. This can be daunting to learn for beginners, but makes use of Blender very efficient for heavy users. Figure 4 Next open the STL file in Blender. Go to the File menu in the upper left, select Import, and select "Stl (.stl)." Then, navigate to the folder for the tutorial files and select the "ankle - talus fracture.stl" file. You probably don't see anything, as is shown in Figure 5. To understand how this happens, you need to know a little bit about how Blender measures distances. Blender uses an arbitrary measure of distance called a "blender unit." One blender unit is equivalent to one of the little squares seen in the viewport. However, in real life distances are measured in real units, such as feet, inches, centimeters, and millimeters. Most STL files that are generated from medical imaging data have default unit of measurement of millimeters. When Blender imports the file it converts the millimeter units to blender units. Since our imported model is the size of human foot, measuring 240 mm or so, the model will be 240 blender units, or 240 of those little squares, in length. We can't see it because the model is too big! Our viewport is zoomed into much! Zoom out using the mouse wheel way, way back until you can see the model as shown in Figure 6. Figure 5: Where is the model? Figure 6: There it is! Correcting the Object Origin You will notice that the origin of the ankle object, as shown by the red blue and green axes (Figure 6), is actually outside of object itself. Left uncorrected, this can be a really annoying issue. When you rotate or pan around the object, you will rotate or pan around these three axes, instead of the ankle object itself. Fortunately, correcting this takes only a moment. In the lower left-hand part of the window select the Object menu. Be sure that you have the ankle object selected first. Then choose Transform, Geometry to Origin. The ankle object is then moved to the red blue and green axes. With the object origin now in the center of the mesh, the mesh will be much easier to work with. Figure 7: The ankle mesh and object origin are now aligned. Inspect the ankle mesh If you look closely at the ankle mesh you can see immediately that it has a lot of problems. In the solid shader mode, the bones look very faceted. The polygons are large, giving the bones a unnatural appearance (Figure 8). Don't worry, will fix this. If you turn on wireframe mode by hitting the "Z" key you can see that there is a lot of extraneous mesh within the bones that represents unwanted mesh from the medullary cavities of these bones (Figure 9). Furthermore, if you check for non-manifold mesh by holding control-shift-alt-M, you'll see that there are innumerable non-manifold mesh defects (Figure 10). Figure 8: Note the very faceted appearance of the bones. Figure 9: There is a significant amount of unneeded and extraneous mesh, particularly within the medullary cavities of the bones. Figure 10: Non-manifold mesh defects. If you are unfamiliar with the term "non-manifold," let me take a moment to explain. A mesh is simply a surface. It is infinitely thin. If the mesh is continuous and unbroken, and has a contained volume within it, then the mesh can be considered to represent something solid. In this case, the mesh surface represents the interface between the inside of the object and the outside of the object, such as the sphere shown in Figure 11. An object like this is considered to be "manifold," or watertight. It represents a solid that can really exist in the physical world, and can thus be 3D printed. Figure 11 If however, I cut a hole in the sphere, as shown in Figure 12, then there is a gap in the mesh. A 3D printer won't know what to do with this. Is this supposed to be solid like a ball, or hollow like a cup? If it is supposed to be like a cup, how thick are the walls supposed to be? The walls in this mesh are infinitesimally thin, so what is the correct thickness? This mesh is not watertight - that is, should water be placed in the structure it would leak out. The mesh is non-manifold. It cannot be 3D printed. If we use the control-shift-alt-M sequence to highlight non-manifold mesh, as shown in Figure 13, we can see that Blender correctly identifies the edge of the hole as having non-manifold mesh. Figure 12 Figure 13 Closing major holes manually in Blender In this particular mesh, there are many, many small mesh errors and two very large ones. The distal tibia and fibula bones have been cut off by the CT scanner, leaving gaping holes in the mesh as shown in Figure 14. Fixing these manually will only take a moment and make things easier down the road, so let's take care of that now. Enter Edit mode by hitting the Tab key, or clicking it in the Mode menu. If you hit control-shift-alt-M to select non-manifold edges, you can clearly see that these bone cuts are a problem as shown in Figure 15. Figure 14 Figure 15 Go to Vertex selection mode by clicking the vertex button or hitting control-tab-1 on the keyboard as shown in Figure 16. Select one of the vertices from the medullary portion of the tibia bone as shown in Figure 17. This mesh represents the medullary cavity of the tibia bone, and is not connected to the rest of the mesh. Hit control-L to select all contiguous vertices (Figure 18). All the unwanted medullary cavity mesh should now be highlighted. Delete this by hitting the "X" key followed by the "V" key, or by hitting the delete and selecting "vertices." There is another small bit of medullary cavity mesh at the edge of the tibia cut. Perform the same routine and delete this as well. Figure 16 Figure 17 Figure 18 Next we will direct our attention to the unwanted medullary mesh of the thinner fibula bone. Click on a vertex in the fibula medullary mesh and hit control L. You will note that the entire mesh is highlighted as shown in Figure 19. This indicates that the medullary mesh is connected to the rest of the mesh in some way. We don't need to manually delete all of the medullary mesh. We just need to get it away from the edge where we will create a new face to close the bone edges. Go to Edge selection mode by hitting control-tab-2 or clicking the edge selection button as shown in Figure 20. Hit the "A" key to unselect everything. Then, click on a single edge along the unwanted medullary mesh, as shown in Figure 21. Figure 19 Figure 20 Figure 21 Next we will by holding down the alt key and right clicking on the edge again. Blender should select the loop around the entire edge as shown in Figure 22. We will now expand the selection by holding down the control tab and hitting the plus key on the number pad. Hit the plus key three times. Your selection should now look like that in Figure 23. Delete the highlighted mesh by hitting the "X" and "V" keys, or hitting the delete key and selecting vertices. Figure 22 Figure 23 Next we are going to close the holes by holding down the alt key and right clicking along the edge of the cut line of the fibula. An entire loop should be selected as shown in Figure 24. Create a face by hitting the "F" key. Convert to triangles by hitting Control-T. The end of the fibula should be closed, as shown in Figure 25. Repeat the same for the open edge of the tibia bone. Afterwards the mesh should look as it does and Figure 26. Figure 24 Figure 25 Figure 26 Creating a Shell of the model using the Shrinkwrap and Remesh modifiers in Blender So how will it ever be possible to correct the hundreds and hundreds of mesh errors in the ankle model? This is the million-dollar question. A mesh of this complexity often cannot be fixed using automated mesh correction software, as we saw with Meshmixer. Correcting this many errors manually is a time-consuming and tedious process. I've spent hundreds of hours correcting mesh errors like this one by one. But, after years of creating 3D printable anatomical models, I've developed a technique to fix these mesh errors in only a few minutes. The secret is this: You don't fix the mesh errors. Leave them alone. You create a new mesh to replace them! Let's start by creating a sphere. If you are in Edit mode, exit that by hitting the Tab key. If you are still in wireframe viewport mode, hit the "Z" key to return to solid viewport shading. In the lower left-hand side of the window, hit the Add menu. Select Mesh, UV sphere and add a sphere. An "Add UV Sphere" panel will show up on the left side of your screen as shown in Figure 27. We want the sphere to have lots of detail. Under Segments enter 256. Under Rings, enter 128. The default size of the sphere is only one blender unit (1 mm) in size. This is too small, we want the thing to be huge. Enter 1000 for size. At this point you should have a very large sphere surrounding your entire scene. Believe it or not, this sphere will eventually be your new ankle object. Let's go ahead and rename it "Ankle skin" as shown in Figure 29. Figure 27: Add a UV sphere Figure 28: Configure the sphere. Segments 256, rings 128, size 1000 Figure 29: Rename the sphere to "Ankle skin" Applying the Shrinkwrap Modifier Select the "Ankle skin" object. Click on the Modifiers tab, it looks like a small wrench (Figure 30). From the Ad Modifier drop-down menu, select the Shrinkwrap item. Specify the Ankle object as "the target. Set off set to 0.5. Check the" Keep Above Surface" box. Your sphere will have shrunken down to envelop the ankle, as shown in Figure 30. Apply the modifier by hitting the "Apply" button. At this point you're thinking that your Ankle skin object hardly looks like an ankle, and you're right. If you try to apply the shrinkwrap modifier again, you won't get any change in the mesh. Blender has shrunken the sphere as best it can given the limited geometry of the sphere. To go further we need to change the geometry a bit, which is where the Remesh modifier comes in. Figure 30: The Shrinkwrap modifier Applying the Remesh Modifier Next go to Add Modifier again, and select Remesh. Set Mode to Smooth, Octree Depth = 8, and uncheck Remove Disconnected Pieces. By now you should have something that looks like Figure 31. Apply the modifier by clicking the Apply button. Figure 31: The Remesh modifier Apply the Shrinkwrap Modifier again Apply the shrinkwrap modifier again, using the same parameters as before. Your Ankle skin object should look like Figure 32. Now we are getting somewhere! There is still a long way to go, but the mesh somewhat resembles the bones of the foot. By repeatedly applying the Shrinkwrap and Remesh modifiers the Ankle skin object, which was originally a sphere, will slowly approximate the surface of the error-filled original ankle mesh. Because of the original skin was a sphere, and hence manifold, as it is shrink-wrapped around the ankle mesh it will preserve (for the most part) it's mesh integrity. There will be no unnecessary internal geometry. Any holes or other defects in the original mesh will be covered. Unfortunately, repeatedly applying the shrinkwrap and remesh modifier again and again is somewhat tedious (although not as tedious as manually correcting all the errors in the original mesh). Fortunately, we can automate this process using Python scripting. This allows us to create a new mesh in a matter of minutes. Figure 32 Automating the Shrinkwrap Process using Python Scripting For those of you less familiar with Blender's more advanced features, you may be surprised to learn that it is fully scriptable. That means that you can program it to perform tasks repeatedly using a Python script. In this case we want to repeatedly execute shrinkwrap and remesh modifiers on our ankle skin object. With each iteration the skin will more closely approximate the surface of the original mesh. If you are familiar with Python scripting, you can write a script yourself to call the necessary modifiers and specify the necessary variables. To make things easier for you, I have written a Python script for you. It is included in the free tutorial file pack. Change the bottom window to the text editor. View button in the bottom left-hand corner as shown in Figure 33. Select Text Editor. Click on the "Open" button and navigate to the folder with the tutorial file pack files as shown in Figure 34. Double-click on the "shrinkwrap loop.txt" file as shown in Figure 35. Figure 33: Select the text editor Figure 34: Click on the Open button Figure 35: Open the "shrinkwrap loop.txt" file The script file should now open in the text editor window. Adjust the target_object variable to be the target you want your skin wrapped around, in this case the "Ankle - Talus Fracture" object. Leave the shrinkwrap_offset variable at 0.5 for now. You can specify how many shrinkwrap-remesh iterations you want to run. For now leave it at 20. Click the "Run Script" button as shown in Figure 36. The script will now run, and it will apply the shrinkwrap-remesh modifiers 20 times. On my machine it takes about one minute for the script to execute. Figure 36 At this point you'll notice that the ankle skin object very closely approximates the original ankle object, as shown in Figure 37. Run the script again using the same settings. At this point the mesh is really looking pretty good. Let's run the script a final time with the smaller offset to more closely approximate the real bones. Set the shrinkwrap_offset variable to 0.3 and run the script again reducing iterations to 10. After completion the mesh should appear as it does in Figure 38. If you compare our new skin mesh as shown in Figure 39 (left) to the original ankle object in Figure 39 (right) you can see that our new skin is actually much more realistic than the original mesh. The highly faceted appearance of the original mesh has been replaced by a smoothed appearance of our shrink-wrapped skin. Furthermore, whereas the original mesh actually had separate bones that were disconnected, the new, shrink-wrapped mesh is a single interconnected object. From a 3D printing standpoint this is much better as the ankle bones will print together as a single unit Figure 37 Figure 38 Figure 39: Comparison of original plus new shrink-wrapped mesh. Finalizing the Ankle Model for 3D printing using Meshmixer. Select the new ankle object. Export the object to the STL file format. From the file menu select Export and then "Stl (.stl)." Let's call the file "ankle corrected.STL." Open the new STL file in Meshmixer. You will notice that Meshmixer immediately identifies some mesh errors as shown in Figure 40. This is because the Remesh modifier in Blender occasionally introduces non-manifold mesh defects. You will note however that the number of defect is significantly less than our original model which was shown in Figure 1. With this smaller number of errors, Meshmixer can fix them automatically. Go to the Analysis button and select Inspector. Meshmixer will highlight the individual mesh defects, as shown in Figure 41. Click on the "Auto Repair All" button. Meshmixer will then automatically repair the mesh defects. The result is shown in Figure 42. Figure 40 Figure 41: Meshmixer inspector Figure 42: Corrected mesh The mesh looks great, and is ready for 3D printing! Export the STL file by going to the File menu in Meshmixer and selecting Export. Save the file as "ankle final result.STL". Please share with the community. If you have found this tutorial helpful and are actively creating 3D printable anatomic models, please consider sharing your work with the Embodi3D community. You can share your models in the File Vault. If you have comments or advice, you can share your expertise in the Forums. If you are interested in blogging about your adventures in medical 3D printing, contact me or one of the administrators and we can set up blogging on your Embodi3D user account. If you wish to hire someone to help you with your anatomical 3D printing project, you can place an ad for free in the Services Needed Forum, If you are doing your own anatomical 3D printing and are willing to help others, list your services for free in the Services Offered Forum. This is a community. We are all helping each other. Please consider giving back if you can. Have fun 3D printing!
  5. 4 points
    Are you working on a cool 3D printing project? If so, let us know and we might feature you and your work in our newsletter. Send a message to me and let me know about what you are doing.
  6. 4 points
    If you want to scan people for fun, you can use your cell phone for photogrammetry with free software. Then you can put the heads on different bodies and to print them. Something like this: For this purpose you can use every 3d printer up to 2000$. I myself prefer my original Prusa MK3, because I'm not an engineer and I prefer something to do all the printing stuff for me. Here is the result: When we're talking about medical 3d printing, we're talking about a whole different topic. The medical models have to be very precise and there is an industrial standards about it. For example, my models have 0,5mm deviation from the original body part at 95% confidence interval. I had a presentation at an morphology symposium about my favorite Lusoria model lately and now I have a lot of orders from the local hospitals, because of the standard, which I can achieve. For medical modeling you have to be an expert in all the morphological specialties (Anatomy, Pathology, Radiology) with some serious clinical background. To reach this level, you need: 1. Medical education. 2. A lot of treated patients, most of which have to stay alive after your job. The death patients are literally skeletons in the closet. 3. Some background in the basic dissection techniques, both the pathological and the anatomical ones. 4. The surgery training is a plus. 5. Some gaming experience or experience with CAD software. The computer games are like bodybuilding for the visual cortex. 6. 1+ years of hard work, everyday modeling, studying, drawing, dissections, consultations with the experts in the field, a lot of tears and some joy. THEN you can do medical modeling, something like this. I started to model, when I was an anatomy assistant professor, with 12 years of experience as an emergency internal physician. I had the chance to find this website with all it resources, tutorials and the awesome support from the administrators and after 1 year of really hard work, I became a professional, (one of the best in my region, in a matter of fact). But still, my biggest nightmare is that, because of my mistakes during the preoperative modeling, a patient will die. So - are we really talking about medical modeling or you just want to do some fun with your client's CT scans?
  7. 4 points
    lillux

    Mandibola

    Version 1.0.0

    330 downloads

    This is a model of a woman's mandible. The TC showed two bone's included 3rd molars (wisdom teeth)

    Free

  8. 4 points
    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
  9. 4 points
    Here is a tutorial for the Grayscale Model Maker in the free program Slicer, specifically for modeling pubic bones since they are used in anthropology for age and sex estimation. The Grayscale Model Maker is very quick and easy! And I can't stand the "flashing" in the Editor. For this example, I am using a scan from TCIA, specifically from the CT Lymph Node collection. Slicer Functions used: Load Data/Load DICOM Volume Rendering Crop Volume Grayscale Model Maker Save Load a DICOM directory or .nrrd file. Hit Ok. Make sure your volume loads into the red, yellow, and green views. Select Volume Rendering from the drop-down. Select a bone preset, such as CT-AAA. Then click on the eye next to "Volume." ...Give it a minute... Use the centering button in the top left of the 3D window to center the volume if needed. Since we only want the pubic bones, we will use the ROI box and Crop Volume tools to isolate that area. To crop the volume check the "Enable" box next to "Crop" and click on the eye next to "Display ROI" to open it. A box appears in all 4 windows. The spheres can be grabbed and dragged in any view to adjust the size of the box. The 3D view is pretty handy for this so you can rotate the model around to get the area you want. The model itself doesn't have to be perfectly symmetrical because you can always edit it later. Once you like the ROI, we can crop the volume. To crop the volume, go to the drop-down in the top toolbar, select "All Modules" and navigate to "Crop Volume." Once the Crop Volume workspace opens, just hit the big Crop button and wait. You won't see a change in the 3D window, but you will see your slice views adjust to the cropped area. At this point, you can Save your subvolume that you worked so hard to isolate in case your software crashes! Select the Save button from the top left of the toolbar and select the .nrrd with "subvolume" in the file name to save. Now we will use the All Modules dropdown to open the Grayscale Model Maker. If you want to clear the 3D window of the volume rendering and ROI box, you can just go back to Volume Rendering, uncheck the Enable box and close the eyes for the Volume and ROI. When using the Grayscale Model Maker, the only tricky thing here is to select your "subvolume" from the "Input Volume" list, otherwise your original uncropped volume will be used. Click on the "Output Geometry" box and select "Create a new Model as..." and type in a name for your model. Now move down to "Grayscale Model Maker Parameters" in the workspace. I like to enter the same name for my Output Geometry into the "Model Name" field. Enter a threshold value: 200 works well for bone, but for lower density bone, you might need to adjust it down. Since the Grayscale Model Maker is so fast, I usually start with 200 and make additional models at lower values to see which works best for the current volume. ***Here is where I adjust settings for pubic bones in order to retain the irregular surfaces of the symphyseal faces.***The default values for the Smoothing and Decimate parameters work well for other bones, but for the pubic symphyses, they tend to smooth out all the relevant features, so I slide them both all the way down. Then hit Apply and wait for the model to appear in the 3D window (it will be gray). You can see from the image above that my model is gray, but still has the beige from the Volume Render on it since I didn't close the Volume Rendering. If for some reason you don't see your model: 1) check your Input Volume to make sure your subvolume is selected, 2) click on that tiny centering button at the top left of your 3D window, or 3) go to the main dropdown and go to "Models." If the model actually generated, it will be there with the name you specified, but sometimes the eye will be closed so just open it to look at your model. Now we an save your subvolume and model using the Save button in the top left of the main toolbar. You can uncheck all the other options and just save the subvolume .nrrd and adjust the file type of your model to .stl. Click on "Change Directory" to specify where you want to save your files and Save! This model still needs some editing to be printable, so stay tuned for Pt. 2 where I will discuss functions in Meshlab and Meshmixer. Thanks for reading and please comment if you have any issues with these steps!
  10. 4 points
    Here is another good case worth sharing: The patient is suffering from a mass in mandible, which is extended into the ramus and mandibular condyle. The mass has perforated the bone and in CT data, air is seen in the ramus. The left mandible is the pathologic and study model. The right one, is made with a technique called "Mirroring". This is a pretty useful technique to produce a rather normal anatomy, so the surgeon will pre-bend the surgical plate on the mirrored model, so after they have resected half of the mandible, they don't have to do the time-consuming plate bending while on the operating table. Our colleagues have reported that this method reduces the time of the surgery up to 2 hours! Please let me know what you think.
  11. 3 points
    Nicola

    Temporal Bone Left

    Version STL

    66 downloads

    This is a .stl file of a left temporal bone ready for 3d printing. I have segmented a CT scan paying attention to all the important bony structures of the ear. In the .stl screenshots you can see the mastoid, malleus, incus, the bony canal of the facial nerve, the stylomastoid foramen Etc. I do this for my training and the idea is to perform a mastoidectomy just in my desktop i have printed my personal 3d plaster model (you can see in the screenshots) but i haven't the courage to destroy it with the drill..... I hope that my work can be of help to anyone who wants to try to drill a faithful model of temporal bone at home or simply want to study the anatomy in a versatile 3d .stl Model Good Job Nicola Di Giuseppe M.D.

    $9.99

  12. 3 points
    Dr. Mike

    Formlabs Fuse 1 SLS printer

    Formlabs now has a low cost nylon SLS printer, the Fuse 1. It is about 10 times cheaper than other selective laser sintering printers. Check it out.
  13. 3 points
    Allen

    3D Printing Safety Tips for Kids

    Now that STEM education is being pushed to the forefront, 3D printers are increasingly becoming more common parts of classrooms around the world. This is a welcome development, of course, as 3D printing and other more advanced manufacturing technologies may prove to be vital parts of one’s skill set in the near future. This development presents an important question – how safe are 3D printers for kids? Can teachers leave students to use 3D printers unsupervised? What safety measures can schools and teachers take to ensure that no untoward incidents happen when kids work with 3D printers? The hazards of 3D printing The first step in establishing effective safety practices is to acknowledge that there are inherent hazards to 3D printing. After all, you’re still dealing with a machine with parts that can be heated beyond 200 °C. If you need to teach kids about using 3D printers, then you might as well tell them about the following hazards as well: Moving parts There are a lot of moving parts in a 3D printer, almost all of which are driven by the rotation of stepper motors. While these gears are typically inaccessible, it’s much easier for the smaller fingers of children to get caught within these moving parts. It’s good practice for both kids and adults to refrain from touching the moving parts of a 3D printer while printing is ongoing. Heat Heat is an important part of 3D printing. It also provides some of its most pervasive hazards. Depending on the filament you’re working with, you might have an extruder temperature that goes as high as 200 to 250 °C. Most 3D printers also have heated print beds that can be heated close to 100 °C. The filament material, of course, is also very hot when it comes out of the extruder nozzle. These are things to watch out for, especially if you’re dealing with a bunch of curious children. Fumes When 3D printing, massive heat is applied to the plastic filament materials. Different filaments react in different ways to this heat, but it is much safer to assume that they all release fumes that can range from irritating to downright toxic. Even if you can’t smell anything, the pressure and heat of extrusion also release plastic micro-particles which can result in long-term respiratory problems in humans. Tools Aside from the 3D printer itself, completing or finishing 3D printing projects will often involve the use of other tools. Some of these tools are sharp and can still cause injury when used improperly or without proper supervision. If absolutely necessary, you may have to incorporate training for using these tools into your 3D printing class. However, there are tools that are simply too dangerous to leave in the hands of small children. In listing down these potential hazards, one must always recognize that children are naturally curious and that they might not have developed a sufficient level of motor skills to work with small parts or tools. This means that there must always be a context in the development of safety practices – a different set of rules will be needed between middle schoolers and very young students. Best 3D printing safety practices for kids The best safety measure is one that eliminates the hazard completely. If this cannot be done, the next best thing is to reduce the hazard or prevent access to it. These will be our guiding principles in formulating safety measures for kids for 3D printing education. Get a 3D printer with an enclosure The best way to keep the kids away from the moving or hot parts of a 3D printer is to simply isolate them. Fortunately, a lot of the new desktop-scale 3D printers being sold nowadays come with built-in enclosures. Models from Flashforge, Dremel, and Monoprice are some good options. These are ideal because they provide protection and isolate the fumes of 3D printing while still allowing students to watch while the 3D printing process unfolds. The physical barrier is highly effective in discouraging kids from poking and prodding the 3D printer while it is still running. You can also set these 3D printers to stop operations as soon as the enclosure or cover is removed, ensuring that no accidents happen even if you’re not actively supervising. Place warning stickers on parts that can get hot We realize that warning stickers don’t always work, especially with kids, but it’s still a good idea to have them, nonetheless. They are a good indicator of which parts of the 3D printer get hot. This is a lesson that most people get to learn the hard way, after all. For best results, we suggest sticking warning labels that are colored bright red. Make sure to use stickers that are actually meant for use in high temperatures, lest you end up with one that gets washed out after just a few weeks. Inspect the 3D printer before use A major responsibility of the instructor is to inspect the 3D printers before use to check for any signs of damage. If there are any exposed wires, then it might be a good idea to have the printer repaired first. Do not touch any parts of a 3D printer while it is running A good general rule of thumb is to tell your students that under no circumstance should they touch any of the parts of a 3D printer while it is still running except for the control panel. This rule applies to students of all ages as well as to you as the instructor – yes, this is a great opportunity to lead by example. Avoid crowding around the 3D printer while it is running Even with all safeguards in place, it is best to enforce a minimum distance between your students and the 3D printer while it is still running. Not only does this help prevent curious fingers from prodding the machine, but it also lessens their exposure to a 3D printer’s harmful fumes. Letting them watch the 3D printer from about five feet away should let them appreciate the process without exposing them to unnecessary hazards. Do not eat or drink near the 3D printer It’s a good idea to treat your 3D printing class like you would a chemistry laboratory – everyone should be wearing the proper protective equipment while working, and there should be no eating or drinking in class. Any food or drink has the potential of getting contaminated with the chemical fumes that 3D printing releases. A spilled drink will also be bad news for any electronics and can result in some extreme accidents. Have students wear goggles, gloves, and respiratory protection A 3D printing class is an excellent avenue to teach students about general safety. Part of safety is making sure that you are wearing safety equipment appropriate to the activity you are doing. In the case of 3D printing, you will want to wear protection for your eyes, mouth, and nose to avoid chemical inhalation or contamination. Heat-resistant gloves are also recommended whenever you need to touch potentially hot parts. Since chemical fumes could be anywhere in the classroom, we recommend having all the students wear eye and breathing protection whenever a 3D printer is running as long as they are in the same room. Make sure to use masks that have been specially designed for chemical fumes and not just common particulates. Print in a well-ventilated area If you have the option to open windows during printing, then do so. This will help disperse the fumes that 3D printers emit. This is a recommended measure even if you’re using a fully enclosed 3D printer with a dedicated filtered vent. If your room does not have large windows, then you might want to reconsider relocating your class to somewhere with better ventilation. Only print with PLA PLA is probably the friendliest filament to work with if you’re teaching 3D printing to kids. It prints at lower temperatures, does not need a heated printing bed, and does not release unpleasant fumes. PLA also isn’t as prone to warping as other 3D printing filaments, making it less likely for your students to go through the frustrating experience of having to start a 3D printing project all over. Watch out for signs of asthma, allergy, or any flu-like symptoms There’s a good chance that the kids in your class have not been exposed to the type of chemical fumes that 3D printers release. Even with breathing protection, you will need to keep a close eye on your students and watch out for adverse reactions. If any of your students show signs of difficulty breathing or allergic reactions, then it would be best to have them step outside the room right away. Get in touch with medical personnel if symptoms don’t improve after a few minutes. As with most safety guidelines, it’s equally important to be receptive to adding or revising the rules as you see fit. Different facilities may require a different set of rules depending on the goals of the course and the available equipment. Final thoughts It wasn’t that long ago when ‘shop class’ was a common thing in schools. Learning woodworking is no longer as common nowadays and have been replaced by more tech-oriented fields. With schools opening courses on 3D printing, we feel it our duty to try and provide assistance on how they can keep these classes safe. The good news is that a lot of desktop-scale 3Dprinters for sale today have been pretty well-designed when it comes to safety. If you can get an enclosed 3D printer with an integrated HEPA filter vent, then that’s already half the battle won. The post 3D Printing Safety Tips for Kids appeared first on 3D Insider. View the full article
  14. 3 points
    If you are planning on using the democratiz3D service to automatically convert a medical scan to a 3D printable STL model, or you just happen to be working with medical scans for another reason, it is important to know if you are working with a CT (Computed Tomography or CAT) or MRI (Magnetic Resonance Imaging) scan. In this tutorial I'll show you how to quickly and easily tell the difference between a CT and MRI. I am a board-certified radiologist, and spent years mastering the subtleties of radiology physics for my board examinations and clinical practice. My goal here is not to bore you with unnecessary detail, although I am capable of that, but rather to give you a quick, easy, and practical way to understand the difference between CT and MRI if you are a non-medical person. Interested in Medical 3D Printing? Here are some resources: Free downloads of hundreds of 3D printable medical models. Automatically generate your own 3D printable medical models from CT scans. Have a question? Post a question or comment in the medical imaging forum. A Brief Overview of How CT and MRI Works For both CT (left) and MRI (right) scans you will lie on a moving table and be put into a circular machine that looks like a big doughnut. The table will move your body into the doughnut hole. The scan will then be performed. You may or may not get IV contrast through an IV. The machines look very similar but the scan pictures are totally different! CT and CAT Scans are the Same A CT scan, from Computed Tomography, and a CAT scan from Computed Axial Tomography are the same thing. CT scans are based on x-rays. A CT scanner is basically a rotating x-ray machine that takes sequential x-ray pictures of your body as it spins around. A computer then takes the data from the individual images, combines that with the known angle and position of the image at the time of exposure, and re-creates a three-dimensional representation of the body. Because CT scans are based on x-rays, bones are white and air is black on a CT scan just as it is on an x-ray as shown in Figure 1 below. Modern CT scanners are very fast, and usually the scan is performed in less than five minutes. Figure 1: A standard chest x-ray. Note that bones are white and air is black. Miscle and fat are shades of gray. CT scans are based on x-ray so body structures have the same color as they don on an x-ray. How does MRI Work? MRI uses a totally different mechanism to generate an image. MRI images are made using hydrogen atoms in your body and magnets. Yes, super strong magnets. Hydrogen is present in water, fat, protein, and most of the "soft tissue" structures of the body. The doughnut of an MRI does not house a rotating x-ray machine as it does in a CT scanner. Rather, it houses a superconducting electromagnet, basically a super strong magnet. The hydrogen atoms in your body line up with the magnetic field. Don't worry, this is perfectly safe and you won't feel anything. A radio transmitter, yes just like an FM radio station transmitter, will send some radio waves into your body, which will knock some of the hydrogen atoms out of alignment. As the hydrogen nuclei return back to their baseline position they emit a signal that can be measured and used to generate an image. MRI Pulse Sequences Differ Among Manufacturers The frequency, intensity, and timing of the radio waves used to excite the hydrogen atoms, called a "pulse sequence," can be modified so that only certain hydrogen atoms are excited and emit a signal. For example, when using a Short Tau Inversion Recovery (STIR) pulse sequence hydrogen atoms attached to fat molecules are turned off. When using a Fluid Attenuation Inversion Recovery (FLAIR) pulse sequence, hydrogen atoms attached to water molecules are turned off. Because there are so many variables that can be tweaked there are literally hundreds if not thousands of ways that pulse sequences can be constructed, each generating a slightly different type of image. To further complicate the matter, medical scanner manufacturers develop their own custom flavors of pulse sequences and give them specific brand names. So a balanced gradient echo pulse sequence is called True FISP on a Siemens scanner, FIESTA on a GE scanner, Balanced FFE on Philips, BASG on Hitachi, and True SSFP on Toshiba machines. Here is a list of pulse sequence names from various MRI manufacturers. This Radiographics article gives more detail about MRI physics if you want to get into the nitty-gritty. Figure 2: Examples of MRI images from the same patient. From left to right, T1, T2, FLAIR, and T1 post-contrast images of the brain in a patient with a right frontal lobe brain tumor. Note that tissue types (fat, water, blood vessels) can appear differently depending on the pulse sequence and presence of IV contrast. How to Tell the Difference Between a CT Scan and an MRI Scan? A Step by Step Guide Step 1: Read the Radiologist's Report The easiest way to tell what kind of a scan you had is to read the radiologist's report. All reports began with a formal title that will say what kind of scan you had, what body part was imaged, and whether IV contrast was used, for example "MRI brain with and without IV contrast," or "CT abdomen and pelvis without contrast." Step 2: Remember Your Experience in the MRI or CT (CAT) Scanner Were you on the scanner table for less than 10 minutes? If so you probably had a CT scan as MRIs take much longer. Did you have to wear earmuffs to protect your hearing from loud banging during the scan? If so, that was an MRI as the shifting magnetic fields cause the internal components of the machine to make noise. Did you have to drink lots of nasty flavored liquid a few hours before the scan? If so, this is oral contrast and is almost always for a CT. How to tell the difference between CT and MRI by looking at the pictures If you don't have access to the radiology report and don't remember the experience in the scanner because the scan was A) not done on you, or you were to drunk/high/sedated to remember, then you may have to figure out what kind of scan you had by looking at the pictures. This can be complicated, but don't fear I'll show you how to figure it out in this section. First, you need to get a copy of your scan. You can usually get this from the radiology or imaging department at the hospital or clinic where you had the scan performed. Typically these come on a CD or DVD. The disc may already have a program that will allow you to view the scan. If it doesn't, you'll have to download a program capable of reading DICOM files, such as 3D Slicer. Open your scan according to the instructions of your specific program. You may notice that your scan is composed of several sets of images, called series. Each series contains a stack of images. For CT scans these are usually images in different planes (axial, coronal, and sagittal) or before and after administration of IV contrast. For MRI each series is usually a different pulse sequence, which may also be before or after IV contrast. Step 3: Does the medical imaging software program tell you what kind of scan you have? Most imaging software programs will tell you what kind of scan you have under a field called "modality." The picture below shows a screen capture from 3D Slicer. Looking at the Modality column makes it pretty obvious that this is a CT scan. Figure 3: A screen capture from the 3D Slicer program shows the kind of scan under the modality column. Step 4: Can you see the CAT scan or MRI table the patient is laying on? If you can see the table that the patient is laying on or a brace that their head or other body part is secured in, you probably have a CT scan. MRI tables and braces are designed of materials that don't give off a signal in the MRI machine, so they are invisible. CT scan tables absorb some of the x-ray photons used to make the picture, so they are visible on the scan. Figure 4: A CT scan (left) and MRI (right) that show the patient table visible on the CT but not the MRI. Step 5: Is fat or water white? MRI usually shows fat and water as white. In MRI scans the fat underneath the skin or reservoirs of water in the body can be either white or dark in appearance, depending on the pulse sequence. For CT however, fat and water are almost never white. Look for fat just underneath the skin in almost any part of the body. Structures that contained mostly water include the cerebrospinal fluid around the spinal cord in the spinal canal and around the brain, the vitreous humor inside the eyeballs, bile within the gallbladder and biliary tree of the liver, urine within the bladder and collecting systems of the kidneys, and in some abnormal states such as pleural fluid in the thorax and ascites in the abdomen. It should be noted that water-containing structures can be made to look white on CT scans by intentional mixing of contrast in the structures in highly specialized scans, such as in a CT urogram or CT myelogram. But in general if either fat or fluid in the body looks white, you are dealing with an MRI. Step 6: Is the bone black? CT never shows bones as black. If you can see bony structures on your scan and they are black or dark gray in coloration, you are dealing with an MRI. On CT scans the bone is always white because the calcium blocks (attenuates) the x-ray photons. The calcium does not emit a signal in MRI scans, and thus appears dark. Bone marrow can be made to also appear dark on certain MRI pulse sequences, such as STIR sequences. If your scan shows dark bones and bone marrow, you are dealing with an MRI. A question I am often asked is "If bones are white on CT scans, if I see white bones can I assume it is a CT?" Unfortunately not. The calcium in bones does not emit signal on MRI and thus appears black. However, many bones also contain bone marrow which has a great deal of fat. Certain MRI sequences like T1 and T2 depict fat as bright white, and thus bone marrow-containing bone will look white on the scans. An expert can look carefully at the bone and discriminate between the calcium containing cortical bone and fat containing medullary bone, but this is beyond what a layperson will notice without specialized training. Self Test: Examples of CT and MRI Scans Here are some examples for you to test your newfound knowledge. Example 1 Figure 5A: A mystery scan of the brain Look at the scan above. Can you see the table that the patient is laying on? No, so this is probably an MRI. Let's not be hasty in our judgment and find further evidence to confirm our suspicion. Is the cerebrospinal fluid surrounding the brain and in the ventricles of the brain white? No, on this scan the CSF appears black. Both CT scans and MRIs can have dark appearing CSF, so this doesn't help us. Is the skin and thin layer of subcutaneous fat on the scalp white? Yes it is. That means this is an MRI. Well, if this is an MRI than the bones of the skull, the calvarium, should be dark, right? Yes, and indeed the calvarium is as shown in Figure 5B. You can see the black egg shaped oval around the brain, which is the calcium containing skull. The only portion of the skull that is white is in the frontal area where fat containing bone marrow is present between two thin layers of calcium containing bony cortex. This is an MRI. Figure 5B: The mystery scan is a T1 spoiled gradient echo MRI image of the brain. Incidentally this person has a brain tumor involving the left frontal lobe. Example 2 Figure 6A: Another mystery scan of the brain Look at the scan above. Let's go through our process to determine if this is a CT or MRI. First of all, can you see the table the patient is lying on or brace? Yes you can, there is a U-shaped brace keeping the head in position for the scan. We can conclude that this is a CT scan. Let's investigate further to confirm our conclusion. Is fat or water white? If either is white, then this is an MRI. In this scan we can see both fat underneath the skin of the cheeks which appears dark gray to black. Additionally, the material in the eyeball is a dark gray, immediately behind the relatively white appearing lenses of the eye. Finally, the cerebrospinal fluid surrounding the brainstem appears gray. This is not clearly an MRI, which further confirms our suspicion that it is a CT. If indeed this is a CT, then the bones of the skull should be white, and indeed they are. You can see the bright white shaped skull surrounding the brain. You can even see part of the cheekbones, the zygomatic arch, extending forward just outside the eyes. This is a CT scan. Figure 6B: The mystery scan is a CT brain without IV contrast. Example 3 Figure 7A: A mystery scan of the abdomen In this example we see an image through the upper abdomen depicting multiple intra-abdominal organs. Let's use our methodology to try and figure out what kind of scan this is. First of all, can you see the table that the patient is laying on? Yes you can. That means we are dealing with the CT. Let's go ahead and look for some additional evidence to confirm our suspicion. Do the bones appear white? Yes they do. You can see the white colored thoracic vertebrae in the center of the image, and multiple ribs are present, also white. If this is indeed a CT scan than any water-containing structures should not be white, and indeed they are not. In this image there are three water-containing structures. The spinal canal contains cerebrospinal fluid (CSF). The pickle shaped gallbladder can be seen just underneath the liver. Also, this patient has a large (and benign) left kidney cyst. All of these structures appear a dark gray. Also, the fat underneath the skin is a dark gray color. This is not in MRI. It is a CT. Figure 7B: The mystery scan is a CT of the abdomen with IV contrast Example 4 Figure 8A: A mystery scan of the left thigh Identifying this scan is challenging. Let's first look for the presence of the table. We don't see one but the image may have been trimmed to exclude it, or the image area may just not be big enough to see the table. We can't be sure a table is in present but just outside the image. Is the fat under the skin or any fluid-filled structures white? If so, this would indicate it is an MRI. The large white colored structure in the middle of the picture is a tumor. The fat underneath the skin is not white, it is dark gray in color. Also, the picture is through the mid thigh and there are no normal water containing structures in this area, so we can't use this to help us. Well, if this is a CT scan than the bone should be white. Is it? The answer is no. We can see a dark donut-shaped structure just to the right of the large white tumor. This is the femur bone, the major bone of the thigh and it is black. This cannot be a CT. It must be an MRI. This example is tricky because a fat suppression pulse sequence was used to turn the normally white colored fat a dark gray. Additionally no normal water containing structures are present on this image. The large tumor in the mid thigh is lighting up like a lightbulb and can be confusing and distracting. But, the presence of black colored bone is a dead giveaway. Figure 8B: The mystery scan is a contrast-enhanced T2 fat-suppressed MRI Conclusion: Now You Can Determine is a Scan is CT or MRI This tutorial outlines a simple process that anybody can use to identify whether a scan is a CT or MRI. The democratiz3D service on this website can be used to convert any CT scan into a 3D printable bone model. Soon, a feature will be added that will allow you to convert a brain MRI into a 3D printable model. Additional features will be forthcoming. The service is free and easy to use, but you do need to tell it what kind of scan your uploading. Hopefully this tutorial will help you identify your scan. If you'd like to learn more about the democratiz3D service click here. Thank you very much and I hope you found this tutorial to be helpful. Nothing in this article should be considered medical advice. If you have a medical question, ask your doctor.
  15. 3 points

    Version 1.0.0

    1,098 downloads

    This is my best selling model for 2019. Download, print, assemble, enjoy. Merry Christmas Originally modded as an engagement ring box, it became really popular birthday gift for the colleague from heart-related departments. I'm selling one of those models for 35$ I'm always bringing few, when I'm going on conference. Really nice gift. I'm printing those with Silk PLA. The metalic colors looks fantastic. I'm using several support blockers for the atrii, because this negates the artefacts and makes the whole upper part hollow. It requires some experience... Slice thickness: 0,15mm Infill: 30% gyroid Circular bottom fill pattern. Six neodymium magnets, 8x2mm. If you use too powerful magnets, the parts are closing so strong, that they can hurt someone. N50 are fine. cyanacrilic glue. Make sure you're gluing the magnets with the right poles!

    Free

  16. 3 points
    After several weeks of multi color/material printing with my FDM printer Prusa MK3 (I have other Printers too) with the Multi Material Unit 2 (MMU2) I'd like to share my results with you. Another interesting product regarding multimaterial is the Mosaic Palette 2. I don't own that unit at the moment but I know people who are using the system and I talked a lot with them about the unit so I will share their experience also with you. First of all, some general info. The Prusa MK3 costs as a build kit 769€ and fully assembled 999€. The MMU2 unit comes only as a kit and costs 300€. It can print with up to 5 materials. It can only be used with a Prusa printer out of the box. (Firmware is open source so in theory you could tinker it to work with other printers). Prusa has also their own (open source) slicer called Slic3er PE. The Palette 2 comes in two versions, the standard and the pro. Both versions can print with up to 4 materials. I highly recommend the pro version because it has a better warranty and comes with better quality parts. I also recommend the canvas hub option because it makes it easier to connect the system to your printer. That would result in a total prise of 878 USD. The Palette 3 can only be used with 3D printers that use 1.75 mm filament. So it can't be used with something like an Ultimaker. One more thing about filament. Prusa has now their own filament called Prusament. It is produced with a tolerance of +/- 0.02 mm in diameter. And you get a QR code with your spool to check the measuring yourself. Every spool is measured 100%. One (and only) advantage of the 2.85 mm filament that Ultimaker is using is that it is easier to produce precisely. If you are using 1.75 mm with +/- 0.02 mm that advantage is gone. First some thoughts on the MMU2. The MK3 produces very nice quality prints especially with high quality PLA like Prusament or PLA/PHA. That is mainly thanks to the Bondtech direct drive extruder. One other nice feature is the removable (magnetic flex steel) PEI bed. I guarantee you that if you are using this feature one time you will never never ever want a printer without it again. The basic principle of the system is that it adds a bowden system with a selector to the direct drive system. So the direct drive system pulls the filament up until the bowden system takes over. Than it switches the filament and the bowden system pushes the filament back to the direct drive gears. And so on ... As already mentioned it comes as a kit. And that is a BIG problem. Assembling it is not easy because you have to make sure that the filament path is as smoothly as possible. When you pull filament out from the hotend you can have tips with large strings or increased diameters. That will cause problems. To form the tips Slic3r PE has something called "ramming sequence". It tries to "form" the tips nicely like with no strings. This works good with Prusas own filament Prusament. It works also usually quite good with other filaments especially high quality ones like PLA/PHA. But there is no guarantee it works with the filament you are using so you might have to try different settings. So you have with the MMU2 basically two main problems. Assembling it so that everything runs perfectly smooth. And getting the ramming sequence settings right. A LOT of people are having problems with that. I had also try a lot out and it was frustrating at the beginning. I have now a working unit and prints are imho amazing. Now some words about the Palette 2 (pro). The principle of the machine is that it cuts the filaments and than splices them (melting) together. So you have one filament going out of the system with the right color combination for your model. It comes basically fully assembled. Installing the system to your printer takes maybe half an hour or so depending on your setup. So a LOT easier that the MMU2. One big problem right now is that their own slicer is very buggy and produces (especially on complex models) mediocre print quality. Sometimes it does even the color changes on the wrong location of the part. Combining your own more sophisticated slicer like Slic3er, Simplify3D or Cura with their system works also not reliably at the moment. Some general thoughts. Both systems produce purge towers. Every time when you change the color you have to get rid of the plastic from the old color in the hot end. How much you have to purge onto the tower is color dependent. E. g. switching from black to white or from PLA to BVOH as extreme scenarios. BUT as I mentioned the Palette splices the filaments together. That produces a color gradient in the filament of a few mm. That has to be purged additionally. So the purge amount of the Palette will always be bigger than the one of the MMU2. Slic3er PE has the option to "purge into infill" so it purges also into the objects infill. That option will come to the Palette 2 in the near future. I print a lot with BVOH and I know that it can work with the Palette too. But in both cases it adds complexity. Slic3er PE has the option for printing only support interface layers or completely supports with soluble material. I will start testing flexible materials in the near future. Customer support is pretty good with both companies. The forums are used very actively and you have also a very helpful chat support at Prusa. MMU2 Print: MMU2 Print: Kidney with tumor and magnet inserts MMU2 Fun prints: Palette slicing problems: Palette color gradient:
  17. 3 points
    In case there is any interest here in the applications of radiology and imaging in forensic science, I wanted to share the link to the next conference in Albuquerque, New Mexico, May 14-16, 2020: https://www.isfri2020.com/. I definitely plan to go and will probably submit some kind of abstract about bones from CT supplementing reference collections for forensic anthropology. The abstract submission deadline is December 12. Terrie
  18. 3 points
    mmkaiser

    Anatomical heart box

    This print worked well. Really liked the addition of the stand and the holes for the magnets.
  19. 3 points
    kopachini

    Quality of models

    At my department we have Intellispace Portal 7 and I am quite pleased with it, depending what you want to do with it. The major thing is that there is possibility to export .stl file from volume rendered recons (short VRT) from version 6 or 7 and above, which is not possible from Siemens Syngo. Also we have Philips Azurion C-arm and when you perform rotational intrarterial angiography it is possible to make VRT 3D model and also export it into Intellispace Portal (I did that only once when Philips aplicator was at my department but will have to do it more when I am back after my final exam). Also, I tried version Intellispace 9 or 10 (not sure which one) at RSNA meeting and it looks pretty nice, too. The thing is that all software in workstations have the same algorithms for automated segmentation and generation VRT models that are based on different threshold values for different tissue density and as said before, the best visualized tissues are those that have significant contrast to other tissue (like bone or contrast blood to surrounding soft tissue). Organs like liver, kidneys etc. are composed of different density tissues that have different density voxels on CT scan that can range from higher HU values in one voxel (blood vessel in post contrast scan of liver) to lower HU values (let say small area of lipids accumulated in hepatocytes), and if that area is near liver capsule where adjacent tissue is fat, you will have artefacts in your automated segmentation of liver. That is why I love manual or semi-automated segmentation for now until AI makes automated segementation more accurate (there was post about application of AI and segmentation in 3D slicer in some other topic).
  20. 3 points
    About a year ago nVidia announced the Clara project which is basically segmentation with AI help. The first release with this functionality is now available for 3D Slicer. Look here -> https://discourse.slicer.org/t/ai-assisted-segmentation-extension/9536 IMHO this is a very big step and even in this early state it looks very promising.
  21. 3 points

    Version 1.0.0

    100 downloads

    STL derived from a CT Lumbar spine and segmented with Slicer3D. lumbar, spine, axial, skeleton, lumbar, spine, .stl, 3d, model, printable, plates, body, intervertebral, disc, spinous, process, transverse, iliac, bone, sacrum, foramina, coccyx, ribs, sacroiliac, joint,

    Free

  22. 3 points
    In the last few decades, the 4th industrial revolution began - a significant advance in the 3D technology and an emerging of a brand new production method - the computer-controlled additive/subtractive manufacturing. It is considered "the new wheel" and it gives the ability to generate a detailed three dimensional object with complicated geometry from various materials (metals, polymers, clay, biological macro molecules) with a robot, controlled by a computer. The size of the object don't really matters - it's possible to construct structures on micron level or entire buildings. The thing, which really matters, is the geometry of the model. The specialists in the 3D technology are able to bend the very fabric of the world in every shape, which is needed. In the medical field, this advancement of the 3D technology was combined with the rise of the computer-assisted imaging and the histological imaging techniques , visualizing the living (or already death) organisms in details, never seen before. This is how the profession of the medical 3D artist emerged, giving new hope and amazing possibilities for the presentation, diagnostics and treatment of the human body. It's a hybrid profession, which requires vast knowledge and experience in the medical, engineering and computer science. If you want to become one and you're wondering can you actually sell your work, this guide will be quite helpful for you. As any other type of scientists, medical 3D artists have to choose his career path. It can lead to a career as academical professor, teaching students and performing theoretical experiments at a university or a science institute or as a industrial R&D specialist, creating practical products for the biomedical corporations. Both career options have their pros and cons, bot of them are saving lives. The difference is in the way of thinking. And the salary. For both of them the entrance requirement is a PhD in the field life or engineering science. So, in order to become a medical 3D artist, you need to go in the academy for a while, to endure the hell of the dissertation/thesis and to keep your sanity at the end. Once achieved, it's really hard to stay unemployed for long, those pesky talent seekers will jump on you like flies on manure. 1. Academical: The academical lives and thrives in his/hers institution. An office, a laboratory, some teaching obligations and the ability to work in the most cutting-edge fields of science and technology. More flexibility/freedom: the academical have a lot of free time, as long as the basic obligations towards the institution are satisfied. Intellectual autonomy: the academical can follow whatever idea he/she wants, as long as it's supported by the institution. Long term results: the academical things and acts in long period of time - one project can take an year, several year or the entire lifespan, depending on the project. Funding/salary issues: the academical is always underfunded and the salary sucks (unless he/she is well quoted, successful professor). This is why the problem-solving abilities and the high IQ are required for this career path. Strong ego and self-confidence: the academical things for themselves as geniuses, much smarter than the rest of the population (and in most cases they are right). Always “speaks theoretically”: the question "what if" is the breath and butter of the academia and it's really hard for the academical to be practical. 2. Industrial R&D specialist: the industrial scientist works in a office or a warehouse, with a team of other specialists, under the supervision of a project manager. He/she develops practical products, which have to be sellable and they have to be developed fast. More constrained (deadlines): the usual industrial project takes several months, under strict supervision and have to satisfy the needs of the marketing department. The deadlines are an issue here. Produces a practical product: the product have a practical, well defined application, shape, quality requirements and price. Pays a lot more: the salaries of the industrial R&D have an additional zero at the end. No funding issues: the industrial projects have more than adequate budget and they can receive an additional funding, if needed. No ego issues – “it’s just a job” - for the industrial specialist, the work is just a meaning for living. A job, as good as any other job. No "special missions" here. Literally “saves the world”: the products of the industry are used as practical applications and are used for diagnostics and treatment on everyday basis. Professional levels: As any other profession, the medical 3D artist goes through several stages, each one with higher requirements and possibilities. Jobber: the lowest level of them all. A sporadic odd jobs, for a low salary, for whoever is willing to pay. This is the first level, which a wannabe medical 3d artist reach and the level, on which most of them stay. Only those, who can achieve the necessary discipline, business ethics and quality can reach the next level. The jobbers are unpredictable, chaotic, they can hardly satisfy the deadlines and they offer the lowest quality possible. Every medical 3D artist in training is also a jobber. Freelancer: the selective few, who are talented and discipline enough to be able to offer NDA, contract, quote statement, production method description and industrial quality control. Those are the medical 3D artists, who doesn't suck, but wants to be free and flexible enough to follow their other interests. The freelancer is hired from companies and institution, which can't support a full-job 3d artist or their specialist are not competent enough to make the job done. A proud, well-respected person, working under strict business ethics, for fixed pay rate, usually calculated per hour or per item. The freelancer works on small projects, for a limited period of time and under well-defined condition, written on an official contract. Every professional medical 3D artist is also a freelancers. The reputation have a big importance in this group, which is why the freelancers are considered predictable, disciplined and competent to do any task, thrown at them. The salary here depends on the negotiating skills of the freelancer. Contractor: Those freelancers, who have the necessary business talent and are willing to take some risks, can make a company with several employees, several 3d printers, a convenient website with good portfolio and a variety of services. Such a company can take bigger orders from large institutions (hospitals or industrial companies), which requires a higher level of expertise, speed of service and quality control. Those contracts are for a longer period of time, under fixed condition, pricing and quality of the service. CEO: Those are the contractors, who are able to survive and to thrive, eventually can become big corporations, with hundreds of employees and millions dollars budgets. All of the current corporations started as small companies. Believe it or not, the biggest 3d printing companies (3D Systems, Stratasys. Ultimaker and many more) started as small, family-oriented companies, which became the gigantic corporations they are today. How they made it? I really want to know the answer of this question. So, most likely, you're a talented young (or not-so-young) individual with medical background, who watched some tutorials, made several models (most likely bones) and 3d printed them with a cheap 3d printer. Confident with your results, you think you can make a living with this amazing job and you're wondering how to start. My start was a bit rough, because I was trying to make a model of Pyramidal neuron in the Telencephalon for my department from a 10Gb Z-stack in Tif format with zero knowledge how to do it. This is how I found this website in first place. Few days later the model was done and when I tried to make my first bone models, it was way too easy, compared to the neuron. The rest is a lot of trails and errors, a lot of youtube tutorials, several kilograms of textbooks and the support of my colleagues. Here are some tips what you need to do in order to become a freelancer: Portfolio: If you want to sell your work, you have to present it first. Sketchfab.com is a very good way to do it, because it have an amazing 3d viewer with various awesome animation options. If you want to present your work, you just have to paste the link, because it's a zero-footrpint system - all you need to use it is a web browser. It's an excellent choice for 3d visualization and it's also free. The more models you're adding, the bigger audience you'll have and you don't have to worry what kind of 3d viewer your potential clients are using. Downloadable models: My personal choice is 30% paid models and 70% free ones. I'm a PhD student, I don't have some immediate need of money, so I can afford that. I'm dividing my models into regular and premium ones. In this way my models can be useful for everyone, both business parties or poor students around the world. It's really hard to find a good medical model for a presentation or a small university project and if you manage to find one, it's most likely from this website. Quote: When you're starting a job for someone, make sure that you have an accurate quote for your task in written format. Something like that: "I will generate ??? 3D models of a ??? (system, organ, structure) from CT/MRI datasets, which will include the following structures (soft tissues, bones, arterial/venous vessels etc. etc.) in ??? days for a ??? USD per hour, ??? hours per model, ??? USD per model". The more accurate you are, the better. This gives you the framework, in which you're working. Everything outside this frameworks is an extra and it should be payed as well. Your clients will try to change the conditions of your quote, this is why you need something written to control this process. Make sure you specify the currency, $ can mean a US dollar or a Mexican peso! NDA: Some clients will requite a mutual non-disclosure agreement, which you have to print, sign, scan and send back to the client. If you don't have such a document signed, you can do whatever you want with the model and you don't have to explain yourself to your client. You can afford a lower price for a model without NDA, because you can sell it or upload it as free download anyway. If you have such a document, just forget about the model, don't share it, don't show it and don't print it - you don't want to be sued by a medical company, they are more powerful than you. Contract: You should have a standard freelancers contract, in which you should apply the quote statement. Most of the cases, the quote statement is enough. Production method: You have to specify your production parameters like software, methods and operations. Something like that: "Segmentation of the abdominal aorta with Slicer 3D, exporting of the model as stl file, modelling and sculpting (smoothing, remeshing, boolean operation etc etc) in Meshmixer, postprocessing (slicing, magnet sockets, hinges etc etc) in Fusion 360, importation of the model into Slicer 3D for subsequent quality control, including ??? measurements of the dataset, the model and generation of average deviation". Don't be too precise, just the basic operations you're using with the corresponding software. Make sure you're not using a cracked software in your production method, everything you're using should be owned by you! 3D printed models: It's a good idea to have a set of 3d printed models, which can be presented on conferences, exhibitions and your social media page. This is a good commercial for your work, which is also a way for popularisation of the medical 3D modelling. Deadlines: Be precise in your work and follow the deadlines! As an old proctologist from my med school used to say - it's better to mess your finger than your reputation. If you're good in your work, you'll be hired again. Invoice: As with the contract, you should have a standard freelancers invoice, which you should send to your client. All those documents increases your credibility and are considered as signs of professionalism. If you're keeping your professional level high, you'll have better clients and higher pay rate. Freelancers websites: It's a good idea to have profiles in several freelancers websites. Most of your clients will contact you in person, but most likely they'll find you on those websites. Linkedin is a must. Patreon and facebook are also a good bet. Pricing: The usual salary for 3d modelling is between 30 and 60$ per hour, depending on the complexity of the task and the presence of an NDA. The most useful pricing for 3d printing is 1,5-2$ per hour of 3d printing. The smaller slide thickness and the bigger models requires significantly more time and a bigger price. You should also include all the postprocessing you're using (sanding, airbrushing, magnets, varnishes etc etc). 3D printing: For small operations, two or three 3d printers are enough. Good budget options are Ender 3 (FDM) and Elegoo Mars (DLP). Prusa MK3 and Form 2 are better, more expensive options, which will make your life much easier. Keep your printers in good condition and provide a regular maintenance. Choose several brands of polymers and stick to them, you don't want surprises, why you're chasing a deadline. Have fun: It doesn't matter what you're doing and how much you're making by doing it. Just have some fun! 3D printing is amazing, highly contagious activity, but it can become a burden, if you're not enjoying it. And always remember - with your work you're developing the medical science and you're literally saving lives.
  23. 3 points
    Dr. Mike

    Full size Thorax 3D print

    A quarter is shown at the bottom for scale.
  24. 3 points
    valchanov

    Atlas and Axis, 3D PDF

    Hello My recent anatomy projects forced me to start importing my 3d models into 3d pdf documents. So I'll share with you some of my findings. The positive things about 3d pdf's are: 1. You can import a big sized 3d model and compress it into a small 3d pdf. 40 Mb stl model is converted into 750 Kb pdf. 2. You can run the 3d pdf on every computer with the recent versions of Adobe Acrobat Reader. Which means literally EVERY computer. 3. You can rotate, pan, zoom in and zoom out 3d models in the 3d pdf. You can add some simple animations like spinning, sequence animations and explosion of multi component models. 4. You can add colors to the models and to create a 3d scene. 5. You can upload it on a website and it can be viewed in the browser (if Adobe Acrobat Reader is installed). The negative things are: 1. Adobe Reader is a buggy 3d viewer. If you import a big model (bigger than 50 Mb) and your computer is business class (core I3 or I5, 4 Gb ram, integrated video card), you'll experience some nasty lag and the animation will look terrible. On the same computer regular 3d viewer will do the trick much better. 2. You can experience some difficulties with multi component models. During the rotation, some of the components will disappear, others will change their color. Also the model navigation toolbar is somewhat hard to control. 3. The transparent and wireframe polygon are not as good as in the regular 3d viewers. The conclusion: If you want to demonstrate your models to a large audience, to sent it via email and to observe them on every computer, 3d pdf is your format. For a presentation it's better to use a regular 3d viewer, even the portable ones will do the trick. But if the performance is not the goal, 3d pdf's are a good alternative. Here is a model of atlas and axis as 3d pfg: https://www.dropbox.com/s/2gm7occq5ur50um/vertebra.pdf?dl=0 Best regards, Peter
  25. 3 points
    So I have seen some questions here on embodi3D asking how to work with MRI data. I believe the main issue to be with attempting to segment the data using a threshold method. The democratiz3D feature of the website simplifies the segmentation process but as far as I can tell relies on thresholding which can work somewhat well for CT scans but for MRI is almost certain to fail. Using 3DSlicer I show the advantage of using a region growing method (FastGrowCut) vs threshold. The scan I am using is of a middle aged woman's foot available here The scan was optimized for segmenting bone and was performed on a 1.5T scanner. While a patient doesn't really have control of scan settings if you are a physician or researcher who does; picking the right settings is critical. Some of these different settings can be found on one of Dr. Mike's blog entries. For comparison purposes I first showed the kind of results achievable when segmenting an MRI using thresholds. With the goal of separating the bones out the result is obviously pretty worthless. To get the bones out of that resultant clump would take a ridiculous amount of effort in blender or similar software: If you read a previous blog entry of mine on using a region growing method I really don't like using thresholding for segmenting anatomy. So once again using a region growing method (FastGrowCut in this case) allows decent results even from an MRI scan. Now this was a relatively quick and rough segmentation of just the hindfoot but already it is much closer to having bones that could be printed. A further step of label map smoothing can further improve the rough results. The above shows just the calcaneous volume smoothed with its associated surface generated. Now I had done a more proper segmentation of this foot in the past where I spent more time to get the below result If the volume above is smoothed (in my case I used some of my matlab code) I can get the below result. Which looks much better. Segmenting a CT scan will still give better results for bone as the cortical bone doesn't show up well in MRI's (why the metatarsals and phalanges get a bit skinny), but CT scans are not always an option. So if you have been trying to segment an MRI scan and only get a messy clump I would encourage you to try a method a bit more modern than thresholding. However, keep in mind there are limits to what can be done with bad data. If the image is really noisy, has large voxels, or is optimized for the wrong type of anatomy there may be no way to get the results you want.
  26. 3 points
    Andras Lasso

    Lumen of vessel in 3D Slicer

    For anybody who stumbles upon this thread: we've added "Hollow" effect to 3D Slicer's new Segment Editor module. It has the option of creating vessel wall inside, outside, or around the surface. The method uses labelmap representation for internal computation therefore it is very robust (there are no degenerate triangles or intersecting surfaces in the generated mesh), you may just need to set the resolution of the segmentation if you want to create models of very thin walls.. Here is a short demo video about how to use it: We constantly improve 3D Slicer's segmentation capabilities and 3D printing is one of the driving applications, so any feedback or feature requests are welcome.
  27. 3 points
    Diogo

    Teeth Micro CT

    Sorry guys been so busy and only now could come back and read your responses. I ended up with Mevislab for segmentation and analysis. Here is an example of what I have been doing. Cheers. Diogo Guerreiro S18T7 Final.mp4
  28. 3 points
    mikefazz

    Give Myself a Hand

    I printed my hand a couple weeks back. The model is available for sale at: Or try your 'hand' at segmenting it from the scan data that is free at: I am still working on getting better transparency to show the internal bones. With FDM true transparency only works for single perimeter prints (like vases) but I am trying some other plastics that should do better than this one done with PLA. The light source is pretty bright, the bones are difficult to see normally.
  29. 3 points
    mikefazz

    Mikes Left Foot

    Version 1.0.0

    123 downloads

    This is the segmented bones from a partial weight bearing CT scan of a healthy 25 year old male (me a few years ago). There is also a model of the outer foot surface (skin) to have the full foot volume. All bones are separate as well as combined as a single file. Shoe size 10.5 for reference. The 3D print is of my other foot (I haven't yet printed my left foot)

    $15.00

  30. 3 points
    This is a time of rapid growth in medical 3D printing. The technology allows us to take an individual patient’s scan information and create physical models, which can be used in any number of clinical applications. The industry standard DICOM image files from CT and MRI scanners can be converted into 3D files, such as STL (for stereolithography) files. These digital models can then be uploaded to a 3D printing service bureau or printed on one of the currently available professional grade printers.The democratization of desktop 3D printers, however, now allows almost anyone with a serious interest in the technology to print models in their own office/workshop. These can be used for educational purposes and for prototyping, and represent an excellent entrée into the technology. Recently, I started printing 3D models of some of my own patient’s scans using a consumer grade desktop printer. The patient’s CTs were acquired on our Toshiba Aquillion 64 Slice CT scanner using our standard acquisition protocols. The DICOM volume data was then burned to a CD for processing. For my initial test prints, I used the Materialise Mimics and 3-matic software under their 30-day free trial period. The images from the appropriate volume were imported into the Mimics software. Thresholding is then performed to isolate the tissues in question, based on its Hounsfield units, a measurement of X-ray density. The particular anatomy of interest is then selected using “region growing” tools and a 3D model is generated. The model is then “wrapped”, to account for the individual CT slices, and to smooth any gaps in the 3D mesh. Choosing the degree of wrapping is where experience comes into play. Too little wrapping can cause gaps to be present on your final models. Too much, and detail can be lost. The 3D model is then exported into the 3-matic program for “local smoothing” of the model. The digital model is then hollowed, depending on the structure and its use. You then export it as a binary STL file. In all of the steps above, clinical knowledge of the anatomy is extremely helpful in creating the most accurate models possible. Understanding how the models will be used informs your decisions in their creation. The STL file is then imported into a slicing software to create the G-code files that instruct the printer how to actually create the physical model. I used the open source Cura software for the generation of the G-code for the printer. An image of the 3D model is seen superimposed in a representation of the build plate of the particular printer, in my case the Ultimaker 2 (Ultimaker B.V.). The model can be rotated to optimize the printing process. The highest resolution of current 3D prints from fused filament printers is in the z-direction: from the bottom on the build plate to the top of the object. The degree of overhang must also be taken into account. Since the filament cannot be deposited in thin air, the slicing software creates a scaffold to support the overhanging material. Keep in mind; this support structure must be physically removed in post-processing. The slicing software also creates a thin base layer of the material (called a brim or raft) that is deposited around the object to facilitate print adherence to the print platform. The generated G-code is saved to an SD card, which is then placed into the printer. In some cases, the files can be transferred wirelessly. I used 2.85 mm PLA filament to create the printed models. PLA is polylactic acid, a biodegradable material derived from cornstarch. PLA based material has been used in orthopedics for sutures, controlled release systems, scaffolding for cartilage regeneration, and fixation screws. The print time takes several hours, depending on the size and complexity of the model, as well as the amount of support structure used. Through trial and error, I found that careful positioning of the 3D model on the virtual build plate can potentially shorten the length of printing time. A full-scale hollow abdominal aortic aneurysm model took about 9 hours to print, while a full-scale scapula took 13 hours. A life-size pediatric skull will take approximately 23 hours to print! The use of 3D printing in medicine presents enormous potential. Exponential development of many new applications will occur if researchers, students and clinicians have access to small-scale 3D printers for prototyping new devices and procedures. The future is only limited by the imagination. A method of reimbursement wouldn’t hurt either. I would like to thank Frank Rybicki, MD, Professor and Chair of Radiology, University of Ottawa, and his team from the Applied Imaging Science Laboratory at Brigham and Women's Hospital for their great 3D Printing Hands-on courses at RSNA 2014. Copyright ©2015 Eric M. Baumel, MD
  31. 3 points
    Hello everyone We have been working on another interesting case recently, and I thought I would share it with you. The patient had been diagnosed with odontogenic myxoma, and had undergone hemimaxillectomy. Due to loss of literally half the face, the patient is seeking a solution to help bring back his facial profile. We designed a prosthesis, using mirroring techniques, and the result turned out to be like this. The next step is to determine how to make the actual prosthesis.
  32. 3 points
    1977: Why would anybody want to use a computer? 1994: Why would anybody want to use the Internet? 2016: Why would anybody want to use 3D printing? I'm glad that you and the members of this community are open minded. This technology is the future, and with it we are going to change medicine and patient care for the better.
  33. 3 points
    This is actually very amazing, and it is really doable with some practice and mastery of the softwares. We have printed numerous models, from crania-maxillofacials to vascular malformations, and also some interesting craniosynostosis cases. It is getting pretty common in the hospital.
  34. 3 points
    descobar3d

    From Dicom to .STL

    There are several options for clinicians to use when converting a patients .dicom data into a 3D printed model. For our 3D Printing Program I use the Mimics Innovation Suite made by Materialise. The software is available for computers running Windows. The software receives regular updates to improve functionality and increase the efficiency and quality of the .dicom to 3D print workflow. It is capable of converting CT, MRI, and 3D ultrasound images into 3D models that are ready for the 3D printer. There are many things that I enjoy when using this software, including:​ Ease of use for beginner users Fast processing time, <30 minutes for many projects Many different features available To give a demonstration on how the software is easy to use, I will use a CT scan of my own head. After the files are loaded, the software detects the appropriate scan studies that are present. You are able to load multiple scans into a single project. Apply thresholding: Mimics has built in presets for CT bone, soft-tissue, etc. I selected the preset for CT bone. After the thresholding is applied a new Mask is created. The mask shows only bone in the scan. Edit mask in 3D: Before i create a new 3D mask, i can edit my current mask to make changes such as removing unwanted pieces and cropping the unwanted areas before moving forward. Region Growing: In order to remove floating voxels and detach unwanted bony anatomy, the Region Growing tool is applied. It will preserve only the bone that is desired in the mask. Calculate 3D from Mask: Once the mask is edited the way you need, you will Calculate 3D object from the Mask. The 3D object can further exported into 3Matic for additional changes or exported as an .stl file for 3D printing. Export to 3Matic: I would demonstrate the tools for cleaning and preparing the part for printingWrap to fill small holes Smoothing to smooth the surfaces Quick label to apply a label to the part Fix wizard to make sure the part is watertight for printing Export 3D PDF as a communication tool [*]Copy-Paste the completed file from 3-matic back to Mimics. Show the contours of the 3D model on the original images. Point out the importance of verifying the accuracy of the part prior to exporting STL. Conclusion: When evaluating software for printing 3D models from patient scans, look at features, cost, compatibility, and ease of use. Ask for a demonstration and trial before purchasing. There are different options for software, it is important to look for one that works with your workflow. Want to learn more? Contact Me David@3dAdvantage.org Visit my site 3DAdvantage
  35. 3 points
    On my last post I gave an overview of the 3D printers I am currently using in our hospital program. Now I will be explaining the different software I have used from one time to another to go from 3D model to 3D print. The software I cover here is available as a free download or for under $500. 1. TinkerCAD: The first software I used was TinkerCAD. It is a web-based CAD design tool, Simply create a free account and start designing. The layout and menu's are simple and basic enough for beginners to naviagate. It offers many pre-made tools to use from adding letters to adding shapes. For creating designs in TinkerCAD it uses a combination of adding and subtracting shapes or using pre-made designs. The main tools I use are Align, Group, Ruler, and Cylinder. When finished you can download your designs for exporting to a 3D printer or use a 3rd party to print your design for you. For being a entry-level software I still use it to add connections between bones, and for simple movement between parts. Importing .stl files is an important function to use when creating files in other software and wanting to edit in TinkerCAD. Use in Healthcare Applications: Adding custom connections between parts, creating simple frames and supports. Pros: Simple design, easy to use, no software to download, free, always available online from any computer. Cons: Pre-loaded shapes can be limiting for complex parts. Amazing results can be achieved with practice and time. 2. 123D Design: This software is part of the Autodesk family. This a free download, geared more towards users with some knowledge of CAD software. Where TinkerCAD requires the user to use shapes to make designs, in 123D you can create from scratch. This software is ideal for designing prototypes and those wanting to becoming more familiar with CAD software. I use 123D when I need more control than what is offered in TinkerCAD. Use in Healthcare Applications: The software provides more customization than TinkerCAD. It allows for custom-made parts used in Rapid Prototyping Design. Pros: Simple to use, free, great for learning CAD software. Cons: Other software is capable of the same functions. 3. Autodesk Fusion360: I recently started using this software. As our 3D printing program grew I started to receive request to design prototypes based on drawings. Fusion360 has been my software of choice when creating prototypes. The software offers many tools from Sculpting, Combining, Importing Mesh, and Press & Pull, to name a few. I can spend countless post just discussing all the features available in Fusion360, best advice is to go use it. The online support is outstanding. Autodesk really has stood behind this product and helping the community, all my questions were answered within hours (during business hours) and customer support always provided screenshots or videos as well as the written steps. Fusion360 also has a new feature that will export directly to the printing software included or a 3rd party software, such as Preform, Simplify3d, Meshmixer, etc. Use in Healthcare Applications: Designing prototypes, creating designs based off of patient scan data, creating a wide range of models from simple to complex, allows for online collaboration with your team. Pros: Many features available, great online/community support, constant updates to software. Cons: Cost associated with purchasing software (minimal) 4. Meshmixer: Another software from the Autodesk family that I use. This is a very powerful & valuable piece of free software to have when 3D printing. Meshmixer gives you control over many different aspects of your model, including Transform, Plane Cut, Sculpt, Analysis, and adding Supports. The Analysis function provides Slicing of your model, it will correct errors and prepare the model for 3D Printing. Meshmixer allows direct exporting to certain printers (*listed in Meshmixer). Using the Support feature allows you to define how supports will be generated. This software also allows you to add or remove supports that are generated by the software, a very useful feature when printing a patient specific model that is dependent on accuracy. Use in Healthcare Applications: This software is a must-have. I use it to double-check for any slicing errors prior to printing. You can also sculpt organic models from scratch (see uterus) Pros: Free. Many editing options available. Will help ensure more successful prints. Cons: Although there are training guides and a community forum. The software can be overwhelming to a first time user. The best recommendation is to search forums and spend time using the software to become familiar with the available features. Conclusion There are many options available when choosing software to use. It is important to evaluate cost, ease of use, available functions, and capability with the 3D printers you will be using. Evaluate the goals of your 3D Printing Program to choose what combination of software you will need and use. Remember as most of the software featured here is free, spend time working with each one. Links to software websites found Here An added extra. Download a 3D Skull ready for Print Click Here Written by David Escobar Check out my site for more information 3DAdvantage.org Twitter: @descobar3d
  36. 3 points
    Michael Holland

    3D printed baby T. rex!

    A few years ago, a friend and colleague of mine was working in the Hell Creek formation of Montana and collected a small fossil jaw fragment. Due to the tiny size and incomplete nature of the bone, along with the need to continue work during the limited time available, he wrapped up the specimen, tentatively labeled it as a crocodilian jaw and moved on. Later, another friend of mine was evaluating this specimen in the museum collection (Museum of the Rockies) and concluded that the jaw was not that of a crocodilian, but rather of a tyrannosaur. Named "Chomper", this specimen generated a lot of excitement, due to the paucity of baby/juvenile T. rex material known and the strong current interest in dinosaur ontogeny. The specimen was sent to Dr. Larry Whitmer, who brought it into the digital domain to realize a very interesting new exhibit feature. After CT-scanning the jaw, Larry and his cohorts digitally created the rest of the skull. To do this, they used scans of another (but substantially larger) juvenile T. rex skull known as "Jane". Using other existing tyrannosaurid fossils for reference, they edited the Jane skull model to shrink it down to the correct proportions needed to fit the tiny jaw bone. Simply scaling down an adult T. rex skull wouldn't do, since growth in the skull is allometric (different areas grow at different times/rates). The resulting skull model was then printed on an Objet printer (a supremely nice machine) and is now being prepared to go on exhibit at the Museum of the Rockies. You can see a nice chronicle of the process on the WhitmerLab Facebook page here: https://www.facebook.com/witmerlab As someone who has spent a lot of time manually sculpting/reconstructing dinosaur skulls by hand, I can appreciate the mix of artistic sensibility and anatomical knowledge needed to do this kind of reconstruction, and I must say that the results of the WhitmerLab crew are fantastic, and this technology allows for many amazing possibilities. Michael
  37. 3 points
    We are happy to receive recognition for being a top influencer in 3D printing. Thanks to all the members of this community who are helping us bring the benefits of biomedical 3D printing to the world! The Management.
  38. 3 points
    mplishka

    Hardware requirements?

    Dr. Mike, here's a blog post I did on the paper printing: https://zenstorming.wordpress.com/2015/03/04/printing-with-paper-the-21st-century-way/ There are links to pdf's in the post with one a case study from Louvain. Enjoy!
  39. 3 points
    Dr. Mike

    Hardware requirements?

    I totally agree with mplishka. The two main firms that do surgical planning models are Medical Modeling (now owned by 3D systems) and Materialise. Reimbursement is a major obstacle. Right now, there is no way to get paid for this, so anything you do clinically must be paid for by the hospital or research grant, or is on your own dime. I just returned from Arizona after attending the Mayo Clinic 3D printing in Medical Practice conference and reimbursement was agreed to be a major obstacle. This is why the very limited 3D printing for surgical planning is mainly being done at wealthy institutions that can absorb the cost (like Mayo). FYI, here are a few of the models that were on display at the conference from both Medical Modeling and Materialise. protohex, I agree that there is a market for a more diverse set of medical 3D printing services, with different price points, materials, turn around times, etc. I've long recognized this. If anybody out there is offering medical 3D printing services (segmentation, design, and printing), please let the community know about your availability by posting in the forums section under services offered. We need more than just two choices!
  40. 3 points
    mplishka

    Hardware requirements?

    3DSystems will do it as will Materialise. There are a couple of other players that their names escape me at the moment, but any 3d printing company can do the printing once they get the STL (heck even individuals with a decent printer with connections can do it!) I've had some in depth discussions with folks from 3DSystems and Materialise and they both point out that it's not about printing per se, it's about workflows. Getting files segmented, cleaned up and then printed in an expeditious manner is the challenge, with emphasis on the 'expeditious' part. Those two companies alone can handle the printing and even the segmentation, but getting their services into hospitals as THE provider is the challenge, especially since there still isn't a reimbursement structure in place for 3d printing. The burden is on the healthcare provider to find a way of getting the prints paid for without losing money.
  41. 2 points
    Selami

    Covid19 infected lung

    Version 1.0.0

    277 downloads

    Covid19 infected lung, infected lung part shown semi-tranparent. Dataset downloaded below, which marked as case4 at site. http://covidctscans.org/ lung, .stl, 3d, model, printable, upper, lower, trachea, covid-19, coronavirus, organ, bronchi, lobes, medium, infection, medical, medicine, bronchi, pneumonia, trachea, cartilage,

    Free

  42. 2 points

    252 downloads

    This anatomically accurate mandible bone (jawbone) was created by Dr. Marco Vettorello, who has graciously given permission to share it here. The mandible forms the lower jaw. It is connected to the rest of skull at the temporomandibular joint. The file is in STL format and compressed with ZIP. This file is also available here. jaw, mandible, jaw, bone, 3d, printing, angle, ramus, coronoid, process, .stl, 3d, model, printable, printing, medicine, medical, incisor, molar, premolar, canine, teeth, tooth, dental, dentistry, foramina, bone,

    Free

  43. 2 points
    Hello This is my first 3D print. I used a 3D model of a kidney, which I made myself from a renal angiography. I printed it with one of my engineer geek friends using a Prusa i3 self-made 3d printer, 0,2 mm nozzle, 0,2mm layer thickness and PLA as material. This was my entering demonstration, which gave me an assignment as a freelancer anatomy assistant professor. My ambitions are to use 2D and 3D models, along with the traditional cadaver techniques in my work as an anatomy teacher and to teach my students how to do it with their own hands. I have 12 years of experience as an internal physician in ER, 4 years as a psychiatrist, 3 years as an acupuncturist and a lifetime as an IT GEEK, I don't have any teaching experience, my english language skills are a bit rusty and I don't know what will come from this, but I'm eager to find out. Wish me luck:)
  44. 2 points
    SJSato

    Lumbar Spine 3D print

    Had some time over Memorial Day weekend so I downloaded Dr. Mike's Lumbar Spine model. Believe it or not, this was a 65 hour print on my Ultimaker 2! All in all, the print came out pretty well. I have a web cam watching over the printer and can monitor progress over my iPhone. I can also shut down the printer remotely if the printer goes haywire.
  45. 2 points
    I was recently asked this question and I am sharing the answer with the group in hopes that somebody will find it helpful. Question: "I am a teacher at a High School in Arizona, we recently built a FAB LAB (digital fabrication facility) and are interested in starting a medical imaging class/club. We have several medical professionals, Dentist, Orthopedic Surgeon, General Practice, Physical Therapist and Medical researchers, who are interested in volunteering in to help with this program. Our goal is twofold, one to increase student interest in pursuing medical professions and two to give students an avenue for employment in the emerging 3D medical imaging field. Ultimately our goal would be to have a Career and Technical Education (CTE) program where students could graduate with some sort of certificate indicating competency. My question is, are there recommended training/certification programs that we need to consider and implement? What are your recommendations for us moving forward with this program. Any information you could provide would be appreciated." Answer: " Hello ______ Just to clarify, are you talking about medical 3D Printing? If so, there is currently no such certification program in this technology. One basic requirement is an understanding of medical imaging technologies, so I would say a bare minimum to do medical 3D printing would be a certification as a CT or MRI technologist, which have established training pathways for post-secondary education. Here is a link. https://study.com/ct_technician.html You would then have to obtain experience with 3D printing, of which there is no formal pathway. Of course, you can obtain greater imaging expertise as a radiologist, which is 4 years of med school and 6 of residency and fellowship after college. Again, there is still no formal pathway for the actual 3D printing component of this. Hope this helps."
  46. 2 points

    Version 1.0.0

    33 downloads

    This 3D printable STL file contains a model of the skull and cervical spine was derived from a medical CT scan. The patient is edentulous (without teeth). This model was created using the democratiz3D 3D model creation service 0522c0909

    Free

  47. 2 points
    Hello Kopachini, I have some news for you. While the new GE machines have the facility to export images form DICOM files in STL format (either as a stand alone model or a relief model), they have unbundled the functionality so that the same functionality can be available using their stand alone software called 4D View where older GE models do not have this functionality built in. This allows you to access a DICOM file and export the image as a STL file. In theory you can download this software for the GE website, but it is rarely successful. And you need to be a member of the Voulson club. The only way I have found is to make friends with an owner of a GE system and ask them to request a demo version of the software. This is what I did. My (small) company 3D Industries is now working on this aspect as one of areas of activity with a view to commercialization. Let me know what you are doing and we may have a common interest. Best regards Peter
  48. 2 points
    Dr. Mike

    Holes in bone models with democratiz3D

    I'd like to elaborate on this topic a bit, as I recently had another member inquire about this issue. The member was creating a model from a CT scan of the clavicles. As you can see, there are holes in the medial (midline) ends of both clavicles. What is causing this? Is it a problem with democratiz3D? How can it be fixed? The issue lies with the patient's anatomy and the quality of the original CT scan. In the human body there are areas where bones are naturally very thin. Sometimes, the bone surface (cortex) can be paper thin. Also, some patients who have conditions like osteoporosis may have very little calcium in their bones. Issues like this make it very hard for the CT scanner to detect the bone wall, as you can see from the image below which shows the area on the left clavicle that has a hole in the final model (red arrow). The problem isn't with democratiz3D, but with the quality of the CT scan or with the patient having thin bones (how dare they!). democratiz3D is actually creating the model exactly as it appears on the CT, its just that the CT has holes we don't want! So, what can be done? If you encounter this problem you have two options. 1) Manually fix the holes in the model with a mesh editor like Meshmixer, or 2) decrease the threshold value in democratiz3D and re-process the scan. Decreasing the threshold tells the system to capture more voxels in your model, potentially capturing more thin or osteoporotic bone. But, be careful. If you reduce the threshold too much (less than 100), you run the risk of starting to capture muscle, organs, and vessels in your bone model. If you are not sure what threshold to use, you can experiment by running your scan through democratiz3D using different thresholds. To save time, I suggest you do this on low or medium quality setting. When you find a threshold that works, you can generate your final model using a higher (and more time consuming) quality setting, like High or Ultra. If you are familiar with mesh editing software, that is probably the fastest way to correct this problem. Just delete the edge of the hole, fill it in with a new face, and run a quick smooth operation on the area. It's a 1 minute fix if you know the keyboard shortcuts. I hope this tip helps. Dr. Mike
  49. 2 points
    Hey! I have used many, like Materialise, 3D Slicer and so on. You have to use an array of softwares. And yes! this is one of the many models I have printed. I use a RepRap printer with PLA (1.75 mm), with 0.2 mm layers. This kind of models like the above picture takes about one whole day to print and sometimes you have to start over due to technical errors. Have you printed any models? And what kind of use do you expect from it? Cheers Amir
  50. 2 points
    The University of Wollongong, Australia has announced a new free online course in 3D bioprinting. Details available from the link below: https://www.engineersaustralia.org.au/portal/news/3d-printing-will-provide-body-parts-future
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