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  1. 5 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. 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
  3. 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!
  4. 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.
  5. 3 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!
  6. 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.
  7. 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.
  8. 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
  9. 3 points
    lillux

    Mandibola

    Version 1.0.0

    76 downloads

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

    Free

  10. 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
  11. 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.
  12. 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.
  13. 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.
  14. 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
  15. 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
  16. 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.
  17. 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!
  18. 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!
  19. 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.
  20. 2 points
    Diogo

    Teeth Micro CT

    Dear all First of all thank you so much Dr Mike for this wonderful website. I am with the University of Michigan and been doing some research on teeth morphology using Micro CTs. I am working mostly with MeVislab frameworks and Mimics. Regarding slicer I would like to ask if it is possible to import TIFF files as slices instead of DICOM files. Each time I try to import data in TIFF my slicer version keeps crashing. Any tips? Best Regards Diogo
  21. 2 points
    No problem! You need to go to All Modules, then Crop Volume, hit Crop and wait. Then you will see your slice windows change to the area you designated. When you go to Save, you will see that there is a second volume that says "subvolume". This is the cropped volume that you can save as .nrrd. This format can be reopened in Slicer or uploaded to the democratiz3d app to get a printable model.
  22. 2 points
    Dr. Mike

    3D printed brain from MRI

    Printed on an Ultimaker 3 extended with white PLA and PVA support.
  23. 2 points
    mikefazz

    Teeth Micro CT

    I haven't tried importing tiff's but one thing to try would be to use ImageJ to convert a stack of tiffs to an nrrd file for loading in 3DSlicer. Mike (not Dr. Mike;)
  24. 2 points
    Ah. There's the problem then. I'm not seeing the crop box at all.
  25. 2 points
    Please note the democratiz3D service was previously named "Imag3D" In this tutorial you will learn how to quickly and easily make 3D printable bone models from medical CT scans using the free online service democratiz3D. The method described here requires no prior knowledge of medical imaging or 3D printing software. Creation of your first model can be completed in as little as 10 minutes. You can download the files used in this tutorial by clicking on this link. You must have a free Embodi3D member account to do so. If you don't have an account, registration is free and takes a minute. It is worth the time to register so you can follow along with the tutorial and use the democratiz3D service. >> DOWNLOAD TUTORIAL FILES AND FOLLOW ALONG << Both video and written tutorials are included in this page. Before we start you'll need to have a copy of a CT scan. If you are interested in 3D printing your own CT scan, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figures 1 and 2 show the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available. Figure 1: The radiology department window at my hospital. Figure 2: An example of what a DVD containing a CT scan looks like. This looks like a standard CD or DVD. Step 1: Register for an Embodi3D account If you haven't already done so, you'll need to register for an embodi3d account. Registration is free and only takes a minute. Once you are registered you'll receive a confirmatory email that verifies you are the owner of the registered email account. Click the link in the email to activate your account. The democratiz3D service will use this email account to send you notifications when your files are ready for download. Step 2: Create an NRRD file with Slicer If you haven't already done so, go to slicer.org and download Slicer for your operating system. Slicer is a free software program for medical imaging research. It also has the ability to save medical imaging scans in a variety of formats, which is what we will use it for in this tutorial. Next, launch Slicer. Insert your CD or DVD containing the CT scan into your computer and open the CD with File Explorer or equivalent file browsing application for your operating system. You should find a folder that contains numerous DICOM files in it, as shown in Figure 3. Drag-and-drop the entire DICOM folder onto the Slicer welcome page, as shown in Figure 4. Click OK when asked to load the study into the DICOM database. Click Copy when asked if you want to copy the images into the local database directory. Figure 3: A typical DICOM data set contains numerous individual DICOM files. Figure 4: Dragging and dropping the DICOM folder onto the Slicer application. This will load the CT scan. Once Slicer has finished loading the study, click the save icon in the upper left-hand corner as shown in Figure 5. One of the files in the list will be of type NRRD. make sure that this file is checked and all other files are unchecked. click on the directory button for the NRRD file and select an appropriate directory to save the file. then click Save, as shown in Figure 6. Figure 5: The Save button Figure 6: The Save File box The NRRD file is much better for uploading then DICOM. Instead of having multiple files in a DICOM data set, the NRRD file encapsulates the entire study in a single file. Also, identifiable patient information is removed from the NRRD file. The file is thus anonymized. This is important when sending information over the Internet because we do not want identifiable patient information transmitted. Step 3: Upload the NRRD file to Embodi3D Now go to www.embodi3d.com, click on the democratiz3D navigation menu and select Launch App, as shown in Figure 7. Drag and drop your NRRD file where indicated. While NRRD file is uploading, fill in the "File Name" and "About This File" fields, as shown in Figure 8. Figure 7: Launching the democratiz3D application Figure 8: Uploading the NRRD file and entering basic information To complete basic information about your NRRD file. Do you want it to be private or do you want to share it with the community? Click on the Private File button if the former. If you are planning on sharing it, do you want it to be a free or a paid (licensed) file? Click the appropriate setting. Also select the License Type. If you are keeping the file private, these settings don't matter as the file will remain private. Make sure you accepted the Terms of Use, as shown in Figure 9. Figure 9: Basic information fields about your uploaded NRRD file Next, turn on democratiz3D Processing by selecting the slider under democratiz3D Processing. Make sure the operation CT NRRD to Bone STL is selected. Leave the default threshold of 150 in place. Choose an appropriate quality. Low quality produces small files quickly but the output resolution is low. Medium quality is good for most applications and produces a relatively good file that is not too large. High quality takes the longest to process and produces large output files. Bear in mind that if you upload a low quality NRRD file don't expect the high quality setting to produce a stellar bone model. Medium quality is good enough for most applications. If you wish, you have the option to specify whether you want your output file to be Private or Shared. If you're not sure, click Private. You can always change the visibility of the file later. If you're happy with your settings, click Save & Submit Files. This is shown in Figure 10. Figure 10: Entering the democratiz3D Processing parameters. Step 4: Review Your Completed Bone Model After about 10 to 20 minutes you should receive an email informing you that your file is ready for download. The actual processing time may vary depending on the size and complexity of the file and the load on the processing servers. Click on the link within the email. If you are already on the embodied site, you can access your file by going to your profile. Click your account in the upper right-hand corner and select Profile, as shown in Figure 11. Figure 11: Finding your profile. Your processed file will have the same name as the uploaded NRRD file, except it will end in "– processed". Renders of your new 3D model will be automatically generated within about 6 to 10 minutes. From your new model page you can click "Download this file" to download. If you wish to share your file with the community, you can toggle the privacy setting by clicking Privacy in the lower right-hand corner. You can edit your file or move it from one category to another under the File Actions button on the lower left. These are shown in Figure 12. Figure 12: Downloading, sharing, and editing your new 3D printable model. If you wish to sell your new file, you can change your selling settings under File Actions, Edit Details. Set the file type to be Paid, and specify a price. Please note that your file must be shared in order for other people to see it. This is shown in Figure 13. If you are going to sell your file, be sure you select General Paid File License from the License Type field, or specify your own customized license. For more information about selling files, click here. Figure 13: Making your new file available for sale on the Embodi3D marketplace. That's it! Now you can create your own 3D printable bone models in minutes for free and share or sell them with the click of a button.If you want to download the STL file created in this tutorial, you can download it here. Happy 3D printing!
  26. 2 points
    Dr. Mike

    Skull without teeth

    Version 1.0.0

    25 downloads

    This 3D printable STL file contains a model of the skull of a edentulous (without teeth) patient was derived from a medical CT scan. This model was created using the Imag3D 3D model creation service 0522c0909

    Free

  27. 2 points
    Romanv825

    Stretched images in 3D Slicer

    i think i just answered myself. Under the Volumes module>Volume Information, i adjusted the Image Spacing and it seems to have worked. maybe this will help someone else down the road.
  28. 2 points
    mikefazz

    Materials for fracture experiments

    Hi Terrie, I am familiar with sawbones are you looking for a material with similar mechanical properties to actual bone? These days there are plenty of materials available yet I have doubts about being able to match the visco-elastic properties. I have played around with altering the internal printing structure of a bone by printing the cortical bone solid and using 'infill' to alter density to simulate trabecular bone. The picture below is from a while back where I printed a bone using 2 materials. The red inside is just the infill material which is similar to a honeycomb structure. Bone as a material is pretty strong so may not be easy to replicate as it is more like a composite. I would be interested in looking into options
  29. 2 points

    Version 1.0.0

    25 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 Imag3D 3D model creation service 0522c0909

    Free

  30. 2 points
    An entirely new 3D printing method that prints 25-100x faster than currently available technologies has been introduced. The new process called Continuous Liquid Interface Production Technology (CLIP) works by using light and oxygen to change a photosensitive liquid resin into a three dimensional solid object. The process is similar to Stereolithography (SLA) where liquid photopolymers are cured using ultraviolet light. However instead of depositing material layer by layer, the object is formed at once. CLIP places a pool of liquid resin over a digital projection system which projects an image for how each layer should form. To create an object, bursts of light and oxygen are applied; light hardens the resin while areas exposed to oxygen are kept from hardening. Proposed advantages of this technology include radically faster processing time and ability to use wide range of materials that make stronger objects. This technology can potentially be extremely useful in the health care industry if models can be printed within a matter of minutes and enable preoperative planning of surgical procedures that may be time sensitive. For a summary of other 3D printing technologies, check out my previous post here Tatiana Kelil, MD
  31. 2 points
    Purpose of this blog: To create a forum where members of the 3D medical printing community can share problems, solutions and practical advice pertaining to all aspects of the 3D printing pipeline. Featured problem: Setting up a new printer Featured printer: Printrbot Metal Plus Printing type: Fused deposition modeling Theme: Don’t put the cart in front of the horse Translation: don’t try to print before you’ve set up the printer If you are at all like me, you are impatient. When your new printer arrives, you want to rip open the packaging, set the printer on the counter, plug it in and hit “print”. If this sounds like you, keep reading. This first blog is a cautionary tale. Lesson 1: Make sure that your printer is properly calibrated. 1. Level, Level, Level While the printer may come “pre-calibrated,” it is always a safe bet to double-check that nothing untoward has happened during shipment. The printing bed needs to be level in relation to the path of the extruder, and therefore both the bed and the extruder railing should be checked and adjusted if not leveled. The more level you can get the print bed with respect to the extruder, the easier your life will be for all of the following steps. There are many reports of warped print beds on the internet; e.g. some of the printrbot simple models seem to have a dip in the center of the print bed. Using a straight edge rather than just a level may help you detect this type of issue. Getting that print bed straight by whatever means necessary is advised. 2. Determine your negative z-value, or get ready to throw out a lot of failed prints You need to determine the optimal distance that the hot end of the extruder should be from the print bed when printing. The number you are determining is the negative z value. Picking your negative z-value is sort of like Goldilocks and the 3 bears: If the negative Z value is too high, your print will look stringy. If the negative Z value is too low, your print will look smashed. So you want it Just Right. To set the negative z value, you need to modify the G-code. G-code? At this moment, let me digress for those not familiar with G-code. G-code is the language that the printing software uses to communicate with the printer. G-code is, in essence, directions given to the printer on how to drive the motors and turn the heaters on and off. This is akin to postscript for laser printers. Different slicing programs will create different g-code; some will do it better than others, depending on how optimized they are for a given printer, etc. This is also why some slicing programs may result in a faster print, based on more optimized/efficient g-code. tip: always enter G code in CAPITAL LETTERS For the Printrbot, you enter the G-code that assigns the negative z-value in Repetier. Go to the manual control tab on the right side of the screen, make sure your printer is connected and then type the following in the G-code line: M501 (shows you what the current X, Y and Z offsets are; output on the bottom of screen) M212 Z0 (The number you type after Z is the negative z value that you are assigning. Start with 0 and see where you land, then go negative in small increments e.g. -0.1 to move closer to the print bed, printing a simple object each time and seeing how it turns out. Positive numbers will move the extruder farther from the bed.) M500 (save) 3. Auto-level before every print. Your printing software should instruct the printer to auto-level before any print. In addition to the basic leveling described in 1., there is an “auto leveling” check designed to determine if the print bed is tilted in any direction. Also referred to as “z probing”, this step is necessary because the quality and success of your print depends on any discrepancies in the distance between the hot end of the extruder and the print bed at a given location being accounted for. This can be done by probing 3 locations on the print bed. Don’t believe leveling the bed matters? Well, here are some problems that can arise from a poorly leveled bed: -Initial print layer does not stick or parts are missing -The hot end of the extruder scrapes the bed -The extruder gathers up plastic from the first or second layer So how does auto-leveling work? -An auto-leveling probe (aka z end-stop sensor) defines the distance between the extruder hot end and the print bed at any given location. The auto-leveling probe is to the right of the extruder and has an orange tip in the picture below. The Printrbot Metal Plus has an “inductive sensor” that detects the print bed via conductivity from the aluminum bed. The theoretical beauty of this design is that the sensor tip can be positioned at a level higher than the tip of hot end of the extruder and thus will not drag through your printing surface the way a touch down sensor would. The potential pitfall is that things that change conductivity (i.e. adjacent metallic objects) may affect the sensor. It is possible that your z end-stop sensor is faulty- if you are the unlucky soul that receives a malfunctioning sensor, you may be in for some hurt if your printer tries to jam the extruder into the table. Even if your sensor works, you may misjudge the distance from the extruder to the bed- for these reasons, be very close to an off switch or the plug when you are calibrating your negative z value. If the extruder is being jammed into the table, by all means, turn the printer off! To auto-level before each print, you need to make sure that the printing software contains the autoleveling G-code and adds it to the beginning of any slicing G-code. You need to set up auto-leveling in each slicing/printing program you use. It does not translate between them. The G code you use in Repetier is: G28 X0 Y0 G29 Below are some links to setting up auto-leveling in Repetier and Cura. Setting up auto-leveling in Repetier on Mac: http://help.printrbot.com/Guide/Setting+Up+Your+Auto-Leveling+Probe+and+Your+First+Print+-+Mac/107 Setting up auto-leveling in Repetier on PC: http://www.repetier.com/documentation/repetier-firmware/z-probing/ Setting up auto-leveling with Cura: http://www.instructables.com/id/Use-Printrbots-Autoleveling-Probe-with-Cura/ Beware: Just because your printer auto-levels itself, it doesn’t necessarily mean it won’t plunge through the printer bed in a desperate attempt to follow your every command. In fact, the printrbot metal plus is NOT smart enough to know when to say no. When we accidentally told it to go down 10 mm in the z direction when it was at Z0, it did so, much to our horror (see picture below). In the background of this picture, a hole in the stage marks the scene of an unfortunate z-axis accident. In the foreground, the outline of an aorta that did not make it (foreshadowing for the next blog entry). 4. Just how accurate is your model? You can check to make sure that the printer motors are appropriately calibrated- i.e. they actually travel the correct distance when told to do so. As described above, the printing software communicates with the printer (and thus the motors) using G-code. To make sure nothing is “lost in translation”, you need to make sure that when the software tells the printer head to move, say, 10 mm in the x-direction and 25 mm in the y-direction, the printer head appropriately translates that g-code into the correct movement. There are 4 motors: -X motor -Y motor -Z motor -Extrusion motor To check the calibration of the x, y and z motors, tell the printer to move 40 mm in the x axis and then measure to determine whether it is accurate. If you measure 40 mm, you are done. If not, you need to do some recalibration (see below). Do the same with the y axis and the z axis. Appropriate calibration in the x, y and z axis matters a lot for medical modeling…you want to make sure you are creating accurate models! To check the calibration of the extrusion motor, heat up the extruder to the recommended temperature for the filament. Use tape to mark a few cm up the filament and then measure from the tape to the entrance into the extruder. Tell the printer to extrude 10 mm of filament and measure again. Rate of extrusion really matters: your printing software assumes it knows the accurate amount of material extruded per given time. If too much is extruded, your print will have globs; if too little is extruded, you have holes or poor matrix This is a great primer on motor calibration and how to fix errors: http://www.instructables.com/id/Calibrating-your-3D-printer-using-minimal-filament/ 5. More advanced calibration/ “tweaking” to optimize your prints: A 3D printing manufacturer who goes by “Ville” recently designed and published an STL test file that can be used to troubleshoot calibration issues with any printer. The print has several challenges, including various overhangs, small details, different sized holes and wall-thicknesses, bridging and different surfaces. The idea is that users can share problems and solutions with each other. Read more at: http://3dprint.com/48922/3d-printer-calibrating-test/ Download this STL test file at: https://www.thingiverse.com/thing:704409 The top picture is what the test model should look like. The bottom picture is what my printer produced. Guess I have some tweaking to do.... In the next post, we will tackle one of the most infamous struggles in 3D printing- getting your model to stick to the print bed. Until then, happy printing! -Beth Ripley
  32. 2 points
    3D Bill

    Video recording and editing tools

    Another paid option for video editing and screen capture is Camtasia. The Mac version is $99 and the Windows version is $299.
  33. 2 points
    A company in Brazil called Artis Tecnologia has developed medical 3D printing technologies to aid in skull resection surgery. They demonstrated their techniques on a volunteer patient who received surgery for free at the university hospital of the Federal University of São Paulo (UNIFESP). They published an article about it two weeks ago in the International Journal of Computer Assisted Radiology and Surgery. Their technologies allow the removal of a skull tumor and the implantation of a prosthesis in a single surgery. The company works with the doctors to plan the surgery and make the mold for the prosthesis. In this case the company donated the mold and the surgical navigator for the computer assisted surgery (CAS). Planning of the prosthesis Surgical planning First, the doctors take a CT scan of the patient, following a specific protocol so that it is precise enough to make the personalized mold. The scans are imported into the company’s EximiusMed software and which is compatible with the surgical navigator. The company is responsible for deciding on the surgery margin, and providing an image of the prosthesis, which is approved by the surgeon. The planning and production of the mold takes four days. Mold production The personalized mold is made with Magics software from Materialise, a company from Belgium. They make the mold for the prosthesis as well as a model of the bone fault, with submillimeter precision, using a 3D printer from 3D Systems, which uses layer-by-layer manufacturing in layers 0.16 inches thick. It is made from a plaster-like material, and finished with an insulator on the inside and scratch proof finish on the outside. Then, the mold and bone fault are packed in blister packaging, sealed with Tyvek, and sterilized by ethylene oxide, before shipping. Images of the mold Making the prosthesis The prosthesis, made from PMMA during surgery, is created using a hand press as shown in the video. The PMMA in plastic phase undergoes a slight contraction, and using 20% extra PMMA and a press, ensures the correct size for the prosthesis. The extra material drains out of the mold and can be easily removed from the prosthesis. The mold also absorbs heat from the exothermic reaction. It is pressed until polymerization is complete which takes ten to twenty minutes. Finally the prosthesis is washed generously with saline solution. Placing the prosthesis on the skull fault The surgeon decides how to perforate and attach the prosthesis, in this case with titanium clips The clips are used to stabilize the prosthesis but not hold it in place. The prosthesis should overlap the edges of the skull fault as shown in the figure so it does not slip into the cranial cavity. Images after surgery
  34. 2 points
    Yes, please. The rendered 3D model (.stl file) should be anonymous, meaning free of any personal identifying information or any headers or metatags from the DICOM data and therefore HIPAA exempt. I agree it is still a good idea and professional courtesy to request permission from the clinician who obtained and supplied the DICOM data to you. If you can upload these anonymous craniofacial .stl files to the marketplace then other members of the community (like myself) can use them for educational projects. Also supplying clinical diagnosis would be very helpful. Thanks!
  35. 2 points
    vlad

    Hominin fossils available online

    There are some excellent academic resources that make high quality 3D scans and downloadable 3D printable files available to the public from various museums and academic institutions. One great resource is African Fossils collection at: http://africanfossils.org/search Another online collection is a joint university collection at Morphosource: http://morphosource.org/index.php/Browse/Index We have embarked on an academic project with LSU Medical School Department of Human Anatomy to produce an exhibit of full scale hominin skulls for study in comparative anatomy to the modern Homo sapien skull. I will post pics of the fossils for this exhibit in an album here: http://www.embodi3d.com/gallery/album/34-hominin-fossils/ This is an ongoing project with the ultimate goal of producing 3D printed replicas of approximately one dozen skulls of evolutionary significance.
  36. 2 points
    Dr. Mike

    Licensing for Models from TCIA CTs

    If you share your models on Embodi3D's file marketplace, nobody can sell those digital files or models except you, unless you specify otherwise. If you decide to distribute your files for free using one of the Creative Commons licenses, you can choose a "Non Commercial" license. That means that people who download your digital model cannot use it for commercial purposes (i.e. sell it). You can also require that the downloader make no derivatives of your work. In other words they can share it but cannot modify it in any way. Or, you can allow them to modify your file but they are required to share that modified file under the same license terms that you shared it with them. In all cases, downloaders who share your file for commercial or non commercial purposes have to properly attribute you as the original author. You also have the option to sell the file, or more accurately a license to use the file, on the marketplace. You can use your own customized license if you have one or use the General Paid File License that Embodi3D provides. The General license allows buyers to make a single 3D print from your file. If they want to make more they have to buy a license from you for each print. I know that practically this is difficult to enforce, but if somebody flagrantly violates your license, for example mass producing your model in a factory in China, you can go after them for violating the license. You can learn more about selling files here. If you have invested great amounts of time in producing high quality models are aren't ready to part with them for free, selling is a good option, especially for very subspecialized models. Embodi3D has worked really hard to make sure that you can share your 3D printable anatomic files on your terms safely. You have many options, and in all cases ownership and control of the model design resides with the creator, YOU. We want to encourage sharing of files and don't want uncertainty about what downloaders can do with files to be a reason why great files aren't shared. If you have any questions, please ask and thanks in advance for sharing!
  37. 2 points
    Amir, that skull is amazing! Fine work!
  38. 2 points
    I've recently discovered two similar peer-reviewed online journals that publish articles related to 3D medical modeling and printing. The first is based out of North America called 3D Printing in Medicine: http://threedmedprint.springeropen.com/articles The second is based out of Australia called Journal of 3D Printing in Medicine: http://www.futuremedicine.com/loi/3dp Let me know if anyone has any feedback about the quality or submission process for papers. Both just started.
  39. 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
  40. 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
  41. 2 points
    Here is a preview of some of the models I am preparing for the 2016 Society of Interventional Radiology meeting. Hope to see some of you there!
  42. 2 points
    In a UK-first, surgeons at Alder Hey Children’s Hospital successfully used a 3D printed model of a spine to help complete an operation. The procedure was the first time NHS doctors have ever used a 3D printed model in the operating room. The model was used by surgeons on the West Derby hospital’s orthopedic team in their efforts to correct the curved back of an eight-year-old patient. The young girl from Whales suffers from kyphoscoliosis, a complicated congenital spinal problem. The plastic model was made with the help of the patient’s CT scans, which were converted into a 3D printable format. The life-size replica was printed in a plastic so it could be sterilized, and then used in the operating room as a guide for the surgeons performing the operation. An NHS First This case is also the first time that a 3D printed model has been taken into the operating room to be used as a reference tool by NHS doctors. Jai Trivedi, Neil Davidson and Colin Bruce were the surgeons who performed the operation. Trivedi, who was lead surgeon, said on Alder Hey’s blog, “There is no doubt the model made this complex procedure operation much safer as it allowed for accurate pre-operative planning and implementation at surgery. Sterile models that can be held during an operation should prove helpful for other surgeons.” The model was made by the 3D printing firm 3D LifePrints. Their representative Henry Pinchbeck said, “We are delighted to be working with the talented surgical teams at Alder Hey who are leading the way in terms of adoption of innovative practices, such as 3D printing.” A Beneficial Collaboration 3D LifePrints has been working closely with a number of Alder Hey doctors in orthopedics, cardio, craniofacial surgery, radiology and other areas to develop 3D models. Both parties believe the models can assist doctors with complex operations, enable easier communication between doctors and patients, and facilitate learning. The successful surgery comes after a new scientific research center was recently opened next to Alder Hey, one component of £260m invested in future development. The center boasts an innovation hub where doctors and scientists can work on building new healthcare technology, as well as facilities for developing and testing new medicines. The innovation service has the goal of harnessing less widely used technologies in healthcare (including 3D printing and bio-sensors) to develop strategies that improve health outcomes for surgery and critical care treatment. This eight-year-old’s successful surgery is just another one of the many examples of how 3D printing can make medical treatment safer and more effective. Image Credits: Alderhey Liverpool Echo
  43. 2 points
    Medical modeling of the coronary arteries:
  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 just finished a 3D print of a rather large AAA. I think it turned out alright. Any thoughts? Anyone else doing work like this?
  46. 2 points
    Dr. Mike this is a great overview. Being that i use patient scans to create 3D prints, i never had this background information provided to me, i had to learn through trial and error.
  47. 2 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
  48. 2 points
    Corbel3D

    First 3D Printer suggestions

    Hi Mike, We printed this model with an objet connex. Model was generated by mimics (running on a trial license). This model was printed with our objet 30. We are planning to get a multi material polyjet this year.
  49. 2 points
    mplishka

    Hardware requirements?

    There is a very cool technology printing with regular paper. It can be done in full color and it's much cheaper than other modes of printing and is quick as well. The challenge is that the print volume is the size of the (double) ream of paper. The models can be designed to be glued together if larger models are needed. The models I have seen are always shrunk a little, so this technology may be better for patient education than for surgical planning, but it's still pretty cool. http://mcortechnologies.com/ http://mcortechnologies.com/solutions/medical/ The folks at Mcor (they're a hop skip and jump away from me) have the same problems with other 3d printers, regarding adoption. Reimbursement being the biggie as well.
  50. 2 points
    Dr. Mike

    Mimics

    I went to the RSNA meeting this year and took the training course in Mimics that Frank Rybicki was giving. It is great software, but very expensive from what I hear from people who have purchased a license. I am working on developing methods of designing 3D printed anatomic models using freeware, and will be publishing a tutorial shortly. Stay tuned. Dr. Mike
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