Leaderboard


Popular Content

Showing most liked content since 09/21/2016 in all areas

  1. 4 likes
    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
  2. 4 likes
    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.
  3. 3 likes
    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!
  4. 3 likes
    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.
  5. 3 likes
    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
  6. 3 likes
    lillux

    Mandibola

    Version 1.0.0

    68 downloads

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

    Free

  7. 3 likes
    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.
  8. 2 likes
    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
  9. 2 likes
    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.
  10. 2 likes
    Printed on an Ultimaker 3 extended with white PLA and PVA support.
  11. 2 likes
    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;)
  12. 2 likes
    Ah. There's the problem then. I'm not seeing the crop box at all.
  13. 2 likes
    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.
  14. 2 likes

    Version 1.0.0

    37 downloads

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

    Free

  15. 2 likes
    Please note that any references to “Imag3D” in this tutorial has been replaced with “democratiz3D” In this tutorial you will learn how to create multiple 3D printable bone models simultaneously using the free online CT scan to bone STL converter, democratiz3D. We will use the free desktop program Slicer to convert our CT scan in DICOM format to NRRD format. We will also make a small section of the CT scan into its own NRRD file to create a second stand-alone model. The NRRD files will then be uploaded to the free democratiz3D online service to be converted into 3D printable STL models. If you haven't already, please see the tutorial A Ridiculously Easy Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes, which provides a good overview of the democratiz3D service. You should download the file pack that accompanies this tutorial. This contains an anonymized DICOM data set that will allow you to follow along with the tutorial. >>> DOWNLOAD THE TUTORIAL FILE PACK <<< Step 1: Register for an Embodi3D account If you haven't already done so, you'll need to register for an embodi3D account. Registration is free and only takes a minute. Once you are registered you'll receive a confirmatory email that verifies you are the owner of the registered email account. Click the link in the email to activate your account. The democratiz3D service will use this email account to send you notifications when your files are ready for download. Step 2: Create NRRD Files from DICOM with Slicer Open Slicer, which can be downloaded for free from www.slicer.org. Take the folder that contains your DICOM scan files and drag and drop it onto the slicer window, as shown in Figure 1. If you downloaded the tutorial file pack, a complete DICOM data set is included. Click OK when asked to load the study into the DICOM database. Click Copy when asked if you want to copy the images into the local database directory. Remember, this only works with CT scans. MRIs cannot be converted at this time. Figure 1: Dragging and dropping the DICOM folder onto the Slicer application. This will load the CT scan. A NRRD file that encompasses the entire scan can easily be created by clicking the save button at this point. Before we do that however, we are going to create a second NRRD file that only contains the lumbar spine, which will allow us to create a second 3D printable bone model of the lumbar spine. Open the CT scan by clicking on the Show DICOM Browser button, selecting the scan and series within the scan, and clicking the Load button. The CT scan will then load within the multipanel viewer. From the drop-down menu at the top left of the Slicer window, select All Modules and then Crop Volume, as shown in Figure 2. You will now want to create a Region Of Interest (ROI) to encompass the smaller volume we want to make. Turn on the ROI visibility button and then under the Input ROI drop-down menu, select "Create new AnnotationROI," As shown in Figure 3. Figure 2: Choosing the Crop Volume module Figure 3: Turn on ROI visibility and Create a new AnnotationROI under the Input ROI drop-down menu. A small cube will then be displayed in the blue volume window. This represents the sub volume that will be made. In its default position, the cube may not overlay the body, and may need to be dragged downward. Grab a control point on the cube and drag it downward (inferiorly) as shown in Figure 4. Figure 4: Grab the sub volume ROI and drag it downwards until it overlaps with the body. Next, use the control points on the volume box to position the volume box over the portion of the scan you wish to be included in the small 3D printable model, as shown in Figure 5. Figure 5: Adjusting the control points on the crop volume box. Once you have the box position where you want it, initiate the volume crop by clicking the Crop! button, as shown in Figure 6. Figure 6: The Crop! button You have now have two scan volumes that can be 3D printed. The first is the entire scan, and the second is the smaller sub volume that contains only the lumbar spine. We are now going to save those individual volumes as NRRD files. Click the Save button in the upper left-hand corner. In the Save Scene window, uncheck all items that do not have NRRD as the file format, as shown in Figure 7. Only NRRD file should be checked. Be sure to specify the directory that you want each file to be saved in. Figure 7: The Save Scene window Your NRRD files should now be saved in the directory you specified. Step 3: Upload your NRRD files and Convert to STL Files Using the Free democratiz3D Service Launch your web browser and go to www.embodi3d.com. If you haven't already register for a account. Registration is free and only takes a minute. Click on the democratiz3D navigation item and select Launch App, as shown in Figure 8. Figure 8: launching the democratiz3D application. Drag-and-drop both of your NRRD files onto the upload panel. Fill in the required fields, including a title, short description, privacy setting (private versus shared), and license type. You must agree to the terms of use. Please note that even though license type is a required field, it only matters if the file is shared. If you keep the file private and thus not available to other members on the site, they will not see it nor be able to download it. Be sure to turn on the democratiz3D Processing slider! If you don't turn this on your file will not be processed but will just be saved in your account on the website. It should be green when turned on. Once you turn on democratiz3D Processing, you'll be presented with some basic processing options, as shown in Figure 9. Leave the default operation as "CT NRRD to Bone STL," which is the operation that creates a basic bone model from a CT scan in NRRD format. Threshold is the Hounsfield attenuation to use for selecting the bones. The default value of 150 is good for most applications, but if you have a specialized model you wish to create, you can adjust this value. Quality denotes the number of polygons in your output file. High-quality may take longer to process and produce larger files. These are more appropriate for very large or detailed structures, such as an entire spinal column. Low quality is best for small structures that are geometrically simple, such as a patella. Medium quality is balanced, and is appropriate for most circumstances. Figure 9: The democratiz3D File Processing Parameters. Once you are satisfied with your processing parameters, click submit. Both of your nrrd files will be processed in two separate bone STL files, as shown in Figure 10. The process takes 10 to 20 minutes and you will receive an email notifying you that your files are ready. Please note, the stl processing will finish first followed by the images. Click on the thumbnails for each model to access the file for download or click the title. Figure 10: Two files have been processed simultaneously and are ready for download Step 4: CT scan conversion is complete your STL bone model files are ready for 3D Printing That's it! Both of your bone models are ready for 3D printing. I hope you enjoyed this tutorial. Please use the democratiz3D service and SHARE the files you create with the community by changing their status from private or shared. Thank you very much and happy 3D printing!
  16. 2 likes
    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!
  17. 2 likes

    Version 1.0.0

    22 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

  18. 2 likes
    Note: This tutorial accompanies a workshop I presented at the 2016 Radiological Society of North America (RSNA) meeting. The workflow and techniques presented in this tutorial and the conference workshop are identical. In this tutorial we will be using two different ways to create a 3-D printable medical model of a head and neck which will be derived from a real contrast-enhanced CT scan. The model will show detailed anatomy of the bones, as well as the veins and arteries. We will independently create this model using two separate methods. First, we will automatically generate the model using the free online service embodi3D.com. Next, we will create the same file using free desktop software programs 3D Slicer and Meshmixer. If you haven't already, please download the associated file pack which contains the files you'll need to follow along with this tutorial. Following along with the actual files used here will make learning these techniques much easier. The file pack is free. You need to be logged into your embodi3D account to download, but registration is also free and only takes a minute. Also, you'll need an embodi3D.com account in order to use the online service. Registration is worth it, so if you haven't already go ahead and register now. >> DOWNLOAD THE FILE PACK NOW << Online Service: embodi3D.com Step 1: Go to the embodi3D.com website and click on the democratiz3D menu item in the naw bar. Click on the "Launch democratizD" link, as shown in Figure 1. Figure 1: Opening the free online 3D model making service service democratiz3D. Step 2: Now you have to upload your imaging file. Drag and drop the file MANIX Angio CT.nrrd from the File Pack, as shown in Figure 2. This contains the CT scan of the head and neck in NRRD file format. If you are using a file other NRRD that provided by the file pack, please be aware the file must contain a CT scan (NOT MRI!) and the file must be in NRRD format. If you don't know how to create an NRRD file, here is a simple tutorial that explains how. Figure 2: Dragging and dropping the NRRD file to start uploading. Step 3: Type in basic information on the file being uploaded, including File name, file description, and whether you want to share the file or keep it private. Bear in mind that this information pertains to the uploaded file, not the file that will be generated by the service. Step 4: Type in basic parameters for file processing. Turn on the processing slider. Here you will enter in basic information about how you would like the file to be processed. Under Operation, select CT NRRD to Bone STL Detailed, as shown in Figure 3. This will convert a CT scan in NRRD format to a bone STL with high detail. You also have the option to create muscle and skin STL files. The standard operation, CT NRRD to Bone STL sacrifices some detail for a smoother output model. Leave the default threshold at 150. Figure 3: Selecting an operation for file conversion. Next, choose the quality of your output file. Low-quality files process quickly and are appropriate for structures with simple geometry. High quality files take longer to process and are appropriate for very complex geometry. The geometry of our model will be quite complex, so choose high quality. This may take a long time to process however, sometimes up to 40 minutes. If you don't wish to wait so long, you can choose medium quality, as shown in Figure 4, and have a pretty decent output file in about 12 minutes or so. Figure 4: Choosing a quality setting. Finally, specify whether you want your processed file to be shared with the community (encouraged) or private and accessible only to you. If you do decide to share you will need to fill out a few items, such as which CreativeCommons license to share under. If you're not sure, the defaults are appropriate for most people. If you do decide to share thanks very much! The 3D printing community thanks you! Click on the submit button and your file will be submitted for processing! Now all you have to do is wait. The service will do all the work for you! Step 5: Download your file. In 5 to 40 minutes you should receive an email indicating that your file is done and is ready for download. Follow the link in the email message or, if you are already on the embodi3D.com website, click on your profile to view your latest activity, including files belonging to you. Open the download page for your file and click on the "Download this file" button to download your newly created STL file! Figure 5: Downloading your newly completed STL file. Desktop software If you haven't already, download 3D Slicer and Meshmixer. Both of these programs are available on Macintosh and Windows platforms. Step 1: Create an STL file with 3D Slicer. Open 3D Slicer. Drag and drop the file MANIX Angio CT.nrrd from the file pack onto the 3D Slicer window. This should load the file into 3D Slicer, as shown in Figure 6. When Slicer asks you to confirm whether you want to add the file, click OK. Figure 6: Opening the NRRD file in 3D Slicer using drag-and-drop. Step 2: Convert the CT scan into an STL file. From within Slicer, open the Modules menu item and choose All Modules, Grayscale Model Maker, as shown in Figure 7. Figure 7: Opening the Grayscale Model Maker module. Next, enter the conversion parameters for Grayscale Model Maker in the parameters window on the left. Under Input Volume select MANIX Angio CT. Under Output Geometry choose "Create new model." Slicer will create a new model with the default name such as "Output Geometry. If you wish to rename this to something more descriptive, choose Rename current model under the same menu. For this tutorial I am calling the model "RSNA model." For Threshold, set the value to 150. Under Decimate, set the value to 0.75. Double check your settings to make sure everything is correct. When everything is filled in correctly click the Apply button, as shown in Figure 8. Slicer will process for about a minute. Figure 8: Filling in the Grayscale Model Maker parameters. Step 3: Save the new model to STL file format. Now it is time to create an STL file from our digital model. Click on the Save button on the upper left-hand corner of the Slicer window. The Save Scene pop-up window is now shown. Find the row that corresponds to the model name you have given the model. In my case it is called "RSNA model." Make sure that the checkbox next to this row is checked, and all other rows are unchecked. Next, under the File Format column make sure to specify STL. Finally, specify the directory that the new STL file is to be saved into. Double check everything. When you are ready, click Saved. This is all shown in Figure 9. Now that you've created an STL file, we need to postprocessing in Meshmixer. Figure 9: Saving your file to STL format. Step 4: Open Meshmixer, and drag-and-drop the newly created STL file onto the Meshmixer window to open it. Once the model opens, you will notice that there are many red dots scattered throughout the model. These represent errors in the mesh and need to be corrected, as shown in Figure 10. Figure 10: Errors in the mesh as shown in Meshmixer. Each red dot corresponds to an error. Step 5: Remove disconnected elements from the mesh. There are many disconnected elements in this model that we do not want in our final model. An example of unwanted mesh are the flat plates on either side of the head from the pillow that was used to secure the head during the CT scan. Let's get rid of this unwanted mesh. First use the select tool and place the cursor over the four head of the model and left click. The area under the cursor should turn orange, indicating that those polygons have been selected, as shown in Figure 11. Figure 11: Selecting a small zone on the forehead. Next, we are going to expand the selection to encompass all geometry that is attached to the area that we currently have selected. Go to the Modify menu item and select Expand to Connected. Alternatively, you can use the keyboard shortcut and select the E key. This operation is shown in Figure 12. Figure 12: Expanding the selection to all connected parts. You will notice that the right clavicle and right scapula have not been selected. This is because these parts are not directly connected to the rest of the skeleton, as shown in Figure 13. We wish to include these in our model, so using the select tool left click on each of these parts to highlight a small area. Then expand the selection to connected again by hitting the E key. Figure 13: The right clavicle and right scapula are not included in the selection because they are not connected to the rest of the skeleton. Individually select these parts and expand the selection again to include them. At this point you should have all the geometry we want included in the model selected in orange, as shown in Figure 14. Figure 14: All the desired geometry is selected in orange Next we are going to delete all the unwanted geometry that is currently unselected. To start this we will first invert the selection. Under the modify menu, select Invert. Alternatively, you can use the keyboard shortcut I, as shown in Figure 15. Figure 15: Inverting the selection. At this point only the undesired geometry should be highlighted in orange, as shown in Figure 16. This unwanted geometry cannot be deleted by going to the Edit menu and selecting Discard. Alternatively you can use the keyboard shortcut X. Figure 16: Only the unwanted geometry is highlighted in orange. This is ready to delete. Step 6: Correcting mesh errors using the Inspector tool. Meshmixer has a nice tool that will automatically fix many mesh errors. Click on the Analysis button and choose Inspector. Meshmixer will now identify all of the errors currently in the mesh. These are indicated by red, blue, and pink balls with lines pointing to the location of the error. As you can see from Figure 17, there are hundreds of errors still within our mesh. We can attempt to auto repair them by clicking on the Auto Repair All button. At the end of the operation most of the errors have been fixed, but if you remain. This can be seen in Figure 18. Figure 17: Errors in the mesh. Most of these can be corrected using the Inspector tool. Figure 18: Only a few errors remain after auto correction with the Inspector tool. Step 7: Correcting the remaining errors using the Remesh tool. Click on the select button to turn on the select tool. Expand the selection to connected parts by choosing Modify, Expand to Connected. The entire model should now be highlighted and origin color. Next under the edit menu choose Remesh, or use the R keyboard shortcut, as shown in Figure 19. This operation will take some time, six or eight minutes depending on the speed of your computer. What remesh does is it recalculates the surface topography of the model and replaces each of the surface triangles with new triangles that are more regular and uniform in appearance. Since our model has a considerable amount of surface area and polygons, the remesh operation takes some time. Remesh also has the ability to eliminate some geometric problems that can prevent all errors from being automatically fixed in Inspector. Figure 19: Using the Remesh tool. Step 8: Fixing the remaining errors using the Inspector tool. Once the remesh operation is completed we will go back and repeat Step 6 and run the Inspector tool again. Click on Analysis and choose Inspector. Inspector will highlight the errors. Currently there are only two, as shown in Figure 20. These two remaining errors can be easily auto repair using the Auto Repair All button. Go ahead and click on this. Figure 20: running the Inspector tool again. At this point the model is now completed and ready for 3D printing as shown in Figure 21. The mesh is error-free and ready to go! Congratulations! Figure 21: The final, error-free model ready for 3D printing. Conclusion Complex bone and vascular models, such as the head and neck model we created in this tutorial, can be created using either the free online service at embodi3D.com or using free desktop software. Each approach has its benefits. The online service is easier to use, faster, and produces high quality models with minimal user input. Additionally, multiple models can be processed simultaneously so it is possible to batch process multiple files at once. The desktop approach using 3D Slicer and Meshmixer requires more user input and thus more time, however the user has greater control over individual design decisions about the model. Both methods are viable for creating high quality 3D printable medical models. Thank you very much for reading this tutorial. Please share your medical 3D printing designs on the embodi3D.com website. Happy 3D printing!
  19. 2 likes
    Hello, Does anyone know how to correct "stretched" sagittal and coronal planes in 3D Slicer? The axial plane is normal. According to the Slicer wiki, i think that using the Orient Scalar Volume may solve this but within the Converters module there is only BSpline to deformation field. There is a parameter set for Create new command line, but that's a bit beyond my skillset. I'll attach a screenshot and if anyone has an easy way to solve this i'd love to hear it. If there's a hard way to solve it i'd love to hear it too but feel free to explain like i'm 5. Slicer wiki page: https://www.slicer.org/wiki/Documentation/4.0/Modules/OrientScalarVolume Currently using Slicer 4.5.0-1 Thanks in advance! Roman
  20. 2 likes
    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.
  21. 2 likes
    I took a look at your models but the privacy setting prevents them from being viewed. I personally find using threshold for segmentation pretty antiquated and use grow/cut for segmentation. This may help for you needs but would be too involved to explain here. I would imagine the issue with the inferior part of the head not having a uniform intensity and giving a rough surface... but I am just guessing
  22. 2 likes
    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
  23. 2 likes

    Version 1.0.0

    21 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

  24. 2 likes
    Cool article about using Finite Element Analysis to predict bone fractures (I love FEA ). https://www.asme.org/engineering-topics/articles/finite-element-analysis/bone-breaking-predictions-put-to-test-with-fea It's very accurate, so to that end, it might not be necessary to create 3d models if the actual bone can be scanned, digitally modelled and then virtually stressed. What types of fracture studies are you planning (if you can share ;-) ) ? Are you looking from a predictive standpoint or from a pure analysis standpoint; perhaps trying to figure out how to prevent certain fractures based upon certain loadings? I think it would be fascinating to print bone with integrated sensors to understand specific deformations at multiple points. It would not necessarily be essential to fail the bone, just understand how forces are transmitted. Printing with multiple materials would be cool in the future to create the ultimate composite bone model. I can see potential problems with micro-anomalies in the bone, or in any of the constraints. The result would false negative/positive failures. One could also do a hybrid approach. Do FEA and at certain points in the analysis, export the deformed file with colors and print it out. You can take the bone apart and see how it's bending/twisting/etc. and what's happening inside it. Just some thoughts Good luck!
  25. 2 likes
    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.
  26. 2 likes
    Collegue of mine, who is interventional radiologist, said to me, why would we use 3D printed model of vessels to educate younger collegues, i trained on pigs... enough said. Other collegues, mostly old school doctors, are skeptical like for any other new technology, but most of younger collegues are more open minded, so maybe, there's bright future for 3d printing in medicine And last BIG obstacle, is money, like you said. Healthcare system here in Croatia doesn't pay for 3d printed bone grafts as treatment, so we must pay with our own money, and for most of people that is not an option. I try to explain to them that in the beginning we invest with our money in those procedures, but maybe one day it will be routinely covered by our healthcare system. V. Kopacin
  27. 2 likes
    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.
  28. 2 likes
  29. 1 like
    These models were designed by embodi3D and printed on an Ultimaker 3 printer and put on display at the 2017 Rapid conference in Pittsburgh, PA.
  30. 1 like
    Glad that worked out. I am also using Slicer (64 bit) and Windows 10 and it works fine.
  31. 1 like

    Version 1.0.0

    25 downloads

    A thoracic vertebra generated by using the contouring tools in 3DSlicer and smoothed in Blender.

    Free

  32. 1 like
    Hi Diogo, I have started working with microCT and can't get them in to Mimics. However, I have had great success with 3DSlicer. It's very slow with the tiff stack, but if I import the tiff stack to Fiji and save it as a .nrrd file, then Slicer reads it much faster. Terrie P.S. What version of Mimics are you using? I have 17 and 18 and they both seem to have a hard time with tiff stacks.
  33. 1 like
    Formlabs has a new wash and cure station for Form 2 and Form 1+ SLA printers. It looks like buying both the wash and cure together will run you $1200 at this time, and they are only taking preorders. But, this is an interesting advance to their line of high quality yet low cost SLA printers.
  34. 1 like
    Hey tsehrhardt, I noticed that your bottom panels already have cropping boxes in them. When I used it, my bottom panels did not. According to the tutorial, you're supposed to drag the cropping box from the main "blue" screen down into the image on the bottom panel? Or is this what Dr. Mike is talking about when he says the crop box is just too small?
  35. 1 like
    Printed well on my Prusa. Lots of support material required, but really helped in show patient the relative size of her mass.
  36. 1 like
    Hi Dr Mike Thanks for this blog post. I came across this one method of designing cranial implants (attached link tutorial video) using the free software MeVisLab....I have yet to try it myself as I was not able to understand the whole method/workflow https://www.youtube.com/watch?v=8epxE8pUMPk Apart from that there is another software , Geomagic Freeform but that too is paid one...
  37. 1 like
    So I began to develop some pain in my right wrist which was later diagnosed as tendinitis. At the same time I had been looking at the CT scan of my abdomen and noticed they also captured my right hand as it was resting on my stomach during the scan (I had injured my right shoulder again). I recalled a concept project a while back I had seen: the CORTEX brace. It presented the idea of replacing the typical plaster cast with a 3D printed one which would prevent the issues of sweating and itchiness… as well as be much more stylish (though not allowing people to sign your cast). I had wanted to apply this to prosthesis sockets initially but never got past the idea stage. Looking around for how to create the ‘webbing’ style I found that meshmixer had the necessary capabilities. So I now had all the tools needed to make my own brace to partially immobilize my wrist. Once the surface model is created and loaded into meshmixer the first step is to cut off anatomy that you don't want in the model using 'plane cut'. Once the general shape of the brace is created the next step is to consider how the brace will be taken on and off. For my design I wanted to have one piece that is flexible enough to slide my wrist in. To create the 'slot' I found that I did a boolean in blender as meshmixer would crash when I tried to create the slot. With the brace model and slot in place the next step was to offset the surface since creating the voroni mesh would generate the tubes on both sides of the surface. This is done back in meshmixer and is fairly computationally intensive so partially reducing the mesh density first is a good idea. The next step is to further decimate the mesh to get the desired voroni mesh pattern. This takes a bit of playing around to get the desired style. Too dense and the resulting web structure will not have many openings which will be stronger but not as breathable. Too rough and the model may not conform to the surface well causing pressure points. The final step is to take the reduced mesh and web like structure using the 'make pattern' feature within meshmixer. There are various settings to be applied within this feature but setting 'Dual Edges' then adjusting the pipe size to double your offset will result in the inner edge of the webbing to just touch the skin of the initial model. Having never made a brace/cast before it took me a few iterations to get a design which I could easily don and doff (put on and take off). I also found that I could make a brace that held my wrist very rigidly but would be too restrictive. Also material selection became important. Initially I used ABS which is more flexible than PLA and I had it in a nice pink skin color. It turned out to be too rigid for the style I was designing. I found PETT (taulman t-glass) to work well as it had a lower modulus of elasticity meaning it was more flexible than ABS. After using the brace on and off for a few weeks I have found that it fits well and is surprisingly comfortable. I have taken a shower with it on as well as slept with it on. It doesn’t seem to smell as bad as the cheap and common cloth type braces. The main downsides have been taking it on and off is a bit challenging still and it is more restrictive of my motion as it behaves somewhere between a brace and a cast. There is definitely a great deal of potential for this type of cast though widespread adoption would require further technical development to simplify the process.
  38. 1 like
    We have just acquired The Beast: an FDM kit from Cultivate3D, an Australian startup down the road in Wyong, NSW. This is the only printer we could source with a build size to take a full pelvis or femur that our public health service could afford. Cost of OrthoBeast kit : A$3000, including heated bed and high volume extruders. Quotes for other printers with 450x450x600 commercially available ranged from $80,000-150,000 and up. The expectations we have are not to have a finished product that we can plug in and use, but how hard can it be? I put it to you that if someone has the skill and patience to reconstruct a bone or joint, building a 3D printer should be achievable... Link to our build journal: The OrthoBeast Build Journal
  39. 1 like
    Hello. I own a 3D Printing Service Bureau (imtyris.com). The out put of our 3D printer is a paper model, either plain white, or in millions of colors. I'm looking for someone to work with to develop CT or MRI data into a full color paper model. Dave Jahnz Imtyris 858 354-4200
  40. 1 like
    Hi Peter, What are you using to combine multiple models? I have used Fiji to combine multiple STLs into one U3D that will expand into a model tree in Acrobat Pro, but it is very slow. Meshlab will create a U3D, but not from multiple models and not for large models. Thanks, Terrie
  41. 1 like
    Examples of historical medical 3D printing on display at RSNA. The green skull is from 1985! We've come a long way since then.
  42. 1 like

    Version 1.0.0

    6 downloads

    Impacted_Canine_H975 - processed

    Free

  43. 1 like
    Dr. Mike

    Skull base

    Version 1.0.0

    2 downloads

    This 3D printable STL file contains a model of the skull base was derived from a medical CT scan. This model was created using the Imag3D 3D model creation service 0522c0909

    Free

  44. 1 like

    Version 1.0.0

    9 downloads

    This CT scan of the jaw, face and cervical spine show the effect that metal dental fillings can have on a 3D printed part. Other than the artifact from dental fillings, the quality of the model is excellent. 0522c90878

    Free

  45. 1 like

    Version 1.0.0

    10 downloads

    c0147 Skull, Male 62yo - processed

    Free

  46. 1 like
    Yay! This works great and I was not able to break it!
  47. 1 like
    Mayo Clinic physicians work closely between Radiology and multi-disciplinary surgical teams composed of 3+ surgical sub-specialties involving complex resection and reconstruction by utilizing 3D rendered digital modeling and 3D printed composite medical models for inter-disciplinary communication, pre-op planning, and simulation of surgery. Link is below: http://www.materialise.com/blog/mimics-innovation-suite-supports-minimally-invasive-surgery-for-rare-lung-cancer-tumor/ Case is a thoracic Pancoast tumor, but methodology is applicable to many areas of complex anatomy, including skull base, thoracic, and pelvic areas.
  48. 1 like
    Q&A with Mayo Radiologists about 3D print lab as surgical service: http://tcbmag.com/News/Recent-News/2016/April/Q-A-How-Mayo-Is-Integrating-3D-Printing-Into-The-O
  49. 1 like

    Version

    317 downloads

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

    Free

  50. 1 like
    Hi, Dr. Mike - This is exciting! A friend of mine (also a talented artist) worked on this specimen at the Academy of Natural Sciences in Philadelphia for several years. I'm not sure if 3D PDF files can be converted to STL, but it wouldn't surprise me if that were possible. MH
This leaderboard is set to Los Angeles/GMT-07:00