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Showing most liked content since 02/24/2017 in all areas

  1. 3 points
    Diogo

    Teeth Micro CT

    Sorry guys been so busy and only now could come back and read your responses. I ended up with Mevislab for segmentation and analysis. Here is an example of what I have been doing. Cheers. Diogo Guerreiro S18T7 Final.mp4
  2. 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.
  3. 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.
  4. 2 points
  5. 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
  6. 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.
  7. 2 points
    Dr. Mike

    3D printed brain from MRI

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

    Version 1.0.0

    61 downloads

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

    Free

  11. 2 points
    lillux

    Mandibola

    Version 1.0.0

    85 downloads

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

    Free

  12. 2 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
  13. 1 point
    Babies in womb please to try to print them with 3d printer! Thank you!
  14. 1 point
    Dr. Mike

    making guides

    Here is a freeware tutorial I wrote for a presentation at RSNA. In it, I discuss the latest information from the FDA on when it is OK to use non-FDA reviewed software.
  15. 1 point
    There are two excellent upcoming conferences that will have lots of information on medical 3D printing. I will be attending and speaking at both. If you are able, please attend. 1) Radiological Society of North American (RSNA) November 26 to Dec 1, 2017. Chicago, IL http://www.rsna.org/Annual_Meeting.aspx 2) Mayo Clinic Collaborative 3D Printing in Medical Practice 2018, Feb 23-25, Scottsdale, Arizona. https://radiologyeducation.mayo.edu/store/collaborative-3d-printing-in-medical-practice-2018
  16. 1 point
    NRRD is a file format for storing and visualizing medical image data. Its main benefit over DICOM, the standard file format for medical imaging, is that NRRD files are anonymized and contain no sensitive patient information. Furthermore NRRD files can store a medical scan in a single file, whereas DICOM data sets are usually comprised of a directory or directories that contain dozens if not hundreds of individual files. NRRD is thus a good file for transferring medical scan data while protecting patient privacy. This tutorial will teach you how to create an NRRD file from a DICOM data set generated from a medical scan, such as a CT, MRI, ultrasound, or x-rays. To complete this tutorial you will need a CD or DVD with your medical imaging scan, or a downloaded DICOM data set from one of many online repositories. If you had a medical scan at a hospital or clinic you can usually obtain a CD or DVD from the radiology department after signing a waiver and paying a small copying fee. Step 1: Download Slicer Slicer is a free software program for medical imaging. It can be downloaded from the www.slicer.org. Once on the Slicer homepage, click on the Download link as shown in Figure 1. Figure 1 Slicer is available for Windows, Mac, and Linux. Choose your operating system and download the latest stable release as shown in Figure 2. Figure 2: Download Slicer Step 2: Copy the DICOM files into Slicer. Insert your CD or DVD containing your medical scan data into your CD or DVD drive, or open the folder containing your DICOM files if you have a downloaded data set. If you navigate into the folder directory, you will notice that there are usually multiple DICOM files in one or more directories, as shown in Figure 3. Navigate to the highest level folder containing all the DICOM files. Figure 3: There are many DICOM files in a study Open Slicer. The welcome screen will show, as demonstrated in Figure 4. Left click on the folder that contains the DICOM files and drop it onto the Welcome panel in Slicer. Slicer will ask you if you want to load the DICOM files into the DICOM database, as shown in Figure 5. Click OK Slicer will then ask you if you want to copy the files or merely add links. Click Copy as shown in Figure 6. Figure 4: Drag and drop the DICOM folder onto the Slicer Welcome window. Figures 5 and 6 After working for a minute or two, Slicer will tell you that the DICOM import was successful, as shown in Figure 7. Click OK Figure 7 Step 3: Open the Medical Scan in Slicer. At this point you should see a window called the DICOM Browser, as shown in Figure 8. The browser has three panels, which show the patient information, study information, and the individual series within each study. If you close the DICOM Browser and need to open it again, you can do so under the Modules menu, as shown in Figure 9. Figure 8: DICOM Browser Figure 9: Finding the DICOM browser Each series in a medical imaging scan is comprised of a stack of images that together make a volume. This volume can be used to make the NRRD file. Modern CT and MRI scans typically have multiple series and different orientations that were collected using different techniques. These multiple views of the same structures allow the doctors reading the scan to have the best chance of making the correct diagnosis. A detailed explanation of the different types of CT and MRI series is beyond the scope of this article, but will be covered in a future tutorial. Click on the single patient, study, and a series of interest. Click the Load button as shown in Figure 8. The series will then begin to load as shown in Figure 10. Figure 10: The study is loading Step 4: Save the Imaging Data in NRRD Format Once the series loads you will see the imaging data displayed in the Slicer windows. Click the Save button on the upper left-hand corner, as shown in Figure 11. Figure 11: Click the Save button The Save Scene dialog box will then appear. Two or more rows may be shown. Put a checkmark next to the row that has a name that ends in ".nrrd". Uncheck all other rows. Click the directory button for the nrrd file and specify the directory to save the file into. Then click the save button, as shown in Figure 12. Figure 12: Check the NRRD file and specify save directory. The NRRD file will now be saved in the directory you specified!
  17. 1 point
    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!
  18. 1 point
    froth

    Lumen of vessel in 3D Slicer

    I am not sure if dealing with solidify modifier is safe procedure. I tried a lot, every time something was wrong. I mean complex geometries of lumen with irregular narrowing from thrombus or atherosclerosis. Every time I lost the ideal lumen of the vessel. Some solution to it, is shrink-wrap modifier, but to be honest it has big limitation like you mention before. I don't think that it would handle with dissections either. So for that moment, I think we don't have perfect solution to mirror the ideal anatomy of vessel lumen. We can be close, but not accurate. Maybe Dr. Mike has different opinion? The second aspect is segmentation. What program you recommend ? Osiris or slicer? I think that when we use the threshold for Hounsfield units for contrast medium , we also segment part of calcium atherosclerosis which has very big Hounsfield value. Around plaque segmentation see a transition zone which corresponds the value of Hounsfield for contrast medium which we see as very irregular surface. Of course we do smoothing as post processing in blender, however its not dealing perfectly with it. Even if it does, we lose ideal shape of lumen. So same again, we are close but not accurate. If anybody knows how to deal with these problem, please share with me.
  19. 1 point
    kopachini

    Lumen of vessel in 3D Slicer

    I don't fill those surfaces, I use solidify modifier so there is no need to merge two edges after offset. And, maybe it is confusing, but even when you do solidify or whatever, you will still have "hidden space" between two surfaces (inner/outer shell...). When printing, 3D printer doesn't recognise that space as empty yet it is prints it as solid, full...
  20. 1 point
    Dr. Mike

    3D slicer set up for windows 10

    Glad that worked out. I am also using Slicer (64 bit) and Windows 10 and it works fine.
  21. 1 point

    Version 1.0.0

    64 downloads

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

    Free

  22. 1 point
    Reinol Gonzalez

    Curiel

    Version 1.0.0

    7 downloads

    CBCT for implant planning

    Free

  23. 1 point
    Cris

    Right proximal humerus Fx

    Version 1.0.0

    1 download

    Right proximal humerus fx from CT-Scan. Printer: Witbox2 (bq) Material: 1,75mm PLA Layer Height: 0,2 Wall, top, bottom thickness: 0,4 Infill: 20% Temperature: 230º Print speed: 60 mm/s Travnel speed: 120 mm/s

    Free

  24. 1 point
    Dr. Mike

    Formlabs new wash and cure station

    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.
  25. 1 point
    If there is a separation, you can click on Edit, Separate Shells in Meshmixer and it will split the model. Did you try uploading the subvolume .nrrd to democratiz3D?
  26. 1 point
    bryanc

    Slicer question on creating new volume

    Woot! I _almost_ got what I wanted! Next question: Is there a way for me to just subtract the pelvis? The slice I have is the head of the femur with acetabulum, which when I import into Meshmixer to subtract pelvis, doesn't have an intact head of femur. The CT scan clearly has separation between the femur and the acetabulum, so that surface must exist....
  27. 1 point
    bryanc

    Slicer question on creating new volume

    Ah ha... ok. So I can get to here. Do I just "Save" this? And if so, there are several options for saving: MRML, NRRD, VP and ACSV. It looks like VolumeProperty is what I want perhaps? Sorry and thanks for walking me through this. Femur crop b.tiff
  28. 1 point
    Dr. Mike

    Teeth Micro CT

    I think it is possible to import a stack of TIFF or JPG files in Slicer using the Add data feature. Once the images are imported you will need to tell Slicer how far apart they are spaced, since unlike a DICOM series, individual TIFF files have no information about slice spacing. I haven't tried this personally, but here is a link. mikefazz is correct about ImageJ, and its derivative, Fiji. I have had some trouble with the left-right and cranial-caudad orientation of the file getting mixed up with Fiji which required me to import the data into Slicer anyway to do a mirror transform. Maybe you will have better luck. If you are creating dental files using Mimics I would suggest you also give the democratiz3D service on this site a try. Once you load your file into Slicer you can export it into NRRD format (anonymized) and upload it to democratiz3D. Conversion to STL takes about 15 minutes and it is scalable, meaning you can upload multiple files and it will process them all concurrently. As of March 20, 2017 there is improved support specifically for dental CT files (see version history here). The main reason to use the automated democratiz3D is that it saves time over Mimics and can do batch processing of multiple jobs simultaneoulsy. Also, it is free compared to thousands of $$$ for Mimics, but since you already have a Mimics license that may not be important to you. On another note, I am planning on doing a dental scan specific tutorial soon. Look for that in the coming weeks. Good luck! Dr. Mike
  29. 1 point
    tsehrhardt

    Meshmixer Plane Cut

    I came across how to use the "Create Pivot" tool in Meshmixer to more precisely place a "Plane Cut," but it doesn't always seem to place the pivot where I want it. My heads are in FH with nasion at x = 0 and I want to make cuts at precise distances from this point or at other known points from the origin (I have nasion at x = 0, left and right porion at y = 0 and z = 0). When I use the default pivot placement, it sometimes places it at the origin, which is perfect because I can use that or use the "Transform" tool to shift the pivot a specific distance. Anyways, even with the same settings, the pivot is not always placed at the origin, so I'm not getting a cut at 0 every single time. Has anybody played with this or have a better way of getting cuts at a precise location? Meshlab has a "Compute Planar Section" which lets me take a cut at say, x = 0, but then I have to extrude it to get a printable layer.
  30. 1 point
    kopachini

    Meshmixer Plane Cut

    Yes, that boolean action gives you flat surface. Somethimes I have troubles with Blender and then I add cube and use Union boolean, then delete flat surfaces of that "model" and add facet where "cut" was made. The result is the same...
  31. 1 point
    Dr. Mike

    Meshmixer Plane Cut

    Hi Terry, Thanks for posting this question. I too have had problems with Meshmixer when I want to perform very precise cuts or moves. For most instances Meshmixer is great when cuts can be "eyeballed," or made visually. But the plane cut tool doesn't seem to have a way to be really precise about it. In these instances, I've used Blender. Basically I will make a "plane" by starting with a cube and making the dimensions something like 1000 x 1000 x 0.1 mm. Technically this isn't a plane since it has volume, but if it is 1/10 of a mm thick for practical purposes that is a plane. You can then set the exact XYZ coordinates and the XYZ rotation of the cut plane in the object parameter pane. Then, do a boolean difference to subtract the intersecting volume between the plane and my target object, effectively making a 0.1 mm thick cut through it. Blender is scriptable, and I've had instances where I have to do multiple identical cuts on multiple objects, and I've written a python script to automate moving the cutting object and performing the cuts. Sorry this isn't specifically a solution for Meshmixer, but hopefully it will help you. Dr. Mike
  32. 1 point
    Toups

    CT scan w/ implants

    Version 1.0.0

    24 downloads

    Face/skill CT scan with implants in place.

    Free

  33. 1 point
    I was also interested into making craniofacial implants, and also i have found MeVisLab free software, but i found it very complex to work with. Than also i tried with Geomagic Sculpt and Freeform, but as Saumyam mentioned they are pretty expencive (retailer in my country said that the price is aroud 2000€ for Sculpt, and 6000 € for Freeform, and 8000 € for Freeform Plus). It was very hard to work with Geomagic sculpt (laggs, unresponsice control etc.), but Freeform was discovery and I am very pleased with that software. Here is model of custom made cranial implant that I made using Geomagic Freeform trial version and Blender. Few details remain to be done on it.
  34. 1 point
    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...
  35. 1 point
    mplishka

    Shells for Hermit Crabs

    Apparently this is few years old, but I just saw a blurb on it the other day. Create a 3D model from a scan of the shell and add a little pizzazz! https://www.wired.com/2013/07/3-d-printed-hermit-crab-shells-based-on-city-skylines/
  36. 1 point
    Dr. Murali Krishna

    11 unnamed

    Version 1.0.0

    6 downloads

    denture scan

    Free

  37. 1 point
    Dr. Mike

    Shells for Hermit Crabs

    What!?!
  38. 1 point
    Not technically 3d printing, but researchers used a spinach leaf to create vasculature http://www.businessinsider.com/spinach-leaf-science-heart-tissue-blood-2017-3 Now thousands of kids won't eat their spinach in the name of science
  39. 1 point
    Researchers at UC San Diego have successfully 3D printed a network of blood vessels. This is an important step towards 3D printing an entire organ. Read the full story here.
  40. 1 point
    kopachini

    ".dicom" to ".stl" softwares

    Try 3D slicer, it is free and you have a lot of tutorials how to use it. OsiriX costs and there is no version for PC :/
  41. 1 point
    3D printing technologies have opened up the capabilities for customization in a wide variety of applications in the medical field. Using bio-compatible and drug-contact materials, medical devices can be produced that are perfectly suited for a particular individual. Another trend enabled by 3D printing is mass customization, in that multiple individualized items can be produced simultaneously, saving time and energy while improving manufacturing efficiency. 3D printers are used to manufacture a variety of medical devices, including those with complex geometry or features that match a patient’s unique anatomy. Some devices are printed from a standard design to make multiple identical copies of the same device. Other devices, called patient-matched or patient-specific devices, are created from a specific patient’s imaging data. Commercially available 3D printed medical devices include: Instrumentation (e.g., guides to assist with proper surgical placement of a device) Implants (e.g., cranial plates or hip joints) External prostheses (e.g., hands) Prescription Glasses Hearing Aids In summary, the 3D Printing medical device market looks exciting and promising, Various Reports and surveys suggest the unexpected growth and demand for 3D Printing in medical device industry and it is expected to blossom more but a number of existing application areas for 3D printing in healthcare sector require specialized materials that meet rigid and stringent bio-compatibility standards, Future 3D printing applications for the medical device field will certainly emerge with the development of suitable additional materials for diagnostic and therapeutic use that meet CE and FDA guidelines.
  42. 1 point

    Version 1.0.0

    4 downloads

    ABD009 from the CT Lymph Nodes Collection of TCIA.

    Free

  43. 1 point
    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!
  44. 1 point
    Examples of historical medical 3D printing on display at RSNA. The green skull is from 1985! We've come a long way since then.
  45. 1 point
    hainebeck

    Joeladaptado

    Version 1.0.0

    13 downloads

    Joeladaptado

    Free

  46. 1 point
    cosmos1985

    MAXILAR SUPERIOR

    Version 1.0.0

    6 downloads

    maxilar superior a maxima calidad threshold 270 hueso sin detallar

    Free

  47. 1 point

    Version 1.0.0

    3 downloads

    Impacted maxillary canine

    Free

  48. 1 point

    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

  49. 1 point
    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.
  50. 1 point
    Dear Dr. Mike: I'm really excited to see the profile of Embodi3D. I commented a few days ago, I got my hands on this tutorial: http://www.makermex.blogspot.com.ar/#!http://makermex.blogspot.com/2015/03/como-convertir-una-tomografia-en.html I honestly was not sure Blender off a possible tool for the development of workflow. But to see what you have accomplished on the page, I put very, very happy. I'm using Blender for about 8 years (www.infografiaeinteriorismo.blogspot.com) a while ago and I'm trying to get 3D printed pieces from information obtained from a CT scanner does. My idea of ​​workflow is: DICOM files tomograph. SLICE 3D processing. Exported in STL format. Import Blender. Clean. 3D printing. I hope and I do urge you to help me if in the way of stumble learning obstacles. Of course, I greatly appreciate your time spent as fantastic video tutorials (I'm looking at right now). Greetings Carlos
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