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How to Create 3D Printable Models from Medical Scans in 30 Minutes Using Free Software: Osirix, Blender, and Meshmixer
If you haven't already done so, please see my tutorial on selecting the best medical scan to create a 3D printed model. If you start your 3D printed model project with the wrong kind of scan, your model will not turn out well. Selecting the right kind of scan is critically important and will save you a lot of frustration. Take a few minutes to look over this brief tutorial. It will be well worth your time. Before you start, DOWNLOAD THE FILE PACK that accompanies this video so you can follow along on your own computer. When you finish the tutorial, you will have your very own 3D printable skull STL file. Download is free for members, and registration for membership is also free and only takes a minute.
Video 1: The video version of this tutorial. It takes you from start to finish in 30 minutes. The written version here has more detail though.
A Few Brief Definitions What is Osirix? Osirix is a Macintosh-only software package for reading medical imaging scans (Figure 1). There are several versions. There is an FDA-approved version designed for doctors reading scans in clinics and hospitals, a 64-bit version for research and other nonclinical activities, and a free, 32-bit version. The main difference between the free 32-bit version and the paid 64-bit version is the 64-bit version can open very large imaging studies, such as MRI exams with thousands of images. The 32-bit version is limited to about 500 images. Additionally, there is a performance boost with the paid versions. If you are just getting into 3D bioprinting, the free, 32-bit version is a great place to start. It can be downloaded at the Osirix website here.
Figure 1: An example of Osirix being used to read a CT scan. What is DICOM? DICOM stands for Digital Imaging and Communications in Medicine. It is the standard file format for most medical imaging scans, such as Computed Tomography (CT), Magnetic Residence Imaging (MRI), ultrasound, and x-ray imaging studies. What is STL? STL, or STereoLithography format , is an engineering file format created by 3D Systems for use with Computer Aided Design software (CAD). The file format is primarily used in engineering, and has become the standard file format for 3D printing. The Problem with 3D Printing Anatomic Structures The major problem with trying to 3D print anatomic structures from medical scans is that the medical scan data is in DICOM format and 3D printers require files in STL format. The two formats are incompatible. There are very expensive, proprietary software packages that can perform the conversion between DICOM and STL. A little-known secret is that this can also be done using free, open-source software. Osirix is the best solution for Macintosh. 3D Slicer is the best solution for Windows and Linux. I will discuss 3D Slicer in an upcoming tutorial. If you haven't already, please download the DICOM data set we will be using in this tutorial. This data set is from a high quality CT scan of the brain and skull. It has been anonymized and has been put in the public domain for research by the US National Cancer Institute. Also included with the download packet are other files we will use for this tutorial, including the final STL file of the skull. The download is free for members, and registration for membership is also free and only takes a minute. From the Macintosh Finder navigate to the folder with the downloaded tutorial file pack and double-click on the file TCGA-06-5410 sharp.zip. Opening the CT scan with Osirix Open Osirix. From the File menu, click Import, Import Files. Click Open. (Figure 2)
Figure 2: Importing the CT scan into Osirix Navigate to the folder that contains your DICOM data set. Click the Open button. Osirix will ask you if you want to copy the DICOM files into the Osirix database, or only copy the links to these files. Click "Copy Files." Osirix will begin to copy the files into the database. A progress bar will be shown on the lower left-hand corner. When the data is imported you'll see a small orange circle with a "+" in it. This orange circle will eventually go away when Osirix is finished analyzing the study, but you can open the study and work with it while Osirix does some cleanup postprocessing. Left click on the study. You will see an icon with a label "FIDUCIALS 1.0 SPO cor, 216 Images." This is a CT scan of the head with coronal slices at 1 mm intervals. Double-click on this icon, Figure 3.
Figure 3: The study when opened Osirix will remind you that you're not supposed to be using it for diagnostic scan reading on real patients unless you are using the more expensive FDA approved version, Osirix MD we're just using it to create a 3D model, so click "I agree." At this point, the study will load. Use the mouse wheel or the bar on the top of the screen to scroll. You can see that this is a pretty decent CT scan of the head for 3D printing. There is not much artifact from metallic dental implants because the maxilla and mandible have been cut off. Segmenting the bony skull and creating a new series We can measure the density of the bony structures using the Region Of Interest or ROI tool. This measures the Hounsfield density, or CT density, of the target area. Select the oval tool from the drop-down menu, Figure 4.
Figure 4: The ROI tool. Choose a region of bone using the oval tool. You will see that information about this region is displayed. What we are interested in is the mean density, which in this case is 1753.194, Figure 5.
Figure 5: Density measurement using ROI tool. The mean density is 1753.194, as shown in maroon field. Use the ROI tool to select another region in the brain. You will see that the mean attenuation, or density, is much less, in this case 1059.137, Figure 6.
Figure 6: Density measurement of the brain tissue. Finally, use the oval tool to choose an area in the air adjacent to the head. You can see that the mean attenuation of this region is 38.514, Figure 7.
Figure 7: Density measurement of air. In this scan the Hounsfield attenuation numbers have been shifted. In a typical scan, air measures about -1000, soft tissue between 30 and 70, and bone typically greater than 300. In this scan those numbers have been increased by 1000. Since we were thorough enough to check the Hounsfield attenuation before moving on, we can easily correct for this shift. Under ROI menu select Grow Region 2D/3D Segmentation, Figure 8.
Figure 8: The Grow Region tool In the Segmentation Parameters window that pops up, set the following:
Lower Threshold 1150
Upper Threshold 3000.
Generate a new series with:
Inside pixels 1000
Outside pixels 0 Be sure to check the checkbox next to the Set Inside Pixels, and Set Outside Pixels fields, Figure 9.
Figure 9: Setting up the Segmentation Parameters window. Next, make sure you select a starting point for the algorithm. Left click on one of the skull bones. Green crosshairs will show. All of the bone that is contiguous with point you clicked will now be highlighted in green, Figure 10.
Figure 10: Setting the starting point for segmentation. The target region turns green. Click the Compute button Osirix will generate a new series with the bones being a single white color with a value of 1000, and everything else being a black color with a value of zero, Figure 11. Creating a separate series just for 3D printing purposes is the secret to getting good 3D models from Osirix. Trying to generate a 3D surface model directly from the 3D Surface Rendering function underneath the 3D Viewer menu is tempting to use, however it will not work well for generating STL files. This is not obvious, and the source of much frustration for beginners trying to use Osirix for 3D printing.
Figure 11: The new bitmapped series shown on right of screen. This series has only two colors, black and white. It is idea for conversion to and STL surface model. Generating an STL file from the new bitmapped series Now we are ready to create our 3D surface model. Make sure that your new bitmapped series is highlighted. Click on the 3D viewer menu and select 3D Surface Rendering, Figure 12. Leave the settings set to their default values. Click OK as shown in Figure 13.
Figure 12: Selecting 3D Surface Rendering
Figure 13: Setting 3D surface rendering settings Osirix will then think for a few moments as it prepares the surface. You can see that a relatively good approximation of the skull has been generated. Use of the left mouse button to rotate the 3D model. Next were going to export the 3D surface model to an STL file. Click Export 3D-SR and choose Export as STL as show in Figure 14. Type the file name "skull file." Click Save.
Figure 14: Exporting model to STL file format. Cleaning up the 3D model in Blender You can see from the 3D rendering that there are many small islands of material that have been included with the STL file. Also, the skull has a very pixelated appearance. It does not have the smooth surface that would be expected on a real skull. In order to fix these problems, we're going to do a little postprocessing in Blender, a free open-source 3D software program. If you don't already have Blender on your computer, you can download it free from blender.org. Blender is available for Windows, Macintosh, and Linux. Select your operating system, preferred installation method, and download mirror. Once Blender is installed on your computer, open it. In the default scene there will be a cube. We don't need this. Right click on the cube to select it. Then delete it using the delete key on a full keyboard or the X key on a laptop keyboard. Blender will ask you to confirm you want to delete the object. Click Delete as shown in Figure 15.
Figure 15: Deleting the default cube. Next, we are going to import the skull STL file. From the File menu select Import, STL, as shown in Figure 16. Navigate to the skull STL file you saved from Osirix, and double-click it. Blender will think for a few seconds and then return to what appears to be an empty scene, as shown in Figure 17. Where is your skull? To find your skull, use the mouse scroll wheel to zoom out. If you zoom out far enough you will see the skull. The skull appears to be gigantic, as shown in Figure 18. This is because the default unit of measurement in the skull is 1 mm. In Blender, an arbitrary unit of measurement called a "blender unit" is used. When the skull was imported, 1 mm of real size was translated into 1 blender unit. Thus the skull appears to be hundreds of blender units large, and appears very big.
Figure 16: Importing the STL file into Blender
Figure 17: The "empty" scene. Where is the skull?
Figure 18: Zoom out and the skull appears! The skull is also offset from the origin. We are going to correct that. Make sure that the skull is still selected by right clicking on it. If it is selected it will have a orange halo. In the lower left corner of the window click on the Object menu. Select Transform, Geometry to Origin as shown in Figure 19. The skull is now centered on the middle of the scene.
Figure 19: Centering the skull in the scene. Deleting Unwanted Mesh Islands First, let's get rid of the extra mesh islands. There is a menu in the lower left-hand corner of the window that says Object Mode. Click on this and go to Edit Mode, as shown in Figure 20.
Figure 20: Entering Edit mode in Blender. Now we are in Edit Mode. In this mode we can edit individual edges and vertices of the model. Right now the entire model is selected because everything is orange. In edit mode you can select vertices, edges, or faces. This is controlled by the small panel of buttons on the bottom toolbar. Make sure that the leftmost or vertex selection mode is highlighted and then right click on a single vertex on the model, as shown in Figure 21. That vertex should become orange and everything else should become gray, because only that single vertex is now selected, Figure 22.
Figure 21: Vertex selection mode
Figure 22: Select a single vertex by right clicking on it. Under the Select menu, click Linked, as shown in Figure 23. Alternatively, you can hit Control-L. This selects every vertex that is connected to the initial vertex you selected. All the parts of the model that are contiguous with that first selection are now highlighted in orange. You can see that the many mesh islands we wish to get rid of are not selected.
Figure 23: Selecting all linked vertices.
We are next going to invert the selection. Do this by again clicking on the Select menu and choosing Inverse, Figure 24. Alternatively, you can hit Control-I. Now, instead of the skull being selected, all of the unwanted mesh islands are selected, as shown in Figure 25. Now we can delete them. Hit the delete key, or alternatively the X key. Blender asks you what you want to delete. Click Vertices, Figure 26. Now all of those unwanted mesh islands have been deleted.
Figure 24: Inverting the selection.
Figure 25: The result after inverting the selection. Only the unwanted mesh islands are selected!
Figure 26: Deleting the unwanted mesh islands. Repairing Open Mesh Holes We can see that on the top of the skull there is a large hole where the skull was cut off by the scanner. Because the bone surface was cut off, Osirix left a gaping defect, Figure 27. Before 3D printing, this will have to be corrected. This is what is called a manifold mesh defect. It is an area where the surface of the model is not intact. A 3D printer will not know what to do with this, such as whether it should be filled in or left hollow. Fortunately, it is relatively easy to correct.
Figure 27: A large open mesh hole at the top of the skull. Using the Select menu in the lower left-hand corner, click on Non-Manifold. This will select all of the non-manifold mesh defects in your model. You can see that the edge of our large hole at the top of the skull has been selected and turned orange. This confirms that this defect has to be fixed. Unselect by hitting the A key. Then, go to Edge select mode by clicking on the Edge Select button along the lower toolbar. Holding down the Alt key, right-click on one of the edges of the target defect, in this case the top of the skull. That familiar orange ring has formed. Your selection should look like Figure 28. Let's fill in this hole by creating a new face. Hit the F key. This creates a new face to close this hole, Figure 29.
Figure 28: The edge of the hole is selected, as indicated by the orange color.
Figure 29: The hole when filled with a new face. Due to the innumerable polygons along the edges, the face is actually quite a complex polygon itself. Let's convert it to a simpler geometry. With the face still selected hit Control T. You can alternatively go to the Mesh menu and select Faces, Triangulate Faces as shown in Figure 30. This will convert the complicated face into simpler triangles. As you can see, some of these triangles are quite large relative to the other triangles along the skull surface. These large triangles may become apparent when smoothing algorithms are applied or 3D printing is performed. Let's reduce their size. Hit the W key and then select Subdivide Smooth, as shown in Figure 31. The triangles are now subdivided. Let's repeat that operation again so that they are even smaller. Hit the W key and again select Subdivide Smooth.
Figure 30: Converting all faces into triangles. ]
Figure 31: Subdividing and smoothing the selected faces. Smoothing the Model Surface Next let's get rid of that pixelated appearance of the model surface. First, we need to convert all of the polygons in the model to triangles. The smoothing algorithms just work better with triangles. Staying in Edit mode, hit the A key. The A key toggles between selecting all and unselecting all. If you need to, hit the A key a second time until the entire model is orange, thus indicating that it is selected. Hit Control-T, or alternatively use the Mesh menu, Faces, Trangulate Faces. This will convert any remaining complex polygons to triangles. Go back to Object mode by hitting the tab button or selecting Object Mode from the bottom toolbar. We are now going to apply a smoothing function, called a modifier, to the skull. Along the right of the screen you'll see a series of icons, one of which is a wrench, as shown in Figure 32. Click on that. This brings up the modifier panel, a series of tools that Blender uses to manipulate digital objects. Click on the Add Modifier button and select the Smooth modifier. Do not select the Laplacian Smooth modifier. That is different. We just want the regular Smooth modifier, as shown in Figure 33. Leaving the Factor value at 0.5, increase the Repeat factor until you are satisfied with the surface appearance of your model. For me, a factor of 20 seemed to work, Figure 34. At this point the modifier is only temporary, and has not been applied to the model. Click on the Apply button. Now the smoothing function has been applied to the model.
Figure 32: The Modifiers toolbar on the right.
Figure 33: The Smooth modifier
Figure 34: Setting the Smooth modifier to repeat 20 times. Rotating and Adjusting the Model Orientation When the model was originally exported from Osirix and opened in Blender, it was at a strange orientation. We can correct to this easily. Click on the View menu from the left portion of the lower now bar and select Front. This orients the model from the frontal view, and you can see that in this orientation we are looking at the top of the skull. To correct this, we will rotate the model along the X axis. First, make sure that the cursor is inside the model window. Then, Hit the R key and then the X key, and type "180." This will rotate the model on the X axis by 180°. Hit the return key to confirm the modification. Don't worry if the skull isn't facing the correct way right now, we will fix that later. Now we are ready to export our cleaned up skull model. Go to the File menu, click Export, STL. Navigate to your desired folder and save your STL file. Since I corrected several defects in this mesh file, I called the file "skull file corrected.stl" Performing a Final Inspection Using Meshmixer If you haven't already done so, go to the Autodesk Meshmixer website at http://www.meshmixer.com/download.html and download and install Meshmixer. The software is free. Once installed open the program and select Import. Navigate to your STL file and double-click it. Meshmixer has a variety of nice features, and one of them is a mesh correction function. Once your file is open click on the Analysis button along the left nav bar. Click on Inspector as shown in Figure 35. Meshmixer will now analyze the STL file for obvious mesh defects. Anything that is detected will be highlighted by red, pink, or blue lines. You can see that our skull model appears to be defect free. Click on the done button and quit Meshmixer.
Figure 35: Running the inspector tool in MeshMixer
Your STL file of the skull is now ready for 3D printing! Conclusion In this tutorial you have learned how to take a DICOM data set from a CT scan and use it to create a 3D printable STL file using free software. First we used the Osirix to segment a CT scan and convert it to an STL file. Then we performed cleanup operations on the STL file using the Blender and Meshmixer, both free programs. For additional information on how to select an appropriate CT or MRI scan for 3D printing please see my previous tutorial. If you want to learn more about using Blender to fix more extensive defects in bone models, you can view to other tutorials I have created: 3D Printing of Bones from CT Scans: A Tutorial on Quickly Correcting Extensive Mesh Errors using Blender and MeshMixer Preparing CT Scans for 3D Printing. Cleaning and Repairing STL Files from Bones using Blender, an advanced tutorial
A variety of useful tutorials for 3D printing is available on the Tutorials page. If you are planning on attending the 2015 Radiological Society of North America (RSNA) meeting in Chicago this November, look for my hands-on course "3D Printing and 3D Modeling with Free and Open-Source Software." I will give more tips and tricks for creating great 3D printed medical models using freeware.
I hope you find this tutorial helpful in creating your own medical and anatomic models for 3D printing. Please stay tuned for my next tutorial on using the free, open-source program 3D Slicer to create medical 3D models on Windows and Linux platforms. If you are creating your own 3D printed medical models, please share your models with the Embodi3D community in the File Vault. If you have questions or comments, please leave a comment below or start a discussion thread in the Forums. Sample free downloads
A Collection of Free Downloadable STL Skulls for you to 3D print yourself.
3D printable human heart in stackable slices, shows amazing internal anatomy.
A Collection of Spine STL files to download and 3D print. Follow Embodi3D on social media Twitter | Facebook | LinkedIn | YouTube | Google+
3D Printed Casts for Healing Fractures
Medical 3D Model Creation: From CT Scan to 3D Printable STL File in 20 Minutes Using Free Software Programs 3D Slicer, Blender, and Meshmixer
Drag and drop the folder that contains your DICOM images onto the slicer welcome window, Figure 1. If you downloaded the file pack, the DICOM folder is the one that begins with "1.3.6" followed by a whole bunch of numbers.
Figure 1: Loading your DICOM data set by dragging and dropping the DICOM folder onto 3D Slicer. Slicer will ask you to select a reader to use for your data. Leave the default setting selected, "Load directory into DICOM database" and click OK. Slicer will ask you if you want to copy the DICOM files into the Slicer database or just add links to the DICOM files. Click Copy, Figure 2.
Figure 2: Telling Slicer to copy the DICOM files into the Slicer database. Slicer will now take a minute or two to load your DICOM data. Once the data has loaded you should get a pop-up box telling you that the study imported successfully. Click OK. At this point a window titled "DICOM Browser" should be showing. Select the study with patient ID TCGA-06-5410. Click on the Load button in the lower left-hand corner, Figure 3.
Figure 3: Loading the CT scan into the active seen within Slicer. At this point you should see a matrix with four boxes in the right half of the Slicer window. In three of the boxes you will see the axial (transverse), sagittal, and coronal views of your imaging study. If you don't see this, you can adjust the viewport layout using the viewport button.
Select the Four-Up viewport layout as shown in Figure 4.
Figure 4: Selecting the Four-up viewport layout. Next, go to the Volume Rendering module. You can access this from the drop-down menu at the top now bar as shown in Figure 5.
Figure 5: Selecting the Volume Rendering module. Once you are in Volume Rendering, turn on volume rendering by clicking the small eyeball to the left of the Volume drop-down menu, as shown in Figure 6. The 3D volume should now be displayed in the fourth square on the right part of the Slicer window. However, the volume is likely not centered. To center the volume click on the small crosshairs at the upper left corner of the volume screen, as shown in Figure 6.
Figure 6: Turning on volume rendering and centering the volume view. You now need to adjust the appearance of your 3D volume. Under the Display section, select a Preset. For this model, select the third icon from the left on the top row, which should be CT-Bone. Slide the Shift slider to the right until the 3D volume looks good. These actions are shown in Figure 7.
Figure 7: Selecting and adjusting a 3D display Preset. Now we are going to start actually constructing our 3D surface model. From the module drop-down menu, Editor, as shown in Figure 8. When asked to create a merge label map, use the default selection GenericAnatomyColors, and click Apply, as shown in Figure 9.
Figure 8: Selecting the Editor module.
Figure 9: Choose the default merge label map. First, we're going to create a label map that denotes the skull. Click on the Threshold Effect Tool button. It looks like this.
The threshold effect tool will then open as shown in Figure 10. We want to select bone, so click on the green rectangle to bring up a choice of label maps. Select 2 – bone. The blinking area should turn a yellow-orange color. Next, define the minimum Threshold Range. If you are using the DICOM data set from the file pack, set this to 1250. If you are using your own scan, this will be a different number, probably closer to 300. Experiment with the values until the blinking region seems to encompass the structures you want to 3D print. Leave the default maximum Threshold Range at 4095. The settings that you need to modify are shown in Figure 11. When you are satisfied with your selection, click Apply.
Figure 10: The Threshold Effect Tool.
Figure 11: The Threshold Effect parameters to set. Now you have created a "label map" that encompasses the bony skull we wish to 3D print. We need to generate a surface model. Click on the Make Model Effect button, which looks like this.
Make sure that the target label is still set to 2 (bone). Click Apply, as shown in Figure 12. 3D Slicer will take about 10 seconds to generate the surface model. When it is completed, you will notice a slight change in the appearance of the 3D rendered image in the upper right view box.
Figure 12: The Make Model Effect tool. You now have a 3D surface model, and need to save it in STL file format. Click on the save button on the left portion of the upper toolbar. 3D Slicer asks you what you want to save. The only thing we are interested in is the bone surface model, so uncheck everything except "bone.vtk." Choose STL for file format and specify the directory you want the file to be saved, as shown in Figure 13.
Figure 13: Saving your 3D surface model as an STL file. You should now have a file called bone.STL. Although tempting to send your new STL file directly to a 3D printer, don't do it. Your file is not yet ready for 3D printing. Fortunately, we can fix most problems with our next software program, Blender. Performing Additional Skull STL File Cleanup in Blender If you haven't already, download the free Blender software program from blender.org. Install it and open Blender.
Delete the default cube that is shown in Blender by hitting the X key followed by the D key. Import the STL file by going to the File menu -> Import -> STL, as shown in Figure 14. Blender may take 10 to 15 seconds to import the file as it is fairly large.
Figure 14: Importing the STL file into Blender. Next, you need to center the skull object in the field of view. Select the Object menu in the lower left-hand corner, then click Transform -> Geometry to Origin, as shown in Figure 15.
Figure 15: Centering the object in the field of view using the Geometry to Origin function. You will notice that the imported skull appears quite large. Don't worry about this. Simply use your scroll wheel on the mouse to scroll out. If you have a middle mouse button, you can use it to rotate the skull. Next, we are going to delete the innumerable disconnected mesh islands in our skull object. Go to Edit Mode, as shown in Figure 16.
Figure 16: Entering Edit Mode. When you are in Edit Mode, you can directly edit the mesh of your object. Initially, the entire mesh is selected, thus the skull appears orange. Right click somewhere on the skull. It does not matter where as long as it is not one of the disconnected mesh islands. By right clicking, you will select a single vertex. Expand the selection to include all connected vertices by clicking Control-L on your keyboard. You will notice that the skull has turned orange, but the disconnected mesh islands are still black. Next, we want to invert the selection by hitting Control-I on your keyboard. The selection is now inverted, and only the disconnected mesh islands should be shown highlighted in orange, as shown in Figure 17.
Figure 17: Selecting the disconnected mesh islands. With the disconnected mesh islands selected, delete them by hitting the X key on the keyboard. A menu of deletion choices is presented. Type "V" for Vertices. This is shown in Figure 18. The disconnected mesh islands are now deleted.
Figure 18: Deleting the vertices of the disconnected mesh islands. Go back to Object Mode by selecting it from the mode button on the lower left as shown in Figure 19.
Figure 19: Returning to Object Mode. From Object Mode select the Modifiers toolbar. It has a button that looks like a small wrench and is located in the right tool column. Modifiers are functions that you can apply to your mesh to change its appearance. In this case, we are going to smooth out our mesh. Click on the Add Modifier menu and select Smooth from the Deform column. DO NOT select Laplacian Smooth. That is a different modifier. The correct selection is shown in Figure 20.
Figure 20: Opening the Smooth Modifier. Set the Repeat field to 30. Blender may take a few seconds to perform the smoothing function. Then, click Apply, as shown in Figure 21.
Figure 21: Settings for the Smooth Modifier. You are now ready to save your smoothed and cleaned-up STL file. From the File menu, select Export -> STL, as shown in Figure 22. Navigate to the folder you want the file to be saved in and type a file name. In this case, we are going to call the file "bone smoothed.stl." Close Blender.
Figure 22: Saving your cleaned-up STL file.
Performing a Final File Check in Meshmixer Before 3D Bioprinting If you haven't already, download Meshmixer from Meshmixer.com. Open Meshmixer.
Click on the Import button as shown in Figure 23. Select your smoothed STL file that you just created in Blender.
Figure 23: Meshmixer's Import button. Meshmixer will take 10 to 15 seconds to import the file. Once imported, you can rotate the orientation of your skull object by using the right mouse button. Click on the Analysis button and choose Inspector as shown in Figure 24. The Inspector tool will check your mesh for the defects that could cause problems during 3D printing. Any problem areas will be highlighted by red, blue, or pink lines. In this case, our mesh looks great, without any errors as shown in Figure 25.
Figure 24: Opening the Inspector tool.
Figure 25: A clean mesh ready to 3D print! That's it! You have now created a defect-free high quality STL file of the skull from a CT scan using free software. You can take the money you saved by not buying proprietary software to do the same thing, and by yourself a new car or something.
Figure 26: The Final 3D printed product. I hope you found this tutorial helpful, and you will begin designing 3D printable medical models from medical scans yourself. Embodi3D is here to help you. If you have questions, post them in the comments below or in the Forums. Share 3D printable models you have designed in the File Vault, or download models that others have shared. You can even sell your 3D printable creations! If you want to learn more about how to create 3D printable medical models, there are many more helpful and free tutorials.
Saving a Spleen with 3D Printing: Pre-Surgical Planning with Medical Models make "Impossible" Surgeries Possible.
I am a board-certified interventional radiologist, and specialize in the minimally-invasive treatment of vascular (involving blood vessels) disorders. My adventure in 3D printing started when a very nice 62-year-old lady was referred to me by another doctor. A CT scan done for another reason had incidentally detected aneurysms in her splenic artery. The splenic artery is the major artery going to the spleen. An aneurysm is a bulging of the artery wall. Aneurysms are dangerous because as they grow they stretch the artery wall, causing it to thin. Like a balloon, the more the aneurysm stretches, the thinner the artery wall becomes, until the wall is too thin to hold back the pressure of the blood and the aneurysm bursts. This can lead to sudden, acute, life-threatening internal bleeding.
Figure 1. Examples of aneurysms. The thin, stretched out walls of the aneurysm predispose it to rupture. The larger the aneurysm, the greater the risk of rupture and bleeding. Source Drugline.org. Medical convention states that when a splenic artery aneurysm is 2 cm or larger, it is at risk for rupture and should be treated. My patient had two aneurysms in her splenic artery, each of which was 2 cm in size. Something needed to be done. A third, smaller aneurysm was also present but it didn't need to be treated at this time. The conventional treatment in this situation is a surgical splenectomy, in which a surgeon, either in an open fashion or laparoscopically, physically removes the splenic artery with its aneurysms. Because the spleen cannot survive without its artery, it must be taken out too. The spleen plays a critical role in the body's ability to fight infections, so after removal of the spleen, patients are at higher risk for certain infections.
Video 1. Digital rendering showing the two large splenic artery aneurysms arising from the splenic artery. The aneurysm are the sphere-like bulges arising from a small artery in the middle of the aorta. The large trunk is the abdominal aorta. Rendering done with Blender. An alternative treatment to surgical removal is splenic artery embolization. In this procedure, a vascular surgeon or interventional radiologist, such as myself, will make a needle puncture in the artery of the hip and navigate a small plastic tube, called a catheter, into the splenic artery using x-ray guidance. A series of small metallic threads, called coils because they coil up once deployed, are then pushed through the catheter into the splenic artery, where they plug up the entire artery. In principle, the technique is similar to putting hair down your bathroom drain. The hair takes up space and eventually plugs the pipe. In the same way, fine thread-like platinum coils can be pushed into the artery one at a time until the artery is plugged up. Any blood in the artery clots, and without any blood flow there is no pressure on the aneurysm wall and thus no risk of the aneurysms rupturing. Unfortunately, the lack of blood flow also causes the spleen to die from insufficient oxygen. The process of the spleen dying from lack of blood flow results in pain for a day or two. Also, without a functional spleen, these patients also are at higher risk for infections. My patient was a very intelligent and determined individual. I explained both options to her in detail, but she would not accept either of the conventional treatments. She did not want to lose her spleen and be at increased risk of future infections. She challenged me to find a way to treat her aneurysms while saving her spleen. I reviewed the case and imaging studies with several of my colleagues, all board-certified specialists in treating this type of problem. Everybody said the spleen couldn't be saved. It was "impossible." She either had to have her spleen removed or her splenic artery embolized. Do nothing and it was just a matter of time until an aneurysm ruptured, probably killing her. I was greatly moved by my patient's doggedness. She wasn't willing to accept the limits of conventional medical treatment, so I didn't think I should either. I kept searching for solutions. I was aware of some specialized catheter equipment that had been specifically designed to treat aneurysms in the brain. Brain aneurysm treatments are very delicate affairs. If an aneurysm in the brain ruptures, it can result in intracranial bleeding, stroke, permanent disability, or death. Brain aneurysms can be treated with placement of metallic coils through a catheter, as long as the coils are only placed in the bulging, aneurysmal part of the artery. There, they cause blood to clot in the aneurysm, which reduces pressure on the aneurysm wall and prevents it from rupturing. These special coils and catheters are designed to treat the aneurysm while preserving blood flow in the parent artery. Because these aneurysms are in the brain, any disruption in the blood flow of the parent artery will result in stroke.
Figure 2: How coils can be used to treat aneurysms in the brain. Using specialized equipment designed for the brain, coils are used to pack the aneurysm while preserving blood flow in the parent artery. (Image source: wix.com) Could the specialized coils and catheters designed to treat aneurysms in the brain work in the splenic artery? Nobody seemed to know. The patient's splenic artery had an unusually large number of loops, which would complicate any procedure. A search of the published medical literature did not produce any useful results. There were many variables that were different. I discussed my thoughts with the patient. I thought there might be a way to treat her aneurysms while sparing her spleen using this specialized brain aneurysm equipment. But the only way to know if the equipment would work would be to try it during an actual procedure. She gave me a puzzled look. "Well isn't there a way for you to practice?," she said. For generations doctors faced with difficult and complex surgical procedures have really had only one true way to know if they will work: try it in a real surgery. We do everything possible to maximize our chance of success, such as ordering scans, consulting colleagues, reading research articles, and imagining the procedure over and over again in our heads. We try to know everything possible about the intended surgical procedure beforehand. But, the only way to truly know how things will go is to actually do it. There really wasn't any way to know how the brain catheter equipment would work in the spleen because nobody had ever done a procedure quite like this before. Yet, I kept thinking about my patient's statement. Why wasn't there a way for me to practice this beforehand? Finding a solution with 3D printing
At that point I had been looking into uses for 3D printing in medicine for about a year. There seemed to be great potential, but at the time few people were using 3D printing in real patient care. I had designed a few simple 3D printable body parts from medical imaging scans. Would it be possible to 3D print a replica of my patient's splenic artery, and practice doing this complex procedure in the 3D printed model? I had never 3D printed an arterial structure of such complexity. Another search of the medical literature revealed that nobody else had either. I was further hampered by the fact that as a private practice doctor, I don't have access to an expensive 3D printer or the costly proprietary software that is needed to create complex 3D printable anatomic models. Nobody was paying me for my time or expenses. I needed to find a solution that was practical but inexpensive. I invested hundreds of hours testing free and open source software packages to see if they could be used to generate the detailed 3D printed splenic artery model I needed. I eventually found that a combination of the software packages Osirix and Blender, the latter of which is typically used for computer animation, would allow me to design a detailed anatomic model from my patient's CT scan. I could then use the low-cost online 3D printing services Shapeways and iMaterialise to actually print my models. I paid for everything out-of-pocket. When the models arrived in the mail I couldn't believe it. They were precise full-scale replicas of the patient's splenic artery.
Figure 3: A precise 3D printed replica of the patient's splenic artery.
I contacted representatives from the companies that manufactured the brain aneurysm equipment. They had never heard of anybody testing their equipment in a 3D printed model before, but enthusiastically supported it. They donated real guidewires, catheters, stents, and coils for use in testing. Several came over to my house and we replicated the entire procedure inside the 3D model. During this testing I learned that some of catheters and wires would work well in the complex curves of the patient's splenic artery, and others would not. I was able to get all of the trial and error done in the model, something that otherwise would have taken place during the actual procedure. The model wasn't exactly the same as a real patient, but I was able to learn a lot about how the catheters and wires handled in the complex and unique geometry of the patient's splenic artery.
Video 2: Time-lapse footage of endovascular wire and catheter testing in the 3D printed model. Numerous problems were encountered with the difficult geometry of the splenic artery, but with trial-and-error a combination of wires and catheters was found that could handle the difficult geometry. With the optimal set of catheters, wires, stents, and coils preselected, I subsequently did the real procedure on the patient. I completed all the necessary paperwork including getting approval from my hospital's research review board. I brought the 3D models into the operating room as a reference, and referred to them many times during the procedure. All of the preselected equipment worked beautifully, just as it had in testing. I was successful in putting coils in the aneurysms while preserving blood flow to the spleen. Even without having to try out different equipment combinations, the procedure was still very difficult and took five hours. If I hadn't had the ability to practice the procedure in the 3D printed model and preselect my equipment, it easily could have taken twice as long. That is, assuming I didn't collapse from exhaustion and dehydration before finishing it. More importantly, the opportunity to practice the procedure beforehand gave me confidence that I could be safe and successful in doing something that had never been done before. Nearly 2 years after the surgery, the aneurysms no longer a threat and the patient's spleen is fully functioning.
Figure 4: Referring to the 3D printed models in the OR during the surgical procedure to correct the splenic artery aneurysms.
Figure 5: positioning a small catheter into the splenic artery via a needle puncture in the arm. 3D Printing Lessons Learned
This experience fundamentally changed my perception about the value of 3D printing in medicine. For safe, easy, and routine medical procedures, 3D printing will probably not have much of an impact in the foreseeable future. It's too time consuming and costly to make 3D printed models. For complicated or high risk procedures, however, it can be invaluable. No doctor wants to take unnecessary risks or have a bad outcome in surgery. Unfortunately, there are many, many unknowns in surgery, particularly with complex and unusual cases. 3D printing an anatomic model before surgery to study and practice reduces those unknown variables, making risky cases much safer. After my experience, I have no doubt that 3D printing will have a significant impact in improving patient care in all fields of medicine. It is my belief in the potential of 3D printing to help doctors and patients that led me to the creation of this website, Embodi3D.com. Embodi3D is a place where 3D printing enthusiasts can help each other in all fields of biomedical sciences. Members can read medical 3D printing news, ask technical questions in the forums, and even download complete 3D printable medical models from the File Vault. There are several tutorials on how to start 3D printing medical models yourself. Everything on the website is free. I ask only that you give back to the community through comments, advice, and sharing of 3D models, if you are able. Below are two 3D printable models used in actual testing. You can download the models yourself for free.
Download the FREE solid, splenic artery aneurysm lumen model. This is the solid model that shows the hollow space inside the artery (the lumen).
Download the FREE hollow splenic artery aneurysm model. This is the hollow model that the catheters and wires were tested in. You can read the official peer-reviewed account of this 3D printing advance in the medical research journal Diagnostic and Interventional Radiology here. If you liked this article, please share it with your friends!
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Choosing the Best Medical Imaging Scan to Create a 3D Printed Medical Model
Figure 1: Standard imaging planes used in medical scans. Source: National Cancer Institute Imaging Modality: CT versus MRI versus ultrasound In order to understand what scans are best used for 3D printing, a very basic understanding of the types, or modalities, of medical scans is needed. The medical physics behind how these scans work can literally fill volumes. Radiology residents are required to take board examinations on the physics and engineering of medical scanners as part of their training. I will attempt to summarize only the most critical information about medical scans into a few short paragraphs to get you up and 3D printing as quickly as possible. Computed Tomography, or CT scans, are created when an x-ray beam is rotated around the patient. An x-ray detector on the opposite side of the emitter records the strength of the beam that emerges from the other side of the patient. Knowing the angle and position of the x-ray emitter and the strength of the beam emerging from the other side of the patient, a computer can calculate the x-ray appearance of the body in three dimensions. An x-ray beam is generally absorbed or deflected by electrons in matter. Since the density of electrons in matter is more or less the same as the actual physical density of matter, a CT scan can be considered to be a density map of the patient. Things that are dense, such as bone or metal, will appear white. Things that are not dense, such as air, appear black. Figure 2 shows how the different densities of tissue appear on a standard CT scan. When intravenous contrast is given, which contains an iodine-containing chemical that is very dense, it appears white. Fat is not very dense and floats on water, thus it has a blackish appearance. What else floats on water? Choices: bread, apples, very small rocks, cider, gravy, cherries, mud, churches, lead, a duck. (This is a joke. If you get the reference, please leave a comment and give yourself a star).
Figure 2: Effect of tissue density on CT scan appearance. This CT scan image of the head at the eyes shows fat in the temporal fossa as black (red arrow), intermediate density brain tissue as gray (green arrow) and dense calcium-laden bone in the skull as white (blue arrow). Magnetic Residence Imaging, or MRI, is a type of imaging that uses very strong magnetic fields to generate an image. The hydrogen atoms that are part of almost all biological structures (water, fat, muscle, protein, etc.) align with the magnetic field. Radio waves can be sent into the scanner causing the hydrogen atoms to flip orientation. When the radio waves are turned off, the hydrogen atoms flip back and emit their own faint radio signal. Based on analysis of these faint radio emissions and by varying the magnetic field strength and timing of the radio wave pulses, a variety of images can be generated. These different pulse sequences can be used to highlight different types of tissue. Take Figure 3 for example. Four different pulse sequences are shown of the same slice of brain: T1, T2, FLAIR, and T1 with gadolinium contrast. On the T1 image tissues with fat are a bright white, as shown by the fat in the skin (white arrow). The hard, calcium-filled tissue of the skull is black, with the exception of a small amount of bone marrow which is gray in color and sandwiched between the inner and outer skull plate (yellow arrow). The watery cerebral spinal fluid in the lateral ventricles are black (red arrow). However, on the T2 image the watery cerebral spinal fluid is bright white (red arrow). T2 images show water very well. In addition to the water in the ventricles, swelling of the brain tissue due to an adjacent brain tumor can be seen as a white appearance (blue arrow). FLAIR images are similar to T2 images except pure water has been subtracted from the image. Thus tissue swelling (blue arrow) is still clearly visible but the cerebral spinal fluid in the ventricle (red arrow) now appears black. Finally, in the T1 images with gadolinium IV contrast small blood vessels are visible. Additionally, you can actually see the brain tumor and meninges turning white from contrast enhancement (purple arrows).
Figure 3: MRI of the brain at the same level using four different pulse sequences. The patient has a left frontal lobe brain tumor. When 3D printing from an MRI scan, it is important to select images from a pulse sequence that will highlight the structure you wish to visualize. Arteries, tumors, body fluid, bones, and general tissue are all best seen on different sequences. If you choose the wrong imaging sequence to generate your 3D model from, you will encounter only frustration. Ultrasound images are generated when soundwaves are sent into the body by an ultrasound emitter. The waves then bounce off various structures and are detected by a receiver, typically built into the emitter. The concept is similar to sonar that is used on ships and submarines. Based on the strength and depth of the soundwave return, an image can be created. Ultrasound images can be used for 3D printing, however it is very difficult to do so because individual images are not registered in a fixed place in space. The images are acquired by sliding the ultrasound transducer on the skin. The exact location in space and angle of the transducer at the time of image acquisition is not known, which makes generation of a 3D volume difficult or impossible. In general, ultrasound is not recommended as a source of imaging data for 3D printing for the beginner. Key features of medical imaging scans used in 3D printing There are certain features common to all scan modalities that can help you to create a good 3D print. When considering making a 3D medical or anatomic model you must first decide what you want the model to show. Should it show bones, arteries, or organs? Having a model with unnecessary structures included not only makes it more difficult to manufacture, but it also diverts attention away from the important parts of the model. Give this careful thought. Once you have decided what you want to show, evaluate the medical scan you want to create your model from carefully. If the scan doesn't have the proper characteristics, you can exponentially increase the difficulty of getting a 3D printable model from it. 1. Presence of Intravenous contrast Take a look at these two axial (transverse) images from CT scans of the upper abdomen (Figure 4). Both images show slices of the upper abdomen at the level of the tops of the kidneys and liver. What is the difference between the two? You'll notice that on the rightmost scan the aorta is white, whereas on the left scan the aorta is gray. Figure 5 is a zoomed image of this region and shows this in more detail. This is because the rightmost scan was performed with intravenous contrast and that contrast is causing the aorta and other vessels to turn a bright white color.
Figure 4: The effect of intravenous contrast.
Figure 5: Close-up view of the abdominal aorta with (right) and without (left) intravenous contrast. Take a closer look at the kidneys. Figure 6 shows a zoomed-in image. The outer part of both kidneys on the contrast-enhanced scan on the right are a light shade of color. This is due to blood mixed with contrast going into the outer cortex of the kidney. With the contrast-enhanced scan you can clearly see the edge of the kidney, even where it touches the liver. On the noncontrast scan the border of the kidney is only discernible where it is adjacent to the darker colored fat. Where it touches the liver it is difficult to see where the kidney ends and the liver begins. If you want to make a print of the kidney, it will be very difficult to discern the edge of the kidney without IV contrast.
Figure 6: Close-up view of the right kidney with (right) and without (left) intravenous contrast. If you are trying to create a 3D printed model of a bone, it is best to create it from a scan without IV contrast. This is because the bone is the only thing that will be a white color in the scan. This allows your software to easily separate the bones from other tissues. The presence of intravenous contrast may trick the software into thinking that blood vessels or organ tissue is actually bone, and it may improperly include these structures in the 3D printable surface model. These unwanted structures can be manually removed, but this can be an incredibly time-consuming and laborious exercise. It is best to avoid this problem in the first place. On the other hand, if you are trying to 3D print a blood vessel, tumor, or organ, then intravenous contrast is absolutely necessary. Vessels and tumors will light up, or enhance, with IV contrast, turning white on a CT scan. Which will make separation of these structures from background tissue more easy to perform. 2. Timing of intravenous contrast If you are creating a 3D printed model of a blood vessel, tumor, or organ, merely having intravenous contrast in your scan is not sufficient. You also must have the proper contrast timing. Contrast injected into a vein before a medical scan is not static. It is a very dynamic entity, and flows through the blood vessels and tissues of the body at different times before being excreted by the kidneys. Intravenous contrast is injected through an IV catheter, typically in the arm immediately before initiation of scanning. The contrast flows with the blood into the superior vena cava, the large vein in the chest, and then into the heart where it is then pumped into the pulmonary arteries. It is at this point, typically about 15 to 20 seconds, that is the best time to perform a scan to clearly visualize the pulmonary arteries. The contrast-filled blood then flows out of the lungs back to the heart where it is pumped into the aorta and its branches. This may be about 30 seconds after contrast injection, and is the best time to see the arteries. The contrast-filled blood then percolates into the capillaries of the tissues throughout the body. This is the point of maximal tissue enhancement, and is usually the best time to see tumors and organs. The blood then leaves the tissues and drains back into the veins, which is the best time to look at the veins. Finally, after about five minutes or so, the contrast begins to be excreted by the kidneys into the urine, and can be seen within the collecting system of the kidneys, the ureters, and the bladder. Take a look at Figure 7. When the scan was performed in the arterial phase (left) you can clearly see the aorta, arteries of the intestine, and outer rim (cortex) of the kidneys have turned white with contrast-enhanced blood (green arrows). After about five minutes the scan was repeated (right), and on these delayed phase images only a small amount of contrast is left within the aorta and blood vessels. However, contrast can be seen concentrated within the central portions of the kidney (red arrow). This is urine mixed with contrast collecting in the renal pelvis and ureter.
Figure 7: Transverse (axial) images from a contrast-enhanced CT scan from a patient with intravenous contrast in the arterial (left) phase and delayed urographic (right) phase. The point I'm trying to make here is that merely having intravenous contrast is not good enough. When the scan was taken relative to the contrast injection, in other words the timing of the contrast, is critically important to visualizing the target structure. 3. Oral contrast In addition to intravenous contrast it is very common for oral contrast to be given prior to CT scans of the abdomen or pelvis. This is that nasty stuff that you are asked to drink about two hours before your scan. Oral contrast is designed to stay within the intestines so they can be clearly seen and evaluated. Take a look at Figure 8. In this CT scan of the abdomen intravenous contrast has clearly been given as the right kidney is white and enhancing (red arrows). Oral contrast has also been given, as several loops of small intestine can be seen filled with a substance that appears white on the CT scan (green arrows). Unless you are trying to 3D print the intestines, for the most part oral contrast is something you do not want in your source imaging scans. If you are trying to separate out bones, organs, or blood vessels for printing, the presence of oral contrast will increase the likelihood that intestines will be accidentally included in your 3D printable model.
Figure 8: The effects of oral contrast on a CT scan of the abdomen. 4. Slice thickness Take a look at these two CT scans of the chest (Figure 9). What is the difference between them? Both of them have IV contrast and both of them are showing the heart. Obviously, the scan on the right is of higher quality than that on the left, but why? The reason has to do with the thickness of the image slices. When CT scans are performed they are reconstructed into slices in the axial (transverse) plane. The axial plane is the plane that is parallel to the ground if you are standing upright. When the axial slices are stacked on top of each other the data can be used to create images in a different plane, such as when viewed from the front (the coronal plane), as in these example images. The axial slices that were used to create the coronal image on the left were 5 mm thick, whereas the axial slices used to create the image on the right were only 1 mm thick. You can see that the thick slices in the leftmost image generate structures with a very coarse appearance. If you try to 3D print an anatomic model from a scan with thick slices, your model will have a similar rough appearance. It is very important to use scans with thin slices, preferably less than 1.25 mm in thickness, when creating a model for 3D printing.
Figure 9: The effect of slice thickness on three-dimensional reconstructions. 5. Imaging artifact Finally, take a look at these two CT scans of the face (Figure 10). What is the difference between them? The scan on the left clearly shows the teeth of the upper jaw as well as the bones of the upper cervical spine. The scan on the right however has white and black lines crisscrossing the mouth and obscuring the teeth. This type of artifact, called a beam hardening artifact, was created by metallic fillings in the teeth. When the CT scan was performed, the x-ray beam could not penetrate the metal fillings in the teeth to reach the detector. Subsequently, the scanner has no information about the x-ray appearance of the tissues along that x-ray path. When it generates an image from the x-ray data, the x-ray path with the missing information is shown as a white or a black line. The same phenomenon can be seen with any metallic object within the body, such as an artificial hip or spine fixation rods. If the scan on the right were converted to an STL file for 3D printing, the white lines would be 3D printed as well and the print would look as if sharp spikes were coming out of the mouth. Metallic objects also cause imaging artifact in MRIs. Metal on MRIs typically looks like a big black blob that obscures everything around it.
Figure 10: Two CT scans through the face and jaw. What is the difference between the two? 6. Reconstruction kernel Take a closer look at the two CT scans of the face (Figure 10). In particular, look closely at the muscle and fat tissue of the neck. The scan on the left shows the muscle and fat tissue as being somewhat noisy. It has a granular type of appearance. On the rightmost scan however, the muscle and fat tissues appear rather smooth. This is because the two scans use a different type of reconstruction kernel. Think of the reconstruction kernel as equivalent to a sharpening or blurring function in Photoshop. The sharper kernel on the left shows the edges of the bones very clearly at the expense of causing a speckled appearance of the muscles and fat. The softer kernel on the right shows the muscle and fat more accurately, at the expense of causing the bones to have a more indistinct edge. Sharp kernels are used to make it easier to find hairline fractures and other difficult to detect abnormalities in the bones. However, for 3D printing smoother reconstruction kernels are generally best. Reconstruction kernel is primarily a factor only in CT scans.
Figure 11: Zoomed image from Figure 10 of the angle of the jaw. Note how the sharp kernel has much more clearly defined bone edges, but also has a speckled, noisy appearance to the soft tissues.
Final thoughts So there you have it. In this tutorial we have gone over the main types of imaging modalities used for 3D printing (CT, and MRI), as well as six very important factors to consider with any type of imaging scan you are thinking about using for 3D printing. There is a saying when it comes to medical 3D printing: "garbage in, garbage out." No matter what your skill level or amount of available free time, if you start the 3D printing process with a problem-laden medical scan, you will encounter nothing but frustration and probably end up with a bad 3D model assuming you can make the model at all. Do yourself a favor and carefully evaluate your medical scan prior to sinking the time and energy into creating a 3D model from it. I hope you enjoyed this tutorial and found it helpful. If you liked this article please look see my next to tutorial on Creating a 3D Printable Medical Model in 30 Minutes Using Free Software: Osirix, Blender, and MeshMixer. Additionally, you may wish to check out the Tutorials section of the website. Also consider registering as a member. Registration is free and allows you to post questions and comments both for blog articles and in the discussion forums. Additionally, you can download free 3D printable models from the file library. Below are a few 3D models to download. If you wish to follow the latest medical 3D printing news, you can follow Embodi3D on various social media platforms. Thank you very much and happy 3D printing! Twitter: https://twitter.com/Embodi3D
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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!
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Figure 21: The download page for your newly created 3D printable skin STL file. Figure 22: Opening the file in Meshmixer for quality control checks. The file is error free and incredibly lifelike. It is ready for 3D printing. Thank you very much! I hope you enjoyed this tutorial. If you use this service to create 3D printable models, please consider sharing your models with the embodi3D community. Here is a detailed tutorial that I wrote on exactly how to do this. This community is built on medical 3D makers helping each other. Please share the models that you create!