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Everything posted by tsehrhardt

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


    This is a skull of a 43yo male that I modeled from TCIA from the QIN-HEADNECK collection, which is available under a Creative Commons Attribution 3.0 Unported License. I modeled it in Mimics and cleaned it up (as best I could) for printing with Meshlab and Meshmixer. I have printed it on a Robo3D. To prep for printing, I used the Plane Cut tool in Meshmixer to slice posterior to the mandible, making a front and back half. Then I cut the front half down the midsagittal line. I used white MakerBot PLA, 200 micron resolution, outer perimeter print speed of 20 mm/s, 3 perimeter shells, 25% infill. I have printed the two halves of the front but not the back yet!


  3. Thanks Dr. Mike! I'm fine with making my models freely available, but I don't like the idea of somebody trying to sell models that I made! I was curious to know how people decide whether to sell, which CC license to choose, or whether to even bother with licensing. I'm working on getting some models up!
  4. How should I license models that I generate from http://www.cancerimagingarchive.net/?Most of the data is available under CCBY 3.0: http://creativecommons.org/licenses/by/3.0/, but can I make models that I generate CCBY-NC?
  5. If laser scans will work for you, this site: https://osteoteaching.wordpress.com/ has scans of fetal bones at various ages. You can request access to their models.
  6. I thought I'd do a quick post on why anthropologists need 3D printed bones in case anybody's interested. Real bones are expensive! Although we have real skeletons for teaching osteology, we are often limited to teaching the identification and examination of whole bones. For both forensic and archaeological contexts, osteologists need to be able to identify bones that are incomplete, scavenged, weathered, burned, or damaged in some other way. In such situations, the first question is whether or not the bone is human. In order to teach this advanced level of identification, we need bone fragments. We can't go around smashing bones to create the fragments, and if you're at an institution without a large archaeological collection of bones, 3D printing, especially of CT scans, can provide some fragments. Because CT scans contain internal structures (as opposed to laser scans of bones), we can digitally slice long bones to create cross-sections or cut models in ways that bone frequently fragments. We can potentially simulate trauma as well, although scans of bones with trauma or pathology would be even better. I've recently started working with the Virtual Curation Laboratory (https://vcuarchaeolo....wordpress.com/) to 3D print bone fragments, whole bones, and bones with pathology or trauma. All of these things can be used to create "case studies" of single individuals or commingled individuals as well, and since they're plastic, we would have no problem using them outside for field exercises and excavations. Having age and/or sex is also important since higher quality 3D printed bones could be analyzed for those traits as well. I've added some pictures from a recent conference at VCU where we presented our preliminary work and displayed a few printed bones. Some of them still have some support structures, but you can see what we're going for. Thanks for reading!
  7. From the album: 3D Bones for Anthropology

    Lumbar vertebrae segmented from a CT scan.
  8. From the album: 3D Bones for Anthropology

    Digitally sliced CT femur to provide fragments and cross-sections for advanced identification.
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