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Terrie S

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Everything posted by Terrie S

  1. Version 1.0.0


    skull, anthropology, sex, estimation, male, female orbit, mandible, maxilla, angle, ramus, coronoid, conduct, inner, frontal, temporal, parietal, occipital, mastoid, process, foramen, foramina, incisor, molar, premolar, canine, teeth, tooth, dental, dentistry, head, zygomatic, arch, Compare traits between male and female skulls as described in: https://www.morphopasse.com/uploads/8/4/0/8/8408493/klales_nij_database_manual_v1_03.29.19_on_website.pdf. Models were generated from TCIA Head and Neck Cetuximab collection (0522c0251 (top) and 0522c0476 (bottom)), originally under National Institute of Justice grant #2014-DN-BX-K005. Vertebrae were removed during segmentation for access to inferior landmarks, so occipital condyles may be flattened. Models are arranged so they can be combined into one viewing space for comparison as shown--import both into Meshlab or 3D Slicer for further visualizations and/or measurements. Sketchfab viewer available here: https://skfb.ly/6UDFQ and can be embedded into Learning Management Systems.


  2. You don't need to create separate DICOM files for the skull and mandible. Depending on the overlap of the teeth, you can erase some of the segmentation in order to create gaps between the skull and mandible--if you are segmenting yourself. If you are uploading to democratiz3d, you can download the model and then either apply a plane cut in Meshmixer or if you want the actual articulations, you can "paint" the parts of the model to delete to create the necessary gaps, then repair the holes. Again, the difficulty would depend on whether you can separate the teeth on the maxilla from the mandible.
  3. Yes definitely! I would definitely like to see it applied more to unidentified remains.
  4. In case there is any interest here in the applications of radiology and imaging in forensic science, I wanted to share the link to the next conference in Albuquerque, New Mexico, May 14-16, 2020: https://www.isfri2020.com/. I definitely plan to go and will probably submit some kind of abstract about bones from CT supplementing reference collections for forensic anthropology. The abstract submission deadline is December 12. Terrie
  5. You can also use the EasyClip tool in 3DSlicer: import your CT volume and your 3D model (or even just your 3D model), then you can use the CT slices as planes to indicate where you want to cut--you can still rotate them if needed. You can save the half you want and even "undo" and save the other side (similar to Meshmixer). Slicer is especially handy if you have landmark coordinates and want to place a cut exactly at a specific coordinate, for example if you have oriented models and nasion is at x = 0--you can type this in to the appropriate slice view (red, yellow, green).
  6. Terrie S


    For tiffs, I like to open the stack in Fiji and save as NRRD--the NRRD opens much faster in Slicer. You can also set the spacing in Fiji for the NRRD to have the correct dimensions in Slicer.
  7. Version 1.0.0


    Skull and face models were generated in Mimics from a CT scan from TCIA (citations: http://doi.org/10.7937/K9/TCIA.2015.K0F5CGLI, https://doi.org/10.7717/peerj.2057, https://link.springer.com/article/10.1007%2Fs10278-013-9622-7) as reference models for visualizing skin-to-bone relationships for forensic craniofacial identification applications. See Figshare for additional project information. Face model was hollowed in Meshlab and extruded to this individual's minimum facial tissue depth (1.6 mm) with Meshmixer (tutorial). Cuts were made in 3D Slicer using the EasyClip plugin to cut at specific landmark coordinate values: skin was cut through x-coordinate of pronasale and right oculus anterius, z-coordinate of bony glabella; bone was cut through x-coordinates of left and right oculus anterius, z-coordinate of glabella, y-plane was adjusted until posterior to cheilion. For 3D printing, I rotated the model until the posterior surface was flat on the bed and added a raft to hold the supports (I left the raft on--see pic), but a custom platform could be added instead with Meshmixer or Tinkercad. I usually leave most of the supports attached to hold the skin layer in place, but remove supports from inside the nasal aperture and sometimes remove supports from the lateral side to reveal the infraorbital foramen. I don't have dual extrusion, but you could probably print the skin in one color and bone in another. The above pics show a print at 300 micron resolution. **Note that this file contains two merged models that can be printed together or separately--to separate, open in Meshlab, right-click the model name in the layer dialog and select "Split into Connected Components" and save each layer as a separate model.


  8. What software did you use to cut the model in the first place? If you use Edit-->Plane Cut in Meshmixer or the EasyClip module in 3DSlicer, it should fill the gap for you with a flat surface.
  9. I know! Anthropologists tend to use Morphosource, although I haven't seen clinically derived data there. As you might have gathered from the survey, there is much discussion in anthropology about the ethics of sharing/posting human skeletal data, especially with clinical CT data becoming more accessible. I have full and cut facial models from TCIA--would that be ok to post here? I have also built 3D html pages that allow interaction with the models that I'm trying to find/build a home for so that I could possibly also cross-reference to printable models here.
  10. For this particular survey, they are requesting only USA residents. The first survey was conducted in Portugal. If a 3rd survey comes out, I'll be sure to post the link for that as well.
  11. It is for anyone. I have mostly seen it shared in anthropology forums, but I think input from the biomedical community would be useful to the survey authors, esp regarding modern human data.
  12. Sharing for another anthropologist in case anybody here is interested in contributing their thoughts about sharing images and 3D models of human bones. This is the link to a survey called "Perspective on the dissemination of three-dimensional models of human skeletal remains online in the United States." https://docs.google.com/forms/d/e/1FAIpQLSc-6lvKD9oPu69YVf_aWrnZC2JFNrBred_DM8Xj3xqfauNveQ/viewform Thanks! Terrie
  13. There are some muscle sets on Sketcfab but I haven't found any that are downloadable. The ATOR site (http://arc-team-open-research.blogspot.com/2013/12/modeling-muscles-and-skin-in-blenders.html) has posts on many facial reconstruction resources, primarily using Blender. I can't find whether Cicero Moraes has provided links to muscle models. If you are not familiar with Blender, Meshmixer might be easier to add primitives and deform them to the appropriate shapes. I have found that you can also import a skull two times into Meshmixer so that you can use the sculpting tools to "pull" the muscles or even tissue depth pegs from one skull mesh while leaving an intact/visible skull mesh underneath.
  14. Wow! What printer was this printed with?
  15. Here is another tutorial on hollowing meshes, specifically head meshes to obtain a face shell, but I use this method to hollow out bones as well. Dr. Mike recently posted a great video tutorial on hollowing a head using Meshmixer: https://www.embodi3d.com/blogs/entry/359-how-to-create-a-hollow-shell-from-a-medical-stl-file-using-meshmixer/. I tend to go back and forth between Meshmixer and Meshlab for different functions to prep a print, but I like to use Meshlab for hollowing because it's quick and you can easily control how much "external" surface is selected, which is especially handy for models that have highly complex internal structures. Note that this workflow is also useful if you simply want a 3D model (for viewing/interacting in software, Sketchfab) of a smaller file size where you don't need the internal structures and/or you don't want to decimate the model to achieve a smaller file size. Here are the steps to hollow a head model in Meshlab. I will post screeshots below which you can also find in the Gallery, https://www.embodi3d.com/gallery/album/73-hollowing-skin-model-with-meshlab/. Step 1: Import a model into Meshlab. Go to Filters --> Color Creation and Processing --> Ambient Occlusion per Vertex. When the new box opens, check the box to select "Use GPU Acceleration" and click "Apply." The default settings are fine for a first step. Once you become comfortable with the workflow, you can play around with applying the light from different axes: "Lighting Direction" and "Directional Bias". Step 2: You will notice that your model is now colorized from light to dark, with "deeper" areas shaded darker. On the main toolbar, select the "transparent wireframe" view. You can now see the internal structures that are shaded completely black. Step 3: We can now use the shading values to select the areas we want to remove. Go to Filters --> Selection --> Select Faces by Vertex Quality. The shading values are stored in the Vertex Quality field of your 3D model, with values from 0 (black) to 1 (white), so we can use these values to select the dark (internal or deep) areas we want to remove. Step 4: When the Selection box opens up, slide the "Min Quality" value all the way to 0 (to the left). Check the "Preview" box so that you can see which areas are selected in red. Adjust the "Max Quality" slider left and right until you see that no external surfaces are selected in red. In the image below, you can see that the bottom edges of the eyelids are still red and some skin below the nostrils is also red. When you find a good value, click "Apply" and Close. **Depending on the model, it may be difficult to adjust the Max slider to a value that doesn't include parts of the eyelids or nose, but I will explain in Step 6 how you can recover these features. Instead of deleting the selection in Step 5, skip to Step 6. Step 5: Once you are happy with your selection from Step 4, you can delete everything selected in red by clicking the button shown in the image below. You can see that the model is now hollow, although there may be some disconnected pieces which we will remove in multiple cleaning steps. Step 6: If you think you may have selected some external features in Step 4 that you don't want deleted, instead of deleting (Step 5), you can move the selected (red) areas to another layer. Sometimes with overhanging eyelids or very deeply set eyes, these areas might have the same shading values as some internal structures and can't be excluded from the red. Go to Filters --> Mesh Layer --> Move selected faces to another layer (if your layer dialog is already open, you can right-click on the model name to access the Mesh Layer menu as well). The layer dialog will open up on the right and you will see the name of your original model as well as the new layer. Use the eye icons to toggle visibility. The Meshlab selection tools can be used to select the areas from the red you want to keep, then move them to another layer. Right-clicking on a mesh name will open the Mesh Layer menu, from which you can "Flatten Visible Layers"--the layers you want to keep can be kept visible and merged into a new mesh. Step 7: This image shows the view from the bottom. The head is empty except for that big flat piece at the top of the head. Step 8: As an initial cleaning step to remove small pieces, go to Filters --> Cleaning and Repairing --> Remove Isolated pieces (wrt Diameter). The default size works well, but you can adjust it up to 40% or so to remove larger pieces. This is a deletion function, so the floating pieces will be removed and gone forever! Try to not to adjust the size too high--we'll remove large pieces in step 9. Step 9: Step 8 will usually not remove large pieces, especially if you're being cautious and only remove small pieces. To remove larger pieces, go to Filters --> Mesh Layer --> Split in Connected Components. The pieces will drop into separate layers in the layer dialog box on the right, and they will be named CC 0, CC 1, etc. You don't want to apply this filter until you've removed small pieces, or you might end up crashing the program because there are too many pieces separating out! As mentioned above, the Mesh Layer menu can also be accessed by right-clicking on the mesh name in the right-hand layer dialog box. Step 10: The largest layer is usually CC 0. Toggle visibility to figure out which layer is the one you want. Left-click on it to highlight it in yellow and then export using File --> Export Mesh as... I prefer to fill holes (Inspector) and create internal walls (Extrude or Offset) in Meshmixer, so you can now import the hollowed model to Meshmixer to fix it up for printing if needed. You can also use the plane cut tool in Meshmixer to remove the flattened edge at the top of the skin model, or apply Ambient Occlusion again in only the z-direction (see Step 1--"Lighting Direction"). This can be an interative process depending on the complexity of the model you're trying to hollow, but it can save on printing time as well as $$ if you're only interested in the external surface. Play around with lighting directions to select the surfaces you want and as always, SAVE meshes along the way in case the program crashes or you make a mistake!
  16. Version 1.0.0


    ABD LYMPH 001 Bones - stl file processed thorax, abdomen, bone, 3dmodel, stl, lumbar, spine


  17. Version 1.0.0


    ABD LYMPH 001 Bones stl, ct with contrast, ct, axial, liver, spleen, muscle,


  18. Version 1.0.0


    skull test - stl file processed skull, bone, 3dmodel, stl, frontal, orbit


  19. Version 1.0.0


    ct with contrast, axial, head, neck, stl, muscle, septum


  20. Terrie S

    Teeth Micro CT

    I know! I just figured out how to create a dicom series in Slicer from the nrrd file. Mimics can read the dicom series, but I had to use Slicer to create the orthogonal views because that's where Mimics was getting hung up for me!
  21. I am running Slicer 4.5.0-1 with Windows 10. Is it possible you downloaded the wrong version for your system? Or I wonder if there's a security setting that is blocking the proper install..
  22. Terrie S

    Teeth Micro CT

    Hi Diogo, I have started working with microCT and can't get them in to Mimics. However, I have had great success with 3DSlicer. It's very slow with the tiff stack, but if I import the tiff stack to Fiji and save it as a .nrrd file, then Slicer reads it much faster. Terrie P.S. What version of Mimics are you using? I have 17 and 18 and they both seem to have a hard time with tiff stacks.
  23. 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?
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