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  2. This tutorial is based on course I taught at the 2018 RSNA meeting in Chicago, Illinois. It is shared here free to the public. In this tutorial, we walk though how to convert a CT scan of the face into a 3D printable file, ready to be sent to a 3D printer. The patient had a gunshot wound to the face. We use only free or open-source software and services for this tutorial. There are two parts to this tutorial: Part 1: How to use free desktop software to create your model Part 2: Use embodi3D's free democratiz3D service to automatically create your model Key Takeaway from this Tutorial: You can make high quality 3D printable models from medical imaging scans using FREE software and services, and it is surprisingly EASY. A note on the FDA (for USA people): There is a lot of confusion about whether expensive, FDA-approved software must be used for medically-related 3D printing in the United States. The FDA recently clarified its stance on the issue.* If you are not using these models for patient-care purposes, this does not concern you. If you have questions please see the FDA website. If you are a DOCTOR, you can use whatever software you think is appropriate for your circumstances under your practice of medicine. If you are a COMPANY, selling 3D printed models for diagnostic use, you need FDA-approved software. If you are designing implants or surgical cutting guides, those are medical devices. Seek FDA feedback. *Kiarashi, N. FDA Current Practices and Regulations, FDA/CDRH-RSNA SIG Meeting on 3D Printed Patient- Specific Anatomic Models. Available at https://www.fda.gov/downloads/MedicalDevices/NewsEvents/WorkshopsConferences/UCM575723.pdf Accessed 11/1/2017. Part 1: Using Desktop software 3D Slicer and Meshmixer Step 1: Download the scan file and required software To start, download the starting CT scan file at the link below. Also, install 3D Slicer (slicer.org) and Meshmixer (meshmixer.com). Step 2: Open 3D Slicer Open Slicer. Drag and drop the scan file gunshot to face.nrrd onto the slicer window. The scan should open in a 4 panel view as shown below in Figure 1. Figure 1: The 4 up view. If your view does not look like this, you can set the 4 up view to display by clicking Four-Up from the View menu, as shown in Figure 2 Figure 2: Choosing the four-up view Step 3: Learning to control the interface Slicer has basic interface controls. Try them out and become accustomed to how the interface works. Note how the patient has injuries from gunshot wound to the face. Left mouse button – Window/Level Right mouse button – Zoom Scroll wheel – Scroll through stack Middle mouse button -- Pan Step 4: Blur the image The CT scan was created using a bone reconstruction kernel. Basically this is an image-enhancement algorithm that makes edges more prominent, which makes detection of fractures easier to see by the human eye. While making fracture detection easier, this algorithm does unnaturally alter the image and makes it appear more "speckled" Figure 3: Noisy, "speckled" appearance of the scan on close up view To fix this issue, we will slightly blur the image. Select Gaussian Blur Image Filter as shown below in Figure 4 Figure 4: Choosing the Gaussian Blur Image Filter Set up the Gaussian Blur parameters. Set Sigma = 1.0. Set the input volume to be Gunshot to face. Create a new output volume called "Gaussian volume" as shown in Figure 5. Figure 5: Setting up the Gaussian parameters When ready, click Apply, as shown in Figure 6. You will notice that the scan becomes slightly blurred. Figure 6: Click Apply to start the Gaussian Blur Image filter. Step 5: Create a 3D model using Grayscale Model Maker Open the Grayscale Model Maker Module as shown below in Figure 7. Figure 7: Opening the Grayscale Model Maker Set up the Grayscale Model Maker parameters. Select the Gaussian volume as the input volume, as shown in Figure 8. Figure 8: Choosing the input volume in Grayscale Model Maker Next, set the output geometry to be a new model called "gunshot model." Set the other parameters: Threshold = 200, smooth 15, Decimate 0.5, Split normals unchecked as shown in Figure 9. Figure 9: Grayscale Model maker parameters When done, click Apply. A new model should be created and will be shown in the upper right hand panel, as shown in Figure 10. Figure 10: The new model Step 6: Save the model as an STL file To start saving the model, click the save button in the upper left of the Slicer window as shown in Figure 11. Figure 11: The save button Be sure that only the 3D model, gunshot model.vtk is selected. Uncheck everything else, as shown in Figure 12. Figure 12: The Save dialog. Check the vtk file Make sure the format of the 3D model is STL as shown in Figure 13. Specify the folder to save into, as shown in Figure 14. Figure 13: Specify the file type Figure 14: Specify the folder to save into within the Save dialog. Step 7: Open the file in Meshmixer for cleanup Open Meshmixer. Drag and drop the newly created STL file on the meshmixer window. The file will open and the model will be displayed as in Figure 15. Figure 15: open the STL file in Meshmixer Get accustomed to the Meshmixer interface as shown in Figure 16. A 3 button mouse is very helpful. Figure 16: Controlling the Meshmixer user interface Choose the Select tool. In is the arrow button along the left of the window. Figure 17: The select tool Click on a portion of the model. The selected portion will turn orange, as shown in Figure 18. Figure 18: Selected areas turn orange. Expand the small selected area to all mesh connected to it. Use Select->Modify->Expand to Connected, or hit the E key. The entire model should turn orange. See Figure 19. Figure 19: Expanding the selection to all connected mesh. Next, Invert the selection so that only disconneced, unwanted mesh is selected. Do this with Select->Modify->Invert, or hit the I key as shown in Figure 20. Figure 20: Inverting the selection At this point, only the unwanted, disconnected mesh should be selected in orange. Delete the unwanted mesh using Select->Edit->Discard, or use the X or DELETE key as shown in Figure 21. At this point, only the desired mesh should remain. Figure 21: Deleting unwanted mesh. Step 8: Run the Inspector tool The Inspector tool will automatically fix most errors in the model mesh. To open it, choose Analysis->Inspector as shown in Figure 22. Figure 22: The Inspector tool The Inspector will identify all of the errors in the mesh. To automatically correct these mesh errors, click Auto Repair All as shown in Figure 23. Figure 23: Auto Repairing using Inspector The Inspector will usually fix all or most errors. In this case however, there is a large hole at the edge of the model where the border of the scan zone was. The Inspector doesn't know how to close it. This is shown in Figure 24. Figure 24: The inspect could not fix 1 mesh error Step 9: Close the remaining hole with manual bridges Using the select tool, select a zone of mesh near the open edge. The Select tool is opened with the arrow button along the left. Choose a brush size -- 40 is good -- as shown in Figure 25. Figure 25: Choosing the select tool The mesh should turn orange when selected, as shown in Figure 26. Figure 26: Selected mesh turns orange. Next, rotate the model and select a zone of mesh opposite the edge from the first selected zone, as shown in Figure 27. Figure 27: Selecting mesh opposite the defect. Once both edges are selected, create a bridge of mesh spanning the two selected areas using the Bridge operation: Select->Edit->Bridge, or CTRL-B, as shown in Figure 28. Figure 28: The bridge tool There should now be a bridge of orange mesh spanning the gap. Click Accept, as shown in Figure 29. Figure 29: The new bridge. Be sure to click Accept. Next, repeat the bridge on the opposite side of the skull. Be sure to deselect the previously selected mesh before working on the opposite side, as shown in Figure 30. Figure 30: Creating a second bridge on the opposite side. Step 10: Rerun the Inspector Rerun the Inspector tool, as shown in Figure 31. Now with the bridges to "help" Meshmixer to know how to fill in the hole, it should succeed. If it fails, create more bridges and try again. Figure 31: Rerun the Inspector tool Next, export your file to STL. ' Figure 32: Export to STL Step 11: 3D print your file! Your STL file is now ready to be sent to the 3D printer of your choice. Figure 33 shows the model after printing. Figure 33: The final print Part 2: Using the democratiz3D service on embodi3d.com democratiz3D automatically converts scans to 3D printable models. It automates the mesh cleanup process and saves time. The service is free for general bone model creation. Step 1: Register Register for a free embodi3D account. The process takes only a minute. You need an account for your processed files to be saved to. Step 2: Upload the NRRD source scan to democratiz3D. From anywhere in the site, click democratiz3D-> Launch App Figure 34: Launching the democratiz3D app. Fill out basic information about your file. That information will be copied to your generated STL file, as shown in Figure 35. Figure 35: Entering basic file information Make sure democratiz3D processing is on. Choose an operation to convert your model. Set threshold to 200, as shown in Figure 36. Figure 36: Operation, threshold, and quality parameters. Click Submit! In 10 to 15 minutes your model should be done. You will receive an email notification. The completed model file will be saved under your account. Download the file and send it to your printer of choice! Figure 37; The final democratiz3D file, ready for download. That's it! I hope this tutorial was helpful to you. If you liked it, please rate it positively. If you want to learn more about democratiz3D, Meshmixer, or Slicer, please see our tutorials page. It has a lot of wonderful resources. Happy 3D printing!
  3. valchanov

    Project Fancy Skull

    I decided to give my Prusa MK3 printer a real challenge, so I cut my best skull model, I added some slots for neodymium magnets and I started to print the parts. I'm done with the half of them and I'll update my post when I'm done.
  4. 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!
  5. Top Orbital and Skull 3D Model STL Files on embodi3D® In our day-to-day lives, we rely on vision more than any of the other four senses, so it only makes sense that human anatomy has adapted to include several features which keep our eyes safe: tear ducts, eyelids, and of course the orbital bone. The orbit (also known as the "eye socket") provides a rigid form of support and protection for some of the most sensitive parts of the eye including the central retinal artery, maeula, retina, choroid, and sclera. The orbit has such complex anatomical features that modeling can prove difficult, and in many instances, the finer features of the orbital bone have been simply been averaged out. The orbital structure isn't one bone, but seven: the frontal, lacrimal, ethmoid, zygomatic, maxillary, and palatine, and sphenoid bones. Can you think of any part of the human body where seven bones converge to fulfill a singular purpose? In recognition of this phenomenal feature of the human anatomy (and one of the most recognizable parts of the human skull), this week's embodi3D® Top Uploads articles, we are featuring several standout uploads — all of which can be used to create an orbital and skull 3D model. As detailed in the scholarly article "Clinical application of three-dimensional printing technology in craniofacial plastic surgery" 3D printing techniques are being used in craniofacial surgeries and especially in reconstruction procedures the require complex modeling. Using the latest 3D printing technology and the STL files converted using democratiz3D®, the contralateral orbit can serve as a point of reference for those in the medical field since the ipsilateral structures taken with a CT scan can be easily converted into an STL file and then fed to a 3D printer. These technologies improve patient consultations, increase the quality of diagnostic information while also helping to improve the planning stage of the surgical process. During surgery, a 3D-printed model of the orbital can be used to orient surgical staff and serve as a guide for surgical resectioning procedures. While these files are available for free on the website, you must register with embodi3D® before you can begin uploading and converting your own CT scans into STL files as well as downloading and 3D printing anatomical models from other users. Every day the collection of anatomical models grows on the embodi3D® website. This is but one of the many ways embodi3D® is seeking to revolutionize medical practices. #1. An Awesome Model of the Orbit's Acute Anatomy The orbits are conical structures dividing the upper facial skeleton from the middle face and surround the organs of vision. Seven bones conjoin to form the orbital structure as we can see in the example below. #2. A 3D Model of the Orbit's Surface in STL Format This excellent 3D model of embodi3D® shows the superficial bony margin of the orbit, which is rectangular with rounded corners. The margin is discontinuous at the lacrimal fossa. The supraorbital notch (seen in the image below) is within the supraorbital rim and is closed to form the supraorbital foramen in 25% of individuals. The supratrochlear notch is medial to the supraorbital notch. #3. A CT Scan of an Orbital Floor Fracture Hisham published this excellent ct scan on embodi3D®. Direct fractures of the orbital floor can extend from fractures of the inferior orbital rim. Indications for repair of the orbital floor in these cases are the same as those for indirect (blowout) fractures. Indirect fractures of the orbital floor are not associated with fracture of the inferior orbital rim. #4. A 3D Model of an Orbital Fracture CT scans with coronal or sagittal views and 3D models help guide treatment. They allow evaluation of fracture size and extraocular muscle relationships, providing information that can be used to help predict enophthalmos and muscle entrapment. #5. 3D Model Showing an Orbital Fracture Dropbear upload this excellent example of a right orbit fracture. #6. An Orbit 3D Model (Printable) Showing Fibrous Dysplasia (FD) for Surgical Demonstration The FD is a benign slowly progressive disorder of bone, where normal cancellous bone is replaced by fibrous tissue and immature woven bone. This entity constitutes about 2.5 % of all bone tumors. References Choi, J. W., & Kim, N. (2015). Clinical application of three-dimensional printing technology in craniofacial plastic surgery. Archives of plastic surgery, 42(3), 267. Bibby, K., & McFadzean, R. (1994). Fibrous dysplasia of the orbit. British journal of ophthalmology, 78(4), 266-270.
  6. Wilmer E.

    Segmentation of a foot MRI scan

    Hello Mike! I have done several tests using Fast GrowCut and I have obtained an .stl file but effectively with contours necessarily far from the precision of a bone, so it is necessary to soften. You comment that you use a MatLab code to perform the smoothing of the bones, could you send us the MatLab code that you use to soften the volume of the 3D model obtained from MRI. Thank you very much in advance.
  7. imagingcentral

    How to Easily Tell the Difference Between MRI and CT Scan

    Great blog! Its the easiest way in which someone must have explained the difference between CT scan and MRI scan. Thanks for sharing such a wonderful blog, most of the people would like it. I would also like to know the difference between Ultrasound, MRI, and CT scan.
  8. 3D-Printed Models of the Spine In this week's post, we want to share with you some of the best 3D-printed models of the spine uploaded by embodi3D® members. We will explore features of this unique anatomy and some of the main uses of 3D printing as it relates to the spine . To convert your own scans and download and 3D-print STL files from other users, all you have to do is register with embodi3D®. It's quick, easy, and costs absolutely nothing to join. Anatomical models have applications in clinical training and surgical planning as well as in medical imaging research. The Wall Street Journal recently ran an article to discuss the many ways 3D printing is changing the face of healthcare. The article also highlighted a case where a 3D model of a pelvis was used to plan a surgical operation on a young female patient. A full-scale, anatomical model of a human lumbar vertebra created with embodi3D®. In terms of clinical applications, the physical interaction with models facilitates learning anatomy and how different structures interact spatially in the body. Simulation-based training with anatomical models reduces the risks of surgical interventions, which are directly linked to patient experience and healthcare costs. Surgical planning 3D printing (3DP) is most frequently utilised in spinal surgery in the pre-operative planning stage. A full-scale, stereoscopic understanding of the pathology allows for more detailed planning and simulation of the procedure. Assessing complex pathologies on a model overcomes many of the issues associated with traditional 3D imaging, such as the lack of realistic anatomical representation and the associated complexity of computer-related skills and techniques. Summary of 3DP in spinal surgery planning 1999 D’Urso et al. (4) Osteogenesis imperfecta, cervicothoracic deformity, lumbar spinal fusion, cervical osteoblastoma 1999 D’Urso et al. (5) Craniofacial, maxillofacial and skull base cervical spine pathologies. 2005 D’Urso et al. (6) Complex spinal disorders. 2007 Guarino et al. (7) Multiplane spinal and pelvic deformities. 2007 Izatt et al. (8) Deformities, spinal tumours. 2007 Paiva et al. (9) Cervical Ewing Sarcoma. 2008 Mizutani et al. (10)Rheumatoid cervical spine. 2009 Madrazo et al. (11)Degenerative cervical disease. 2010 Mao et al. (12) Kyphoscoliosis, congenital malformations, neuromuscular disease. 2010 Yang et al. (13) Kyphoscoliosis. 2011 Wu et al.(14) Severe congenital scoliosis. 2013 Toyoda et al. (15) Atlantoaxial subluxation. 2014 Yang et al. (16) Atlantoaxial instability. 2015 Li et al.(17) Revision lumbar discectomy. 2015 Kim et al. (18)Thoracic tumours. 2015 Sugimoto et al. (19) Congenital kyphosis. 2015 Yang et al. (20) Adolescent idiopathic scoliosis. 2016 Goel et al. (21) Craniovertebral junction anomalies. 2016 Wang et al. (22) Congenital scoliosis, atlas neoplasm, atlantoaxial dislocation. 2016 Xiao et al. (23) Cervical bone tumours. 2017 Guo et al. (24) Cervical spine diseases. Imaging Anatomy There are 33 spinal vertebrae, which comprise two components: A cylindrical ventral bone mass, which is the vertebral body,and the dorsal arch. 7 cervical, 12 thoracic, 5 lumbar bodies • 5 fused elements form the sacrum • 4-5 irregular ossicles form the coccyx Arch • 2 pedicles, 2 laminae, 7 processes (1 spinous, 4 articular, 2 transverse) • Pedicles attach to the dorsolateral aspect of the body • Pedicles unite with a pair of arched flat laminae • Lamina capped by dorsal projection called the spinous process • Transverse processes arise from the sides of the arches The two articular processes (zygapophyses) are diarthrodial joints. • (1) Superior process bearing a facet with the surface directed dorsally • (2) Inferior process bearing a facet with the surface directed ventrally Pars interarticularis is the part of the arch that lies between the superior and inferior articular facets of all subatlantal movable elements. The pars are positioned to receive biomechanical stresses of translational forces displacing superior facets ventrally, whereas inferior facets remain attached to dorsal arch (spondylolysis). C2 exhibits a unique anterior relation between the superior facet and the posteriorly placed inferior facet. This relationship leads to an elongated C2 pars interarticularis, which is the site of the hangman's fracture. 1. An Exceptional Human Lumbar Vertebra Converted from a CT Scan with embodi3D® An anatomically accurate full-size human lumbar vertebra created from a real CT scan. The lumbar vertebral bodies are large, wide and thick, and lack a transverse foramen or costal articular facets. The pedicles are strong and directed posteriorly. The superior articular processes are directed dorsomedially and almost face each other. The inferior articular processes are directed anteriorly and laterally. 2. Create Your Own Lumbar Spine Model with a 3D-Printable STL File A 3D printable STL file and medical model of the lumbar spine was generated from real CT scan data and is thus anatomically accurate as it comes from a real person. It shows the detailed anatomy of the lumbar (lower back) spine, including the vertebral bodies, facets, neural foramina and spinous proceses. 3. A 3D Printer-Ready Spinal Column in Amazing Detail Thoracic bodies are heart-shaped and increase in size from superior to inferior. Facets are present for rib articulation and the laminae are broad and thick. Spinous processes are long, directed obliquely caudally. Superior facets are thin and directed posteriorly. The T1 vertebral body shows a complete facet for the capitulum of the first rib, and an inferior demifacet for capitulum of second rib. The T12 body has transitional anatomy, and resembles the upper lumbar bodies with the inferior facet directed more laterally 4. Create a 3D-Printed Model of Lumbar Vertebrae The lumbar spine is formed by 5 lumbar vertebrae labelled L1-L5 and the intervening discs. Its main function is to provide stability and permits movement. The lumbar vertebral body is formed of 3 parts : Body, arch and spinal processes. The body of the lumbar vertebrae is large, its transverse diameter is larger than is AP diameter, and is more thickened anteriorly. The arch of the lumbar vertebra on the other hand is formed of pedicle, a strong structure that is projected from the back of the upper part of the vertebrae, and lamina which forms the posterior portion of the arch. Another well reported benefit of 3DP models is improved patient education. A physical model is much easier for a patient to understand than complex MRI and CT scans. 5. An NRRD File Showing the Whole Spine — See the Future of Medical 3D Printing A Whole Spine (Dorsal-Lumbar-Sacral) and Aorta NRRD file from CT Scan for Medical 3D Printing As 3DP technology continues to become cheaper, faster and more accurate, its use in the setting of spinal surgery is likely to become routine, and in a greater number of procedures. 6. Download a 3D-Printable Thoracic Spine with Prevalent Scoliosis A 3D printable STL file contains a model of the thoracic spine derived from a CT. The spine has significant scoliosis. In a recent embodi3D® article, we touched on the topic of how medical 3D printing is being used to plan spinal surgeries, such as in correcting the spinal curvature in scoliosis patients. Scoliosis is considered to be present when there is a coronal plane curvature of the spine measuring at least 10°. However, treatment is not generally instituted unless the curvature is > 20-25°. The curvature may be balanced (returning to midline) or unbalanced. The vertebrae at the ends of the curve are designated the terminal (or end) vertebrae, while the apical vertebra is at the curve apex. Curvatures are described by the side to which they deviate. A dextroscoliosis is convex to the right, with its apex to the right of midline. A levoscoliosis is convex to the left, with its apex to the left of midline. Curvatures can be categorized as flexible (normalizing with lateral bending toward the side of the curve) or structural (failing to correct). Most scoliotic curvatures are associated with abnormal curvature in the sagittal plane. These are described as kyphosis (apex dorsal) or lordosis (apex ventral). Morphology of the Curvature Scoliosis due to fracture, congenital anomaly, or infection typically has an angular configuration. Other causes of scoliosis tend to have a smooth curvature. Scoliosis most commonly involves the thoracic spine, followed by the thoracolumbar spine. In the past, curves were categorized as primary and secondary (compensatory), but it is often difficult to make the distinction and so these designations are no longer commonly used. Measurement of Scoliosis The Cobb method is most commonly used to measure scoliosis. The vertebrae at each end of the curve (the terminal vertebrae) are chosen. These are the endplates with the greatest deviation from the horizontal. The curvature is the angle between a line drawn along the superior endplate of superior terminal vertebra and a line along the inferior endplate of the inferior terminal vertebra. In severe curvatures, the endplates are often difficult to see. In that case, the inferior cortex of the pedicle can be used as the landmark for making the measurement. If measurements are made on hard copy radiographs, it is usually necessary to draw lines perpendicular to the endplates and measure the angle between the perpendicular lines. Scoliosis is almost always associated with abnormal curvature in the sagittal plane. The most common finding is loss of normal thoracic kyphosis. The Cobb method can be used to determine sagittal plane deformity. Rotational deformity is often present but can only be grossly assessed on radiographs. It can be measured on CT scan by superimposing the apical and terminal vertebrae. Normally, the T1 vertebra is centered over the L5 vertebra in both the coronal and sagittal planes. Coronal or sagittal plane imbalance can be measured as the horizontal distance between the center of the L5 vertebral body and a plumb line drawn through the center of the T1 vertebral body. 7. Dr. Mike's Excellent Tutorial on Converting CT Scans to 3D Printer-Ready STL Models An excellent tutorial of A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes which allows you to follow along with the tutorial. Included is an anonymized chest abdomen pelvis CT in both DICOM and NRRD formats. 8. An MRI of a Lumbar Spine with Disc Bulge at L4-L5 and L5-S1 The term bulge is used to describe a generalized extension greater than 50% of the circumference of the disc tissues, extending a short distance (< 3 mm) beyond the edges of the adjacent apophyses. A bulge is not a herniation, although 1 portion of the disc may be bulging and another portion of the disc may herniate. A bulge is often a normal variant, particularly in children in whom all normal discs appear to extend slightly beyond the vertebral body margin. Bulge may also be associated with disc degeneration or may occur as a response to axial loading or angular motion with ligamentous laxity. Occasionally, a bulge in 1 plane is really a central subligamentous disc herniation in another plane. Asymmetric bulging of disc tissue greater than 25% of the disc circumference may be seen as an adaptation to adjacent deformity, and is not considered a form of herniation. Herniations are a localized displacement of disc material beyond the limits of the intervertebral disc space in any direction. 9. Using 3D Modeling to Understand the Severity of a Scoliosis Case A 3D model of a severe scoliosis. CT scan should always be performed with reformatted images. Angled reformatted images and 3D reformations are often useful in assessment of severe curvatures. Some physicians find it useful to obtain both SPECT and CT images of degenerative scoliosis. An area of arthritis on CT scan, which shows increased uptake on SPECT, is probably a pain generator. MR can be difficult to interpret when scoliosis is severe. Angled axial images should be obtained based on both sagittal and coronal scout images and angled along the plane of the vertebral endplate on both scouts. Sagittal images should be angled along each segment of the curvature. The coronal plane is often the most useful for evaluating bony anomalies, spondylolysis, or degeneration of the discs and facet joints. References 1. Bücking, T. M., Hill, E. R., Robertson, J. L., Maneas, E., Plumb, A. A., & Nikitichev, D. I. (2017). From medical imaging data to 3D printed anatomical models. PloS one, 12(5), e0178540. 2. Wilcox, B., Mobbs, R. J., Wu, A. M., & Phan, K. (2017). Systematic review of 3D printing in spinal surgery: the current state of play. Journal of Spine Surgery, 3(3), 433. 3. Ross, J. S., Moore, K. R., Bryson Borg, M. D., Julia Crim, M. D., & Shah, L. M. (2010). Diagnostic imaging: spine: published by Amirsys®. Lippincott Williams & Wilkins, Baltimore. 4. D'Urso PS, Askin G, Earwaker JS, et al. Spinal biomodeling.Spine (Phila Pa 1976) 1999;24:1247-51. 10.1097/00007632-199906150-00013. 5. D'Urso PS, Barker TM, Earwaker WJ, et al. Stereolithographic biomodelling in cranio-maxillofacial surgery: a prospective trial. J Craniomaxillofac Surg 1999;27:30-7. 10.1016/S1010-5182(99)80007-9 6. D'Urso PS, Williamson OD, Thompson RG. Biomodeling as an aid to spinal instrumentation. Spine (Phila Pa 1976) 2005;30:2841-5. 10.1097/01.brs.0000190886.56895.3d 7. Guarino J, Tennyson S, McCain G, et al. Rapid prototyping technology for surgeries of the pediatric spine and pelvis: benefits analysis. J Pediatr Orthop 2007;27:955-60. 10.1097/bpo.0b013e3181594ced 8. Izatt MT, Thorpe PL, Thompson RG, et al. The use of physical biomodelling in complex spinal surgery. Eur Spine J 2007;16:1507-18. 10.1007/s00586-006-0289-3 9. Paiva WS, Amorim R, Bezerra DA, et al. Aplication of the stereolithography technique in complex spine surgery. Arq Neuropsiquiatr 2007;65:443-5. 10.1590/S0004-282X2007000300015 10. Mizutani J, Matsubara T, Fukuoka M, et al. Application of full-scale three-dimensional models in patients with rheumatoid cervical spine. Eur Spine J 2008;17:644-9. 10.1007/s00586-008-0611-3 11. Mao K, Wang Y, Xiao S, et al. Clinical application of computer-designed polystyrene models in complex severe spinal deformities: a pilot study. Eur Spine J 2010;19:797-802. 10.1007/s00586-010-1359-0 12. Yang JC, Ma XY, Lin J, et al. Personalised modified osteotomy using computer-aided design-rapid prototyping to correct thoracic deformities. Int Orthop 2011;35:1827-32. 10.1007/s00264-010-1155-9 13. Wu ZX, Huang LY, Sang HX, et al. Accuracy and safety assessment of pedicle screw placement using the rapid prototyping technique in severe congenital scoliosis. J Spinal Disord Tech2011;24:444-50. 10.1097/BSD.0b013e318201be2a 14. Toyoda K, Urasaki E, Yamakawa Y. Novel approach for the efficient use of a full-scale, 3-dimensional model for cervical posterior fixation: a technical case report. Spine (Phila Pa 1976)2013;38:E1357-60. 10.1097/BRS.0b013e3182a1f1bd 15. Yang JC, Ma XY, Xia H, et al. Clinical application of computer-aided design-rapid prototyping in C1-C2 operation techniques for complex atlantoaxial instability. J Spinal Disord Tech 2014;27:E143-50. 16. Li C, Yang M, Xie Y, et al. Application of the polystyrene model made by 3-D printing rapid prototyping technology for operation planning in revision lumbar discectomy. J Orthop Sci 2015;20:475-80. 10.1007/s00776-015-0706-8 17. Kim MP, Ta AH, Ellsworth WA, 4th, et al. Three dimensional model for surgical planning in resection of thoracic tumors. Int J Surg Case Rep 2015;16:127-9. 10.1016/j.ijscr.2015.09.037 18. Sugimoto Y, Tanaka M, Nakahara R, et al. Surgical treatment for congenital kyphosis correction using both spinal navigation and a 3-dimensional model. Acta Med Okayama 2012;66:499-502. 19. Yang M, Li C, Li Y, et al. Application of 3D rapid prototyping technology in posterior corrective surgery for Lenke 1 adolescent idiopathic scoliosis patients. Medicine (Baltimore) 2015;94:e582. 10.1097/MD.0000000000000582 20. Goel A, Jankharia B, Shah A, et al. Three-dimensional models: an emerging investigational revolution for craniovertebral junction surgery. J Neurosurg Spine 2016;25:740-4. 10.3171/2016.4.SPINE151268 21. Wang YT, Yang XJ, Yan B, et al. Clinical application of three-dimensional printing in the personalized treatment of complex spinal disorders. Chin J Traumatol 2016;19:31-4. 10.1016/j.cjtee.2015.09.009 22. Xiao JR, Huang WD, Yang XH, et al. En Bloc Resection of Primary Malignant Bone Tumor in the Cervical Spine Based on 3-Dimensional Printing Technology. Orthop Surg 2016;8:171-8. 10.1111/os.12234 23. Guo F, Dai J, Zhang J, et al. Individualized 3D printing navigation template for pedicle screw fixation in upper cervical spine. PLoS One 2017;12:e0171509. 10.1371/journal.pone.0171509
  9. Dear Dr Mike, We used this workflow in our facility to make a tibial fracture model. By doing so, printing time was reduced from 26hr to 13hr (using uPrint SE plus) without loosing details. Thank you for the great tutorial and educational materials, Itamar
  10. This week we would like to share the most downloaded 3D models and resources from our site. These may be good resources for educational purposes as they demonstrate the detailed anatomy of the human body. We have a list of the top human heart STL files and another list of free human anatomy STL files. The 1st place is for Dr. Mike’s tutorial on how to create 3D printable bone models. 3D printing is an evolving technology that enables the creation of unique organic and inorganic structures with high precision. In medicine, this technology has demonstrated potential uses for both patient treatment and education as well as in clinical practice. Learning how to create 3D models and taking this technology as a great advantage for medical education and practice is important for all of us as physicians and this tutorial makes it easy to learn. The list also includes other great 3D models, like skull and heart. Let’s then take a look into this ten awesome models. Don’t forget to register in order to download the models, you can do it by clicking here. 1. 2.952 Downloads An improved tutorial that shows you how to create 3D printable bone models even more easily and for free on any operating system. Try it! https://www.embodi3d.com/files/file/115-file-pack-for-3d-printing-with-osirix-tutorial/ 2. 913 Downloads 3D printable model of a human heart was generated from a contrast enhanced CT scan. https://www.embodi3d.com/files/file/64-3d-printable-human-heart-model-with-stackable-slices/ 3. 893 Downloads 3D printable brain is from an MRI scan of a 24 year old human female. https://www.embodi3d.com/files/file/30-human-brain-from-mri-scan/ 4. 714 Downloads This full-size skull with web-like texture was created from a real CT scan. https://www.embodi3d.com/files/file/26-3d-printable-lace-skull-full-size/ 5. 648 Downloads 3D printable model of stroke. https://www.embodi3d.com/files/file/6378-3d-printing-brain-model-with-stroke-stl-files-available-for-download/ 6. 609 Downloads Skull with web-like texture was created from a real CT scan. https://www.embodi3d.com/files/file/25-3d-printable-lace-skull-half-size/ 7. 422 Downloads Anatomically accurate heart and pulmonary artery tree was extracted from a CT angiogram. https://www.embodi3d.com/files/file/59-heart-and-pulmonary-artery-tree-from-ct-angiogram/ 8. 396 Downloads Tutorial: "3D Printing of Bones from CT Scans: A Tutorial on Quickly Correcting Extensive Mesh Errors using Blender and MeshMixer” https://www.embodi3d.com/files/file/89-tutorial-file-pack/ 9. 392 Downloads Tutorial A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes https://www.embodi3d.com/files/file/6441-imag3d-tutorial-support-files-dicom-and-nrrd/ 10. 373 Downloads Bony anatomy and skin surface of the L and R feet. https://www.embodi3d.com/files/file/52-feet-from-ct-scan/ References 1. Colaco, M., Igel, D. A., & Atala, A. (2018). The potential of 3D printing in urological research and patient care. Nature Reviews Urology.
  11. michaelmplatt

    Segmentation of a foot MRI scan

    I haven't checked it out recently but I will, thank you! I'm a big fan of 3DSlicer. I'll let you know if I have any questions.
  12. Andras Lasso

    Segmentation of a foot MRI scan

    Have you tried 3D Slicer recently? We've completely reworked segmentation by adding a new Segment Editor, which should be comparable and in a couple of things much better than commercial software (not just in price, flexibility and extensibility but in capabilities as well). Segment editor supports overlapping segments, advanced masking, real-time slice/3D view synchronization, hugely improved Fast GrowCut ("Grow from seeds"), contour interpolation, hollowing, smoothing, cutting, Boolean operations, input volume switching, editing on oblique slices, etc. You can find a couple of tutorials and demos on our lab's YouTube channel and you can find some step-by-step tutorials here. If you install SlicerRT extension, then you can load RT structure sets directly into Slicer and edit them using Segment Editor (or compare them, register, transform them, export them to DICOM, compute DVH, etc.). See for example this module for DICOM import, automatic registration of prostate MRI to ultrasound, and DICOM export: If you have any specific request or recommendation then let us know. There may be many things that are easy to implement and make your work much easier.
  13. Hi Devarsh, I am working on a Color MRI software for viewing and interpretting MRI images. It is a free and opensource plugin for Osirix image viewer, which works on MacOs. You can download the plugin here. Plugin main page and documentation is here. It is in alpha phase and has known issues. Please feel free to report additonal bugs while being the first using it. The plugin generates 24bit color images in which fat is yellow, water is cyan and muscles are dark red. One of the secondary benefits I expect from plugin is better segmentation from MRI data. Fat, muscle and water each will have distinct colors and should be easy for segmentation. The other advancement I expect from Osirix Color MRI plugin is the creation of Color medical 3D prints from MRI data. Nevit Note: Dr. Mike's tutorial has good introductory info about Osirix. Sample Color MRI image:
  14. valchanov

    Intellectual property protection

    I shared one of my models with an acquaintance of mine, because he wanted to test his new Prusa 3D printer with it. Later he posted it on a website for selling. I approached the problem personally, he removed the model from the site and apologized to me, this is why I won't share details about the issue (he had to print some of my models for free, of course). Now all my models are watermarked and if I have such a case, I can contact the administrator instead, my name and my institution are inserted in the mesh itself.
  15. hello...i did all the steps to crop de dicom surce file....but there isn t a crop button in the latest 3d slicer version....how can i saved just the cropped part ? i tried to and upload it to democratiz3d but there ws some kinf of error...
  16. Dr. Mike

    Intellectual property protection

    Thanks for the reference. Can you elaborate on the IP theft you mentioned? What happened?
  17. valchanov

    Intellectual property protection

    The protection of the intellectual property of the 3D models can be a serious issue for every 3D modeler. It sucks when your model is posted for selling at a webside without your consent with a juicy price and you're gaining NOTHING from it. Some 3D artists are adding watermarks to their models, which can be easily removed by an amateur with a free surface modelling program (Meshmixer, Meshlab etc.). But there is an easy solution for this injustice - an invisible watermark. On Watermark3D you can add such watermark, incorporated into the mesh of your 3D model itself, which is hard for removing and can be checked on the same website during an intellectual property dispute. For the removing of the watermark you have to remesh the whole model, which will decrease the overall quality of the model substantially. I hope that I'll spare you the pain, which I experienced recently. Enjoy
  18. Hello the Biomedical 3D Printing community, it's Devarsh Vyas here writing after a really long time! This time i'd like to share my personal experience and challenges faced with respect to medical 3D Printing from the MRI data. This can be a knowledge sharing and a debatable topic and I am looking forward to hear and know what other experts here think of this as well with utmost respect. In the Just recently concluded RSNA conference at Chicago had a wave of technology advancements like AI and 3D Printing in radiology. Apart from that the shift of radiologists using more and more MR studies for investigations and the advancements with the MRI technology have forced radiologists and radiology centers (Private or Hospitals) to rely heavily on MRI studies. We are seeing medical 3D Printing becoming mainstream and gaining traction and excitement in the entire medical fraternity, for designers who use the dicom to 3D softwares, whether opensource or FDA approved software know that designing from CT is fairly automated because of the segmentation based on the CT hounsifield units however seldom we see the community discuss designing from MRI, Automation of segmentation from MRI data, Protocols for MRI scan for 3D Printing, Segmentation of soft tissues or organs from MRI data or working on an MRI scan for accurate 3D modeling. Currently designing from MRI is feasible, but implementation is challenging and time consuming. We should also note reading a MRI scan is a lot different than reading a CT scan, MRI requires high level of anatomical knowledge and expertise to be able to read, differentiate and understand the ROI to be 3D Printed. MRI shows a lot more detailed data which maybe unwanted in the model that we design. Although few MRI studies like the contrast MRI of the brain, Heart and MRI angiograms can be automatically segmented but scans like MRI of the spine or MRI of the liver, Kidney or MRI of knee for example would involve a lot of efforts, expertise and manual work to be done in order to reconstruct and 3D Print it just like how the surgeon would want it. Another challenge MRI 3D printing faces is the scan protocols, In CT the demand of high quality thin slices are met quite easily but in MRI if we go for protocols for T1 & T2 weighted isotropic data with equal matrix size and less than 1mm cuts, it would increase the scan time drastically which the patient has to bear in the gantry and the efficiency of the radiology department or center is affected. There is a lot of excitement to create 3D printed anatomical models from the ultrasound data as well and a lot of research is already being carried out in that direction, What i strongly believe is the community also need advancements in terms of MRI segmentation for 3D printing. MRI, in particular, holds great potential for 3D printing, given its excellent tissue characterization and lack of ionizing radiation but model accuracy, manual efforts in segmentation, scan protocols and expertise in reading and understanding the data for engineers have come up as a challenge the biomedical 3D printing community needs to address. These are all my personal views and experiences I've had with 3D Printing from MRI data. I'm open to and welcome any tips, discussions and knowledge sharing from all the other members, experts or enthusiasts who read this. Thank you very much!
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