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  1. 3 likes
    So I have seen some questions here on embodi3D asking how to work with MRI data. I believe the main issue to be with attempting to segment the data using a threshold method. The democratiz3D feature of the website simplifies the segmentation process but as far as I can tell relies on thresholding which can work somewhat well for CT scans but for MRI is almost certain to fail. Using 3DSlicer I show the advantage of using a region growing method (FastGrowCut) vs threshold. The scan I am using is of a middle aged woman's foot available here The scan was optimized for segmenting bone and was performed on a 1.5T scanner. While a patient doesn't really have control of scan settings if you are a physician or researcher who does; picking the right settings is critical. Some of these different settings can be found on one of Dr. Mike's blog entries. For comparison purposes I first showed the kind of results achievable when segmenting an MRI using thresholds. With the goal of separating the bones out the result is obviously pretty worthless. To get the bones out of that resultant clump would take a ridiculous amount of effort in blender or similar software: If you read a previous blog entry of mine on using a region growing method I really don't like using thresholding for segmenting anatomy. So once again using a region growing method (FastGrowCut in this case) allows decent results even from an MRI scan. Now this was a relatively quick and rough segmentation of just the hindfoot but already it is much closer to having bones that could be printed. A further step of label map smoothing can further improve the rough results. The above shows just the calcaneous volume smoothed with its associated surface generated. Now I had done a more proper segmentation of this foot in the past where I spent more time to get the below result If the volume above is smoothed (in my case I used some of my matlab code) I can get the below result. Which looks much better. Segmenting a CT scan will still give better results for bone as the cortical bone doesn't show up well in MRI's (why the metatarsals and phalanges get a bit skinny), but CT scans are not always an option. So if you have been trying to segment an MRI scan and only get a messy clump I would encourage you to try a method a bit more modern than thresholding. However, keep in mind there are limits to what can be done with bad data. If the image is really noisy, has large voxels, or is optimized for the wrong type of anatomy there may be no way to get the results you want.
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    Version 1.0.0


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


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    I printed my hand a couple weeks back. The model is available for sale at: Or try your 'hand' at segmenting it from the scan data that is free at: I am still working on getting better transparency to show the internal bones. With FDM true transparency only works for single perimeter prints (like vases) but I am trying some other plastics that should do better than this one done with PLA. The light source is pretty bright, the bones are difficult to see normally.
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    I've recently discovered two similar peer-reviewed online journals that publish articles related to 3D medical modeling and printing. The first is based out of North America called 3D Printing in Medicine: http://threedmedprint.springeropen.com/articles The second is based out of Australia called Journal of 3D Printing in Medicine: http://www.futuremedicine.com/loi/3dp Let me know if anyone has any feedback about the quality or submission process for papers. Both just started.
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    Version 1.0.0

    1 download

    Proximal humerus fracture


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    I came across how to use the "Create Pivot" tool in Meshmixer to more precisely place a "Plane Cut," but it doesn't always seem to place the pivot where I want it. My heads are in FH with nasion at x = 0 and I want to make cuts at precise distances from this point or at other known points from the origin (I have nasion at x = 0, left and right porion at y = 0 and z = 0). When I use the default pivot placement, it sometimes places it at the origin, which is perfect because I can use that or use the "Transform" tool to shift the pivot a specific distance. Anyways, even with the same settings, the pivot is not always placed at the origin, so I'm not getting a cut at 0 every single time. Has anybody played with this or have a better way of getting cuts at a precise location? Meshlab has a "Compute Planar Section" which lets me take a cut at say, x = 0, but then I have to extrude it to get a printable layer.
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    You can see and adjust the cropping box in both the 3D window and in the slices below. In the 3D window, you can left-click and drag anywhere to rotate the volume and box around in 3D to see the adjustable points on each surface. The box always starts out around your whole volume, but you can grab the top dot (light blue) and drag it down.
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    Yes, that boolean action gives you flat surface. Somethimes I have troubles with Blender and then I add cube and use Union boolean, then delete flat surfaces of that "model" and add facet where "cut" was made. The result is the same...
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    Hi Terry, Thanks for posting this question. I too have had problems with Meshmixer when I want to perform very precise cuts or moves. For most instances Meshmixer is great when cuts can be "eyeballed," or made visually. But the plane cut tool doesn't seem to have a way to be really precise about it. In these instances, I've used Blender. Basically I will make a "plane" by starting with a cube and making the dimensions something like 1000 x 1000 x 0.1 mm. Technically this isn't a plane since it has volume, but if it is 1/10 of a mm thick for practical purposes that is a plane. You can then set the exact XYZ coordinates and the XYZ rotation of the cut plane in the object parameter pane. Then, do a boolean difference to subtract the intersecting volume between the plane and my target object, effectively making a 0.1 mm thick cut through it. Blender is scriptable, and I've had instances where I have to do multiple identical cuts on multiple objects, and I've written a python script to automate moving the cutting object and performing the cuts. Sorry this isn't specifically a solution for Meshmixer, but hopefully it will help you. Dr. Mike
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    Hi I am assuming you have a scan from a gated MRI or a CT scan. If so I would try region growing as shown in my MRI segmentation tutorial:
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    Printed well on my Prusa. Lots of support material required, but really helped in show patient the relative size of her mass.
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    Thanks for posting this link, will try them. I came across this article relevant to this post https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615389/
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    I receive a lot of inquiries to my account. I'm going to try to share them with the community in the hope that any information that is shared can help many others. A member recently contacted me and asked the following: "I am a Biomaterials and Tissue Engineer by profession and recently got into 3d printing of medical implants. I would be greatly obliged if you could please advice me on designing 'cranial mesh' My task is to design titanium based cranial mesh. I would like to know if you can suggest me any tutorial on the same." Another member asks, " I am a resident in neurosurgery in Brazil and I have a dream to allow cheap cranioplasty for those in need that depend on Brazilian public health system. If you have some sort of tutorial using free software to make those prosthetic cranial grafts of a cheap way to make a mold out of it I will be glad to hear from you. I am planning on buying the ultimaker 2 printer which allows direct PEEK print and also PLA print for mold to go through autoclave." I must admit that I have limited experience with craniofacial implants. I know that the physicians at Walter Reed Army Medical Center in Bethesda Maryland are doing pioneering work in the field. Regarding making titanium-based implants I am unaware of any tutorials, but a search on Pubmed has yielded a few helpful articles. Here is one https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073471/ From what I have seen most of these implants are designed using the Mimics system by Materialise. Regarding the low-cost solution for cranial implants, I'm not familiar with any freeware software that specifically does implants. From the hardware perspective, you may want to consider a Form 2 stereolithographic printer in addition to the Ultimaker 2 (FYI, there is a new Ultimaker 3 printer out). Formlabs, the makers of the Form 2 have a tutorial on using their printer to make molds for casting. https://formlabs.com/blog/3d-printing-for-injection-molding/ Formlabs has a dental biocompatible resin that I know some hospitals (Mayo Clinic) are using for in-surgery cutting guides. I heard them talk about that at a conference I recently attended. Whatever you do, make sure you follow the health safety rules in your country and take all necessary steps for patient safety.
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    There are tutorials you can combine from there maybe http://support1.geomagic.com/Support/5605/5668/en-US/Article/View/2368/Geomagic-Freeform-Tutorials
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    I was also interested into making craniofacial implants, and also i have found MeVisLab free software, but i found it very complex to work with. Than also i tried with Geomagic Sculpt and Freeform, but as Saumyam mentioned they are pretty expencive (retailer in my country said that the price is aroud 2000€ for Sculpt, and 6000 € for Freeform, and 8000 € for Freeform Plus). It was very hard to work with Geomagic sculpt (laggs, unresponsice control etc.), but Freeform was discovery and I am very pleased with that software. Here is model of custom made cranial implant that I made using Geomagic Freeform trial version and Blender. Few details remain to be done on it.
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    Hi Dr Mike Thanks for this blog post. I came across this one method of designing cranial implants (attached link tutorial video) using the free software MeVisLab....I have yet to try it myself as I was not able to understand the whole method/workflow https://www.youtube.com/watch?v=8epxE8pUMPk Apart from that there is another software , Geomagic Freeform but that too is paid one...
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    Apparently this is few years old, but I just saw a blurb on it the other day. Create a 3D model from a scan of the shell and add a little pizzazz! https://www.wired.com/2013/07/3-d-printed-hermit-crab-shells-based-on-city-skylines/
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    I recently attending this conference in Scottsdale Arizona. A lot of great models were on display. Here are a few for your enjoyment.
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    Hopefully it will be cheaper than Mimics. Can you let us know pricing information when you get it?
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    Not technically 3d printing, but researchers used a spinach leaf to create vasculature http://www.businessinsider.com/spinach-leaf-science-heart-tissue-blood-2017-3 Now thousands of kids won't eat their spinach in the name of science
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    Researchers at UC San Diego have successfully 3D printed a network of blood vessels. This is an important step towards 3D printing an entire organ. Read the full story here.
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    Examples of historical medical 3D printing on display at RSNA. The green skull is from 1985! We've come a long way since then.
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