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  • embodi3d

    Selling Your Medical Model Files on Embodi3D.com

    By embodi3d

    Dear Community Members,
    After many months of work, we are happy to announce the addition of a feature that will allow you to sell medical models you have designed on Embodi3D.com. While we always have encouraged our members to consider allowing their medical STL files to be downloaded for free, we understand that when a ton of time is invested in creating a valuable and high-quality model, it is reasonable to ask for something in return. Now Embodi3D members have two options: 1) You can share your medical models for free, or 2) you can charge for them. We hope these two options encourage more sharing and file uploads. The more models available, the more it helps the medical 3D printing community.   For more details on how to sell your medical masterpieces on Embodi3D, go to the selling page.         Thanks, and happy 3D printing!
    • 0 comments
    • 652 views
  • Dr. Mike

    A Ridiculously Easy Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes

    By Dr. Mike

    Please note the democratiz3D service was previously named "Imag3D" In this tutorial you will learn how to quickly and easily make 3D printable bone models from medical CT scans using the free online service democratiz3D®. The method described here requires no prior knowledge of medical imaging or 3D printing software. Creation of your first model can be completed in as little as 10 minutes.   You can download the files used in this tutorial by clicking on this link. You must have a free Embodi3D member account to do so. If you don't have an account, registration is free and takes a minute. It is worth the time to register so you can follow along with the tutorial and use the democratiz3D service.   >> DOWNLOAD TUTORIAL FILES AND FOLLOW ALONG << Both video and written tutorials are included in this page.           Before we start you'll need to have a copy of a CT scan. If you are interested in 3D printing your own CT scan, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figures 1 and 2 show the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available.     Figure 1: The radiology department window at my hospital.       Figure 2: An example of what a DVD containing a CT scan looks like. This looks like a standard CD or DVD.       Step 1: Register for an Embodi3D account   If you haven't already done so, you'll need to register for an embodi3d account. Registration is free and only takes a minute. Once you are registered you'll receive a confirmatory email that verifies you are the owner of the registered email account. Click the link in the email to activate your account. The democratiz3D service will use this email account to send you notifications when your files are ready for download.   Step 2: Create an NRRD file with Slicer If you haven't already done so, go to slicer.org and download Slicer for your operating system. Slicer is a free software program for medical imaging research. It also has the ability to save medical imaging scans in a variety of formats, which is what we will use it for in this tutorial. Next, launch Slicer. Insert your CD or DVD containing the CT scan into your computer and open the CD with File Explorer or equivalent file browsing application for your operating system. You should find a folder that contains numerous DICOM files in it, as shown in Figure 3. Drag-and-drop the entire DICOM folder onto the Slicer welcome page, as shown in Figure 4. Click OK when asked to load the study into the DICOM database. Click Copy when asked if you want to copy the images into the local database directory.     Figure 3: A typical DICOM data set contains numerous individual DICOM files.     Figure 4: Dragging and dropping the DICOM folder onto the Slicer application. This will load the CT scan.   Once Slicer has finished loading the study, click the save icon in the upper left-hand corner as shown in Figure 5. One of the files in the list will be of type NRRD. make sure that this file is checked and all other files are unchecked. click on the directory button for the NRRD file and select an appropriate directory to save the file. then click Save, as shown in Figure 6.     Figure 5: The Save button     Figure 6: The Save File box   The NRRD file is much better for uploading then DICOM. Instead of having multiple files in a DICOM data set, the NRRD file encapsulates the entire study in a single file. Also, identifiable patient information is removed from the NRRD file. The file is thus anonymized. This is important when sending information over the Internet because we do not want identifiable patient information transmitted.   Step 3: Upload the NRRD file to Embodi3D   Now go to www.embodi3d.com, click on the democratiz3D navigation menu and select Launch App, as shown in Figure 7. Drag and drop your NRRD file where indicated. While NRRD file is uploading, fill in the "File Name" and "About This File" fields, as shown in Figure 8.     Figure 7: Launching the democratiz3D application     Figure 8: Uploading the NRRD file and entering basic information To complete basic information about your NRRD file. Do you want it to be private or do you want to share it with the community? Click on the Private File button if the former. If you are planning on sharing it, do you want it to be a free or a paid (licensed) file? Click the appropriate setting. Also select the License Type. If you are keeping the file private, these settings don't matter as the file will remain private. Make sure you accepted the Terms of Use, as shown in Figure 9.     Figure 9: Basic information fields about your uploaded NRRD file   Next, turn on democratiz3D Processing by selecting the slider under democratiz3D Processing. Make sure the operation CT NRRD to Bone STL is selected. Leave the default threshold of 150 in place. Choose an appropriate quality. Low quality produces small files quickly but the output resolution is low. Medium quality is good for most applications and produces a relatively good file that is not too large. High quality takes the longest to process and produces large output files. Bear in mind that if you upload a low quality NRRD file don't expect the high quality setting to produce a stellar bone model. Medium quality is good enough for most applications. If you wish, you have the option to specify whether you want your output file to be Private or Shared. If you're not sure, click Private. You can always change the visibility of the file later. If you're happy with your settings, click Save & Submit Files. This is shown in Figure 10.     Figure 10: Entering the democratiz3D Processing parameters.       Step 4: Review Your Completed Bone Model After about 10 to 20 minutes you should receive an email informing you that your file is ready for download. The actual processing time may vary depending on the size and complexity of the file and the load on the processing servers. Click on the link within the email. If you are already on the embodied site, you can access your file by going to your profile. Click your account in the upper right-hand corner and select Profile, as shown in Figure 11.     Figure 11: Finding your profile.   Your processed file will have the same name as the uploaded NRRD file, except it will end in "– processed". Renders of your new 3D model will be automatically generated within about 6 to 10 minutes. From your new model page you can click "Download this file" to download. If you wish to share your file with the community, you can toggle the privacy setting by clicking Privacy in the lower right-hand corner. You can edit your file or move it from one category to another under the File Actions button on the lower left. These are shown in Figure 12.     Figure 12: Downloading, sharing, and editing your new 3D printable model.   If you wish to sell your new file, you can change your selling settings under File Actions, Edit Details. Set the file type to be Paid, and specify a price. Please note that your file must be shared in order for other people to see it. This is shown in Figure 13. If you are going to sell your file, be sure you select General Paid File License from the License Type field, or specify your own customized license. For more information about selling files, click here.     Figure 13: Making your new file available for sale on the Embodi3D marketplace.     That's it! Now you can create your own 3D printable bone models in minutes for free and share or sell them with the click of a button.If you want to download the STL file created in this tutorial, you can download it here. Happy 3D printing!  
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    • 24,930 views
  • Dr. Mike

    Easily Create 3D Printable Muscle and Skin STL Files from Medical CT Scans

    By Dr. Mike

    In this tutorial we will learn how to use the free medical imaging conversion service on embodi3D.com to create detailed anatomic muscle and skin 3D printable models in STL file format from medical CT scans. Muscle models show the detailed musculature by subtracting away the skin and fat. Even when created from a scan of an obese person, the model looks like it comes from a bodybuilder, Figure 1A. Skin models show an exact replica of the skin surface. The finest details are captured, including wrinkles and veins underneath the skin. Hair however is not captured in a CT scan and thus the model does not have any hair, Figure 1B. Figure 1A (left): A muscle 3D printable model. Figure 1B (right): A skin 3D printable model   These models can be used for a variety of purposes such as medical and scientific education and research. Additionally, the skin models can be used to re-create a person's likeness in 3D from a medical scan. If you have had a CT scan of the head, you can create a lifelike replica of your head. You can create replicas of your friends, family, or even pets if they have had a medical CT scan. Alternatively, if you have a loved one who passed away but had a CT scan prior to death, you can use the scan to re-create an exact replica of their face. Even scans that are years old can be used for this purpose. Some people may consider this to be a little creepy, so if you are considering doing this think carefully first.   Before proceeding please register for an embodi3D.com account if you haven't already. You will need an account to use the service. It is highly recommended that you download the associated file pack for this tutorial so that you can follow along with the exact same files that are used in this tutorial.   >> DOWNLOAD THE FREE FILE PACK BY CLICKING HERE <<   If you are interested in learning how to use the free embodi3D.com service, see my prior tutorials on creating bone models, processing multiple models simultaneously, and sharing and selling your models on the embodi3D.com website.       If you are interested in converting your own CT scan or that of a friend or family member, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figure 2 shows the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available. If you have downloaded the file pack for this tutorial, example CT scans are included   Figure 2A, the Image Management (radiology) department at my hospital, where you can pick up a DVD of your CT scan as shown in Figure 2B (right). My hospital does this for free, but some may charge a trivial fee.   PART 1: Creating a Muscle STL model from NRRD File   Before we begin please bear in mind that this process only works for CT scan images. It will not work for MRI images. Before proceeding please check that the scan you wish to convert is a CT (CAT) scan!   Step 1: Convert Your CT scan to an Anonymized NRRD File with 3D Slicer Open 3D Slicer. If you don't have the software program you can download it for free from slicer.org. Once Slicer has opened, take the folder from the download pack that is called STS_004. This folder contains anonymized DICOM images from a CT scan of the legs of a 24-year-old woman who had a muscle tumor. Drag and drop the entire folder onto the Slicer window, as shown in Figure 3. Slicer will ask you if you want to load the images into the DICOM database. Click OK. Slicer will also ask you if it should copy the images into the database, click Copy. Slicer will take about one minute to load the scanned. Figure 3: Drag-and-drop the STS_004 DICOM folder from the file pack onto the Slicer window   Next, load the scan into the active wor king area in slicer. If the DICOM browser is not open, click on the Show DICOM browser button, as shown in Figure 4. Click on the STS_004 patient and series, and click the Load button, as shown in Figure 4. The leg CT scan will now load into the active seen within Slicer, as shown in Figure 5.   Figure 4: Open the DICOM browser and load the study into the active seen   Figure 5: The leg CT scan is shown in the active seen   Step 2: Trim the Scan so that only the Right Thigh is included. Click on the Volume Rendering module from the Modules drop-down menu as shown in Figure 6. Turn on volume rendering by clicking on the eyeball button, as shown in Figure 7. Then, center the model in the 3D pane by clicking on the crosshairs button, Figure 7. If you don't have the same window layout as shown in Figure 7, you can correct this by clicking on the Four-Up window layout from the window layout drop-down menu, as shown in Figure 8.   Figure 6: Turn on the volume rendering module   Figure 7: Center the rendered volume.   Figure 8: Make sure you are in the Four-Up window layout   Next we are going to crop the volume so that we exclude everything other than the right knee and thigh. From the modules menu, select All Modules, Crop Volume, as shown in Figure 9. Turn on ROI visibility by clicking on the eyeball button, as shown in Figure 10. Then, move the region of interest box so that it only encapsulates the right thigh, as shown in Figure 10. You can adjust the size of the box by grabbing on the colored circular handles and moving the sides of the box as needed.   Figure 9: The Crop Volume module.   Figure 10: Turning on and adjusting the crop volume ROI (Region Of Interest) Once the crop volume ROI is adjusted to the area that you want, perform the crop by clicking on the Crop button, Figure 11.   Figure 11: the Crop button.   The new, smaller volume that encompasses the right fight and knee has been assigned a cryptic name. The entire scan had a name of "2: CT IMAGES – RESEARCH," and the new thigh volume has a name "2: CT IMAGES-RESEARCH-subvolume-scale_1." That's a mouthful and I want to rename it to something more descriptive. I'm going to select the Volumes module, and then select the "2: CT IMAGES-RESEARCH-subvolume-scale_1" from the Active Volume drop-down menu. Then, from the same drop-down menu I'm going to select "Rename Current Volume". Type in whatever name you want. In this case I'm choosing "right thigh."   Figure 12: Renaming the newly cropped volume.   Step 3: Save the right thigh volume as an anonymized NRRD file.   Click on the Save button in the upper left-hand corner. The save window is then shown. All the checkboxes on the left except for the one that corresponds to the right by. Make sure the file format for this line says NRRD (.nrrd). Make sure you specify the proper directory you want the file to be saved as. When you are satisfied click on save. This is demonstrated in Figure 13. In the specified directory you should see a called right thigh.nrrd. Figure 13: The save file options.   Step 4: Upload the NRRD file to embodi3D.com   Make sure you are logged into your embodi3D.com account. Click on Imag3D from the nav bar, Launch App. Then drag-and-drop your NRRD file onto the upload pain, as shown in Figure 14. Figure 14: Uploading the NRRD file to embodi3D.com.   While the file is uploading, fill in the required fields, including the name of the uploaded file, a brief description, file privacy, and license type. Except the terms of use. next, turn on Imag3D processing.  Under operation, select "CT NRRD to Muscle STL."  Leave the threshold value unchanged. Under quality, select medium or high. Specify your privacy preference for your output STL file. If you are going to share this file, you can choose to share it for free or sell it. Please see my separate tutorial on how to share and sell your files on the embodi3D.com website for additional details. When you're happy with your choices, save the file, as shown in Figure 15: Figure 15: File processing options.   Step 5: Download your new STL file after processing is completed.   In about 5 to 15 minutes you should receive an email that says your file has finished processing and is ready to download. Follow the link in the email or access the new file via your profile on the embodi3D.com website. Your newly created STL file should have several rendered thumbnails associated with it on its download page. If you want to download the file click on the Download button, as shown in Figure 16. Figure 16: the download page for your new muscle STL file   I opened the file in AutoDesk MeshMixer to have another look at it, and it looks terrific, as shown in Figure 17. This file is ready to 3D print! Figure 17: The final 3D printable muscle model. PART 2: Creating a Skin Model STL File Ready for 3D Printing Creating a skin model is essentially identical to creating the muscle model, except instead of choosing the CT NRRD to Muscle STL on the embodi3D.com service, we choose CT NRRD to Skin STL. Step 1: Load DICOM image set into Slicer   Launch Slicer. From the tutorial file pack drag and drop the MANIX folder onto the Slicer window to load this head and neck CT scan data set. This is shown in Figure 18.   Figure 18: Loading the head and neck CT scan into Slicer. It may take a minute or two to load. From the DICOM browser, click on the ANGIO CT series as shown in Figure 19.   Figure 19: Loading the ANGIO CT series from the MANIX data set   Step 2: Skip the trimming and crop volume operations   In this case we don't need to trim and crop a volume as we did with the muscle file above. We can skip Step 2. Step 3: Save the CT scan in NRRD format. Just as with the muscle file above, save the volume in NRRD format. Click on the save button, make sure that the checkbox for the nrrd file is selected and all other checkboxes are deselected. Specify the correct directory you want the file to be saved in, and click Save.   Step 4: Upload your NRRD file of the head to the embodi3D website. Just as with the muscle file process as shown above, upload the head NRRD file to the embodi3D.com website. Enter in the required fields. In this case, however, under Operation choose the CT NRRD to Skin STL operation, as shown in Figure 20. Figure 20: Selecting the CT NRRD to Skin STL file operation   Step 5: Download your new Skin STL file   After about 5 to 15 minutes, you should receive an email that says your file processing has been completed. Follow the link in the email or look for your file in the list the files you own in your profile. You should see that your skin STL file has been completed, with several rendered images, as shown in Figure 21. Go ahead and download your file. You can then check the quality of your file in Meshmixer as shown in Figure 22. In this instance everything looks great and the file is error free and ready for 3D printing.  
    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!
     
    • 2 comments
    • 4,510 views
 

Fighting Obesity with 3D Printing

Since the 1980s, three-dimensional (3D) medical printing and bioprinting technologies have been influencing almost every aspect of the human life. Most people are, however, surprised at the kind of impact additive printing is having in the field of medicine. The technology is helping diagnose and treat complex illnesses ranging from cancer and heart disease to arthritis and infections. In recent months, several innovative 3D tools have also been created to overcome obesity. More than two-thirds of adults in the United States are obese or overweight. The prevalence of obesity has doubled in children and quadrupled in adolescents in the last 30 years. This has increased the risk of Type II diabetes, cancer and other serious conditions in men and women of all ages and abilities. Both government agencies and nonprofit organizations have spent millions of dollars creating awareness about the issue. Consequently, many people now understand the importance of healthy diet and exercise. They, however, lack resources that will help them accomplish such goals. Physicians are also looking for tools that will assist them in treating morbid obesity more effectively. Thankfully, 3D printing technology is offering some novel solutions to everyone, and researchers believe that it will ultimately bolster the efforts aimed at reducing weight and enhancing fitness levels. Liposuction Tools BioSculpture Technology, under the leadership of New York Downtown Hospitals and the Presbyterian New York affiliated plastic surgeon Robert Cucin, is relying on 3D printing to develop an innovative line of surgical instruments to perform liposuction. The technology is also allowing surgeons to create exact replicas of the patient’s organs and practice the procedure before the actual intervention. Together, these products are making liposuction more accessible and safe. Liposuction is an invasive procedure that involves removal of excess fat from various parts of the body and is commonly used treat obesity. Close to 400,000 people underwent this surgery in 2015, as per the American Society of Aesthetic Plastic Surgery. Tracking Devices Exertion Games Lab in Melbourne, Australia, has created a simple device that can print 3D models of the user’s physical activity time, sleep time, and heart rate during the week to motivate and encourage them to set new challenges. Unlike smartphones and pedometers, the Exertion Games Lab device caters to the needs of children as it helps them grasp complex fitness-related information with ease. Children can also hold these models in their hands and share their enthusiasm with their peers. The Potential These examples just form the tip of the iceberg. The impact of 3D printing on the fight against obesity is expected to go beyond creating mechanical devices and surgical instruments. Tamara Nair, a Research Fellow at the Centre for Non-traditional Security (NTS) Studies in the S. Rajaratnam School of International Studies (RSIS), believes that the technology can also be used to create food products with higher nutritional value. Such foods may help obese and overweight individuals manage calorie intake according to their activity level. The 3D printing technology can also make nutritious foods more palatable, says Nair. These potential benefits may appear like science fiction to some readers. Nonetheless, if the recent advances in the 3D printing and bioprinting technologies are anything to go by, they may turn into reality very soon.

mattjohnson

mattjohnson

 

Hacks to make your medical 3D Print Cheaper

Cutting down costs for 3D prints is the number one concern for many Doctors and Patients. In order to achieve this, we need to understand how costs for 3D prints are calculated. Probably the most important variable is the amount of material that is needed for printing your medical object. So all we need to do is to make sure to use as little material as possible.   Here are our some top tips for more successful 3D printing. They're short and to the point, and if you follow them, you'll find your models will stand straight and look beautiful.      Create a hollow 3D model & 3D print with Escape Holes if needed.  A hollow model means that the interior of your object will not be solid. Solid designs are not necessarily a problem – they will be stronger and harder to break (depending on the material), but they will also be more expensive as more 3D printing material will be used.With a hollow model the interior of your print will be empty (in theory). However, since our printers print layer by layer, 3D printing material can get trapped in the interior of your model. If you would like to avoid this, you can add ‘escape holes’ to your design. Material that is not used for building your 3D print can then be removed. However, creating a 3D model with an empty interior can be a bit tricky, you need to know how to hollow your model in the 3D modeling software you’re using, you need to define a wall thickness that is strong enough for your model not to break, and it probably makes sense to add so-called ‘escape holes’ to your model Why do I need escape holes? As already pointed out, our 3D prints are created layer by layer. With a hollow interior, this means that 3D printing materials can get trapped inside the object. A hollow model full of trapped powder is in danger of deforming. Escape holes are recommended for getting ‘trapped’ 3D printing material out of your 3D print. We typically use pressurized air for cleaning the excess powder off.   How do I design escape holes? Again, the exact procedure depends on your software but the idea is often the same: create a cylinder at the bottom of your model and extrude or subtract from its wall    Use supports If you plan on printing out a figure as one solid piece, you'll want to consider placing supports at overhang areas. Some slicing/preference software will do this automatically.  The Infill for FDM 3D Printing The Slicing softwares lets you adjust the infill percentage and infill type to print your model in FDM. Choosing the correct percentage and type of infill depending on how strong you want your model to be can reduce the volume of your model making it cheaper.     Know your materials Learn the tolerances of the various materials used. It's better to err on the larger side, because you can always sand or trim down the piece afterwards.   Happy 3D Printing!!   

DevarshVyas

DevarshVyas

 

Region Growing Image Segmentation

I wanted to take some time to look into a brief history of medical image segmentation before moving into what I consider the more modern method of segmentation.  (be warned video is rather long)     First to be clear the goal of segmentation is to separate the bones or anatomy of interest from 3D scan data.  This is done most easily when there is a sharp contrast between the anatomy of interest and what surrounds it.  If you have a CT scan of an engine block this is pretty straight forward.  The density of metal to air is hard to beat, but for anatomy and especially MRI scans this is a whole other story.  Anatomical boundaries are often more of gradients than sharp edges.   Over the years there have been many approaches to make the process of segmenting anatomy faster, easier, and less subjective then the dreaded 'manual segmentation'.  When I first started working with medical images back around 2003 the group I was at was trying an alternative to their previous method.  Their previous method involved using ImageJ to separate each bone of the foot by applying a threshold then going in and 'fixing' that by painting... They wanted to segment the bones of the foot and it would take like 10 hours of tedious labor... fortunately that was before my time. I was tasked with figuring out how to get 3DViewNix to work.  It was basically a research project that ran on linux (which I hadn't used before).  Its had a special algorithm called 'live-wire' which allowed clicking on a few points around the edge of the bone on each slice to get a closed contour that matched the bone edge then doing that for each scan slice for each bone.  This resulted in about 3 hours a foot of still rather mind numbing effort.     After a while a radiologist with a PhD electrical engineering student let us know that there were much better ways.  His student had some software written in IDL that allowed using 'seeds' in each bone that would then grow out in 3D to the edges of the bones.  After some time to get setup we were able to segment a foot in less than an hour with a good portion of that being computer time.   My background is as an ME so I don't pretend to fully understand the image processing algorithms but I have used them in various forms.  This year I got more familiar with 3DSlicer which I have found to be the best open source medical imaging program yet.  It is built off of VTK and ITK and has a very nice GUI making seeding far more convenient (other programs I've used didn't really allow zooming).  It took me a while to find something similar to what I had used before but eventually I found the extension 'FastGrowCut' gives very good results, enough to move away from the special software I had been using before that wasn't free.   My basic explanation of 'FastGrowCut' and similar region growing algorithms is; you start with 'seeds' which are labeled voxels for the different anatomy of interest.       The algorithm then grows the seeds until it reaches the edge of the bone/anatomy or a different growing seed.  There is then a back and forth until it stabilizes on what the edge really is.  The result is a 'label' file which has all the voxels labeled as background or one of the entities of interest.       Once everything is segmented to the level that you like I prefer to do volumetric smoothing of each entity (bone) before creating the surface models.     These algorithms are an active area of research typically in image processing groups within university electrical engineering departments.  The algorithms are not a silver bullet that works on all situations, there are a variety of other methods (some as extensions to 3DSlicer) for specific situations.  Thin features, long tubular features, noisy data (metal artifacts), low quality scans (scouts), will still take more time and effort to get good results.  No algorithm can take a low resolution, low quality scan and give you a nice model... garbage in = garbage out.    Now I have been surprised bemoaned to find thresholding used as a common segmentation technique, often as the main tool even in expensive commercial programs.  That style typically involves applying a threshold then going in and cleaning up the model until you get something close to what you want.  To me this seems rather antiquated but for quickly viewing data or creating a quick and rough model it really can't be beat... but for creating high quality models to be printed there are better ways.

mikefazz

mikefazz

 

Registration with 3DSlicer

In this entry we look at registering one scan to another from the same subject pre and post op.     There may come a time when you have multiple scans of the same subject which you want to compare to each other.  This could be a CT and an MRI or a pre and post op scan as in this example.  Since the scans were taken at different times and possibly different places they will not line up with each other when they are loaded.  Registration is the process that can find the transformation that moves one volume to line up with the other.    The first step after loading the data is to perform an initial alignment.  If the two volumes are far apart the difference will likely be too much for the registration algorithm to properly work.  The initial alignment is done using the 'transforms' menu within 3DSlicer.  After creating a new transform pick which volume you will be moving as the other one (fixed image) will stay stationary through the whole process.  Now adjust the 3 translation and 3 rotation sliders until you get a decent alignment by eye.  It can help to center each volume first if they have a large origin offset.  Also changing the way one of the volumes is colored can make visual alignment easier.   With the two volumes roughly lined up find the BRAINS registration within the Registration group under the main menu.  Before performing the registration set the: Fixed Image Moving Image Output Image Volume Initialization Transform Registration Phases, set to Rigid (6 Degrees Of Freedom).     When you click 'Apply 'the registration will run until it finds the best match between the scans.  Registration quality is typically measured in therms of 'Mutual Information' which is basically the union between the two volumes.   Full volume rigid registration will not work for all situations such as two scans of a foot which are flexed in a different way.  Rigid registration works best when the two scans are from the same person and the volume in question doesn't change shape (such as head scans).  Other types of registration will allows the 'moving' volume to be distorted until it matches the 'fixed' volume.  This can be simple affine (scaling) all the way to template matching (warping).   Find the scans used at: PreOp   PostOp   And of course 3DSlicer - https://www.slicer.org/

mikefazz

mikefazz

 

Dicom Primer

In this tutorial I will cover some of the basics on working with dicom data with a focus on anatomizing, and reading into medical imaging software as well as how to potentially fix problematic scans.     So first of all what is DICOM data?  It is a standard file type for basically all medical imaging devices (CT, MRI, US, PET, X-ray, etc), DICOM stands for Digital Imaging and COmmunication in Medicine and along with the file format, and the tags, it is designed to be transferred and stored with PACS.  The DICOM standard can be found at their homepage.     The useful bits for the purpose of creating anatomical models and particularly values that define the volume geometry can be found in 'tags'.  These are in each image/slice header file (metadata).  They are two 4 digit hexadecimal values assigned to a particular type of value like:   (0018, 0088) Spacing Between Slices   To find the official library of these tags go to the standard on the dicom home page and go down to "Part 6: Data Dictionary".  When opened scrolling down will reveal just how immense the dicom standard is.  Now this library just gives you the tag and the name but not much information about that tag.  To get a bit more of a description use Dicom Lookup and type in the tag or name to find more information.   Before looking at data a mention on anatomizing data.  The goal is to remove any information that can be traced back to the original person without removing other important information like modality, etc...  To get an official type of list of these values go to HIPPA and find there de-identification guidance document.  In general (pages 7 and 8) remove all names, dates, addresses, times, and other sensitive information like SSN.   Now to actually look at the data I have for years used ImageJ which has been updated to Fiji.  Open an image from the scan CD and click 'CNTR+I' to open the header file and see what is in there.     Fiji (ImageJ) is a very simple and useful program for looking at data.  It is mostly made for working in 2D so in that way is kind of outdated compared to modern medical imaging software like 3DSlicer but it still has its place.  Fiji can save a stack of images as an nrrd file so if for some reason 3DSlicer doesn't want to load a scan correctly Fiji gives you another option.   So as useful as Fiji is; for anonymising and changing the values of tags I would suggest Dicom Browser.  I personally use some code in Matlab to automate the process but that is an expensive and cumbersome tool for the average user.  Open the folder with the data in Dicom Browser and when the main folder is selected the values from each slice are stacked on top of each other.  To anonymise the data select a value and set it to 'clear'     Find all relevant information and clear it or change its value to something that can't be traced to the person (like patient A001).  This is also where geometrical values like slice thickness can be changed if that is necessary to get a scan to load properly.  Once all the values are changed save the new dicom files and open the new ones again in ImageJ just to check that it all worked and that no PID (Patient Identifier Data) was missed.   As to fixing data the most common issue I have come across is an incorrect slice spacing which causes the scan to be shrunk or stretched.  There are a few values that control this and different programs will use different values.  'SliceThickness' is sometimes used which is bad.  The best is to use the 'ImagePositionPatient' which changes for each slice/image.  'SliceSpacing' is often used as well which is better than 'SliceThickness'.  If you suspect your slice spacing value is wrong calculate the difference between two consecutive 'ImagePositionPatient' values and check it against the slice spacing if they are not equal something is amiss.    Now you have anonymized and potentially fixed data that you can send to a friend, share here on embodi3D or load up in medical imaging software like my favorite 3DSlicer.   When dicom data (anonymized or not) is loaded into 3DSlicer and saved to an nrrd file (see Dr. Mike's tutorial) you will have a single volume file which is inherently anonymized.  Opening the *.nrrd file in a text editor like notepad++ there are a few lines at the top which are basically your new header file.  It is very minimal and doesn't include a great deal of the information that was in the original dicom files like modality, scan type and settings.  This is fine if all you want to do is create a model from it but it can be helpful to have other information then what you have in an nrrd file, so anonymized dicom will be better in some situations.

mikefazz

mikefazz

 

embodi3D November 2016 Newsletter

Welcome to our November 2016 newsletter! We will discuss our medical 3D printing tool and highlight a new website feature.   Dr. Mike is at the RSNA Annual Meeting in Chicago. If you are attending the conference, make sure to check out the expanded 3D printing exhibits and attend one of Dr. Mike’s workshops “3D Printing Hands-on with Open Source Software”.   democratiz3D: Medical 3D Printing for All At the end of September we launched a tool that converts a medical CT scan into a bone STL model and optimizes it for 3D printing. Once complete, you can download your file, share it with the community, or sell it in our Marketplace. We have made so many improvements in the last 2 months that we are renaming the service “democratiz3D(TM)” – reflecting our mission to democratize medical 3D printing by making it easily accessible to anyone, through tutorials, blogs, discussion forums, a marketplace, and now software. What used to require expensive software or complicated workflows is now done in minutes with democratiz3D(TM). Dr. Mike has put together several tutorials showing how to use this tool.     democratiz3D currently lets our members convert a medical CT scan into: a bone STL model a muscle STL model a skin STL model Do you need a different type of file conversion or medical model? Let us know, as we keep adding more features. embodi3D's Improved Website Our website, embodi3d.com, recently underwent a major upgrade, making the site easier to navigate. A new feature we want to highlight is the Activity menu navigation tab. This is where you can find recent site updates at a glance. You can set up streams to get updates on content created by members you follow, making it easier for you to track content you are most interested in. A snapshot of a portion of the November activity feed is below.   We Want Your Feedback We would like to thank our members who have provided feedback and thus contributed to the improvements we covered in this newsletter. Please keep sending us your feedback and making the experience better for everyone!   Let's grow our community together! The Embodi3D Team

embodi3d

embodi3d

 

Creating 3D Printable Medical Models and STL Files for Free: Online Services vs. Desktop Software - Slicer and Meshmixer

Note: This tutorial accompanies a workshop I presented at the 2016 Radiological Society of North America (RSNA) meeting. The workflow and techniques presented in this tutorial and the conference workshop are identical.     In this tutorial we will be using two different ways to create a 3-D printable medical model of a head and neck which will be derived from a real contrast-enhanced CT scan. The model will show detailed anatomy of the bones, as well as the veins and arteries. We will independently create this model using two separate methods. First, we will automatically generate the model using the free online service embodi3D.com. Next, we will create the same file using free desktop software programs 3D Slicer and Meshmixer.   If you haven't already, please download the associated file pack which contains the files you'll need to follow along with this tutorial. Following along with the actual files used here will make learning these techniques much easier. The file pack is free. You need to be logged into your embodi3D account to download, but registration is also free and only takes a minute. Also, you'll need an embodi3D.com account in order to use the online service. Registration is worth it, so if you haven't already go ahead and register now.   >> DOWNLOAD THE FILE PACK NOW <<   Online Service: embodi3D.com     Step 1: Go to the embodi3D.com website and click on the democratiz3D menu item in the naw bar. Click on the "Launch democratizD" link, as shown in Figure 1.   Figure 1: Opening the free online 3D model making service service democratiz3D.   Step 2: Now you have to upload your imaging file. Drag and drop the file MANIX Angio CT.nrrd from the File Pack, as shown in Figure 2. This contains the CT scan of the head and neck in NRRD file format. If you are using a file other NRRD that provided by the file pack, please be aware the file must contain a CT scan (NOT MRI!) and the file must be in NRRD format. If you don't know how to create an NRRD file, here is a simple tutorial that explains how.   Figure 2: Dragging and dropping the NRRD file to start uploading.   Step 3: Type in basic information on the file being uploaded, including File name, file description, and whether you want to share the file or keep it private. Bear in mind that this information pertains to the uploaded file, not the file that will be generated by the service.
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!

Dr. Mike

Dr. Mike

 

How to Create a Hollow Shell from a Medical STL File Using MeshMixer

In this brief tutorial we will go over how to use Meshmixer to create a hollow shell from a medical 3D printable STL file. Hollowing out the shell, as shown in the pictures below, can allow you to 3D print the model using much less material that printing a solid piece. The print will take less time and cost less money.   For this tutorial we will use a head that we created from a real medical CT scan in a prior tutorial, " Easily Create 3D Printable Muscle and Skin STL Files from Medical CT Scans" If you haven't seen the prior tutorial, please check it out.     To follow along with the tutorial, please download the accompanying file. This will enable you to replicate the process exactly as it is shown in the tutorial.    >> DOWNLOAD THE TUTORIAL FILE NOW <<      

Dr. Mike

Dr. Mike

 

Role of 3D Printing in Scoliosis Correction Surgery

Role of 3D Printing in Scoliosis Correction Surgery     Scoliosis is a medical condition in which a person's spine has a sideways curve. The curve is usually "S" or "C" shaped. Scoliosis occurs most often during the growth spurt just before puberty.  In some cases, the person suffering from the disease can be left unable to stand up straight, to walk, or even, in the most severe cases, to breathe properly. In the most severe scoliosis cases, however, surgery is the only option. Back surgery is never a minor procedure, and scoliosis surgery is especially tricky, as it requires screws or wires to be placed throughout multiple vertebrae and then connected to stabilize the back         Fig: Scoliosis Example     3D printing has done quite a bit to make scoliosis treatment less agonizing for even severe cases. Here is an over view of how 3D Printing is a complete package in diagnosing, treatment and rehabilitation for scoliosis patients.     ·        3D Printed Patient Specific Models for Pre-Surgical Planning       Recognition of complex anatomical structures in scoliosis can sometimes be difficult to attain from simple 2D radio-graphic views. 3D models of patients’ anatomy facilitate this task and allow doctors to familiarize themselves with a specific patient. This approach proved to reduce drastically OT time, especially in complex scoliosis cases. Getting to know patients’ anatomy before entering an OT allows to plan the exact approach, helps to predict bottlenecks and even test procedures beforehand.          Fig: Scoliosis Pre operative model to be 3D Printed.     No standard models nor 2D images can replace 3D printing as the first do not represent the specific case in debate and the latter may hide important details, especially in the spatial relationship between structures. 3D prints may be as well used by a doctor to explain to a patient his or her condition. Offering a patient possibility to understand his case and procedure may be reassuring and produce better treatment outcome by reducing stress and insecurity.     ·        3D Printed Patient Specific Surgical Guides in Scoliosis      Another recent advancement in the 3D Printing applications for spine surgeries are the 3D-printed Patient specific pedicle screw guides, realized in a customized manner with 3D printers. Their aim is to orient and guide in a precise fashion the placement of the screw in the pedicle. In complex scoliosis cases and revision surgeries it is very difficult to find the pedicle and the entry point for the screw guides. 3D Printing addresses this challenge and proves to be accurate, this level of accuracy is absolutely useful for patients with scoliosis, whose common anatomical landmarks can be in an abnormal position or might be not easily recognizable.       Fig: Patient specific 3D printed guides.       The guides involve surgical planning and software assisting surgical placement of pedicle screws designed specifically for a patients' unique anatomy. It is essentially a 3D printed surgical tool that fits the patient's unique anatomy. The 3D Printed surgical guides are printed in SLS and are bio compatible to be used on the patient's body. It is easy to see how these new customizable tools can greatly improve Scoliosis Surgery outcomes. These enhanced tools promise to improve patient satisfaction and physician performance, using the tailor-made patient-specific guides for the spine vertebrae utilizing proprietary CT scan algorithms and sophisticated 3-D medical printing technology.     ·        3D Printed Patient Specific Braces for Scoliosis     Moderately severe scoliosis (30-45 degrees) in a child who is still growing may require bracing. The main goal of 3D Printed scoliosis brace is to combine fashion, design, and technology to create a brace far more appealing to patients, and, as a result, far more effective medically.       Fig: 3D Printed scoliosis Brace.     The 3D Printed patient specific brace represents a meaningful innovation in scoliosis treatment. Using advanced 3D scanning and printing technology, the Scoliosis Brace addresses the most common objections to traditional bracing. The 3D Printed braces are usually printed in SLS (Selective Laser Sintering) for its strength durability and aesthetic features along with bio compatibility. This is what happens when Design innovation meets Medical Innovation.     To conclude the use of three dimensional printing in scoliosis surgeries has a wide range of applications from pre operative models to patient specific guides and orthotics proving to be a complete package in aiding Scoliosis surgeries and treatment.

DevarshVyas

DevarshVyas

 

Increasing Role of 3D Printing in Cancer Screening

In spite of extensive research, the medical fraternity has not reached a consensus on what causes cancer and how it should be treated. Nonetheless, almost everyone agrees that early and accurate diagnosis is crucial for successful recovery. In fact, early detection can lead to a 70 percent decline in cervical cancer mortality, as per the Canary Foundation. Early diagnoses of colon cancer can increase the patient’s five-year survival rate from 11 percent to 91 percent. Almost 100 percent of the patients with breast and prostate cancer survive for more than five years when the condition is revealed at an early stage. Consequently, millions of dollars are being spent on developing and improving diagnostic techniques such as MRI scans, CT scans, PAP smears and mammograms. While these procedures have been immensely successful, they can be very expensive and may not be accessible to everyone. Some screening methods are associated with bleeding and other unwanted side effects. They can also lead to false-positive and false-negative reactions. Surprisingly, three-dimensional (3D) medical printing and bioprinting technology is paving the way for newer cancer screening techniques that are more sensitive, specific and cost effective. The technology allows the user to deposit desired materials on a substrate in a specific pattern to create medical devices, implants and prosthetics as per the needs of the patient. Simplified Blood Testing Miriam, a 3D printed blood testing device from Miroculus, uses proprietary microRNA detection technology and digital microfluids to identify early stage cancer at the molecular level. The company is focusing on gastric cancer at this time and has collaborated with the National Institute of Health to conduct clinical trials for the diagnostic device. The goal is to provide doctors with a simple tool to identify patients who require additional testing. This can help save thousands of dollars in the long run and make cancer screening available to patients in the poorest parts of the world.   Printing the Ducts Another major challenge is to identify malignant tumors accurately. Doctors estimate that about 20 to 50 percent of breast tumors become invasive. However, the oncologists cannot determine which ones would worsen with time and hence, end up treating every patient with expensive and harmful medications. Researchers at University of Pittsburgh Medical Center and Carnegie Mellon University are relying on the 3D printing technology to print the duct between the mammary gland and the nipple. They hope to use the duct to grow breast tumors artificially in the lab and detect biomarkers that identify potentially malignant tumors. Mobile Devices Israeli startup MobileODT has developed a 3D printed mobile accessory known as the Mobile Coloscope. The doctors can attach the accessory to any smartphone and use it to click magnified images of the cervix. The images can help diagnose cervical cancer at an early stage. A disproportionately large number of women die of cervical cancer in the developing world due to inaccurate and delayed diagnosis. MobileODT hopes their device will help physicians overcome this hurdle. The success of these prototypes is inspiring other scientists to find novel cancer screening methods using 3D printing. Several projects have received millions of dollars in grant money with both healthcare professionals and scientists betting heavily on this technology. Soon, 3D printed devices may change the way physicians diagnose and treat cancer, and thereby help lower mortality rates significantly.

mattjohnson

mattjohnson

 

Easily Create 3D Printable Muscle and Skin STL Files from Medical CT Scans

In this tutorial we will learn how to use the free medical imaging conversion service on embodi3D.com to create detailed anatomic muscle and skin 3D printable models in STL file format from medical CT scans. Muscle models show the detailed musculature by subtracting away the skin and fat. Even when created from a scan of an obese person, the model looks like it comes from a bodybuilder, Figure 1A. Skin models show an exact replica of the skin surface. The finest details are captured, including wrinkles and veins underneath the skin. Hair however is not captured in a CT scan and thus the model does not have any hair, Figure 1B. Figure 1A (left): A muscle 3D printable model. Figure 1B (right): A skin 3D printable model   These models can be used for a variety of purposes such as medical and scientific education and research. Additionally, the skin models can be used to re-create a person's likeness in 3D from a medical scan. If you have had a CT scan of the head, you can create a lifelike replica of your head. You can create replicas of your friends, family, or even pets if they have had a medical CT scan. Alternatively, if you have a loved one who passed away but had a CT scan prior to death, you can use the scan to re-create an exact replica of their face. Even scans that are years old can be used for this purpose. Some people may consider this to be a little creepy, so if you are considering doing this think carefully first.   Before proceeding please register for an embodi3D.com account if you haven't already. You will need an account to use the service. It is highly recommended that you download the associated file pack for this tutorial so that you can follow along with the exact same files that are used in this tutorial.   >> DOWNLOAD THE FREE FILE PACK BY CLICKING HERE <<   If you are interested in learning how to use the free embodi3D.com service, see my prior tutorials on creating bone models, processing multiple models simultaneously, and sharing and selling your models on the embodi3D.com website.       If you are interested in converting your own CT scan or that of a friend or family member, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figure 2 shows the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available. If you have downloaded the file pack for this tutorial, example CT scans are included   Figure 2A, the Image Management (radiology) department at my hospital, where you can pick up a DVD of your CT scan as shown in Figure 2B (right). My hospital does this for free, but some may charge a trivial fee.   PART 1: Creating a Muscle STL model from NRRD File   Before we begin please bear in mind that this process only works for CT scan images. It will not work for MRI images. Before proceeding please check that the scan you wish to convert is a CT (CAT) scan!   Step 1: Convert Your CT scan to an Anonymized NRRD File with 3D Slicer Open 3D Slicer. If you don't have the software program you can download it for free from slicer.org. Once Slicer has opened, take the folder from the download pack that is called STS_004. This folder contains anonymized DICOM images from a CT scan of the legs of a 24-year-old woman who had a muscle tumor. Drag and drop the entire folder onto the Slicer window, as shown in Figure 3. Slicer will ask you if you want to load the images into the DICOM database. Click OK. Slicer will also ask you if it should copy the images into the database, click Copy. Slicer will take about one minute to load the scanned. Figure 3: Drag-and-drop the STS_004 DICOM folder from the file pack onto the Slicer window   Next, load the scan into the active wor king area in slicer. If the DICOM browser is not open, click on the Show DICOM browser button, as shown in Figure 4. Click on the STS_004 patient and series, and click the Load button, as shown in Figure 4. The leg CT scan will now load into the active seen within Slicer, as shown in Figure 5.   Figure 4: Open the DICOM browser and load the study into the active seen   Figure 5: The leg CT scan is shown in the active seen   Step 2: Trim the Scan so that only the Right Thigh is included. Click on the Volume Rendering module from the Modules drop-down menu as shown in Figure 6. Turn on volume rendering by clicking on the eyeball button, as shown in Figure 7. Then, center the model in the 3D pane by clicking on the crosshairs button, Figure 7. If you don't have the same window layout as shown in Figure 7, you can correct this by clicking on the Four-Up window layout from the window layout drop-down menu, as shown in Figure 8.   Figure 6: Turn on the volume rendering module   Figure 7: Center the rendered volume.   Figure 8: Make sure you are in the Four-Up window layout   Next we are going to crop the volume so that we exclude everything other than the right knee and thigh. From the modules menu, select All Modules, Crop Volume, as shown in Figure 9. Turn on ROI visibility by clicking on the eyeball button, as shown in Figure 10. Then, move the region of interest box so that it only encapsulates the right thigh, as shown in Figure 10. You can adjust the size of the box by grabbing on the colored circular handles and moving the sides of the box as needed.   Figure 9: The Crop Volume module.   Figure 10: Turning on and adjusting the crop volume ROI (Region Of Interest) Once the crop volume ROI is adjusted to the area that you want, perform the crop by clicking on the Crop button, Figure 11.   Figure 11: the Crop button.   The new, smaller volume that encompasses the right fight and knee has been assigned a cryptic name. The entire scan had a name of "2: CT IMAGES – RESEARCH," and the new thigh volume has a name "2: CT IMAGES-RESEARCH-subvolume-scale_1." That's a mouthful and I want to rename it to something more descriptive. I'm going to select the Volumes module, and then select the "2: CT IMAGES-RESEARCH-subvolume-scale_1" from the Active Volume drop-down menu. Then, from the same drop-down menu I'm going to select "Rename Current Volume". Type in whatever name you want. In this case I'm choosing "right thigh."   Figure 12: Renaming the newly cropped volume.   Step 3: Save the right thigh volume as an anonymized NRRD file.   Click on the Save button in the upper left-hand corner. The save window is then shown. All the checkboxes on the left except for the one that corresponds to the right by. Make sure the file format for this line says NRRD (.nrrd). Make sure you specify the proper directory you want the file to be saved as. When you are satisfied click on save. This is demonstrated in Figure 13. In the specified directory you should see a called right thigh.nrrd. Figure 13: The save file options.   Step 4: Upload the NRRD file to embodi3D.com   Make sure you are logged into your embodi3D.com account. Click on Imag3D from the nav bar, Launch App. Then drag-and-drop your NRRD file onto the upload pain, as shown in Figure 14. Figure 14: Uploading the NRRD file to embodi3D.com.   While the file is uploading, fill in the required fields, including the name of the uploaded file, a brief description, file privacy, and license type. Except the terms of use. next, turn on Imag3D processing.  Under operation, select "CT NRRD to Muscle STL."  Leave the threshold value unchanged. Under quality, select medium or high. Specify your privacy preference for your output STL file. If you are going to share this file, you can choose to share it for free or sell it. Please see my separate tutorial on how to share and sell your files on the embodi3D.com website for additional details. When you're happy with your choices, save the file, as shown in Figure 15: Figure 15: File processing options.   Step 5: Download your new STL file after processing is completed.   In about 5 to 15 minutes you should receive an email that says your file has finished processing and is ready to download. Follow the link in the email or access the new file via your profile on the embodi3D.com website. Your newly created STL file should have several rendered thumbnails associated with it on its download page. If you want to download the file click on the Download button, as shown in Figure 16. Figure 16: the download page for your new muscle STL file   I opened the file in AutoDesk MeshMixer to have another look at it, and it looks terrific, as shown in Figure 17. This file is ready to 3D print! Figure 17: The final 3D printable muscle model. PART 2: Creating a Skin Model STL File Ready for 3D Printing Creating a skin model is essentially identical to creating the muscle model, except instead of choosing the CT NRRD to Muscle STL on the embodi3D.com service, we choose CT NRRD to Skin STL. Step 1: Load DICOM image set into Slicer   Launch Slicer. From the tutorial file pack drag and drop the MANIX folder onto the Slicer window to load this head and neck CT scan data set. This is shown in Figure 18.   Figure 18: Loading the head and neck CT scan into Slicer. It may take a minute or two to load. From the DICOM browser, click on the ANGIO CT series as shown in Figure 19.   Figure 19: Loading the ANGIO CT series from the MANIX data set   Step 2: Skip the trimming and crop volume operations   In this case we don't need to trim and crop a volume as we did with the muscle file above. We can skip Step 2. Step 3: Save the CT scan in NRRD format. Just as with the muscle file above, save the volume in NRRD format. Click on the save button, make sure that the checkbox for the nrrd file is selected and all other checkboxes are deselected. Specify the correct directory you want the file to be saved in, and click Save.   Step 4: Upload your NRRD file of the head to the embodi3D website. Just as with the muscle file process as shown above, upload the head NRRD file to the embodi3D.com website. Enter in the required fields. In this case, however, under Operation choose the CT NRRD to Skin STL operation, as shown in Figure 20. Figure 20: Selecting the CT NRRD to Skin STL file operation   Step 5: Download your new Skin STL file   After about 5 to 15 minutes, you should receive an email that says your file processing has been completed. Follow the link in the email or look for your file in the list the files you own in your profile. You should see that your skin STL file has been completed, with several rendered images, as shown in Figure 21. Go ahead and download your file. You can then check the quality of your file in Meshmixer as shown in Figure 22. In this instance everything looks great and the file is error free and ready for 3D printing.  
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!
 

Dr. Mike

Dr. Mike

 

Will 3D printed organs-on-chips replace animal testing?

Harvard University researchers have 3D printed the first organ-on-a-chip with integrated sensors. This new technology could revolutionize the biomedical research field, which has relied on expensive and time-consuming animal studies and cell cultures for decades. Organs-on-chips, or microphysiological systems (MPS), are microchips that recapitulate the microarchitecture and functions of living human organs in vitro. The Wyss Institute at Harvard University explains MPS as follows: “Each individual organ-on-chip is composed of a clear flexible polymer about the size of a computer memory stick that contains hollow microfluidic channels lined by living human cells interfaced with a human endothelial cell-lined artificial vasculature, and mechanical forces can be applied to mimic the physical microenvironment of living organs.”  Typically, MPS are made in clean rooms using a complex, multi-step lithographic process. Collecting data requires microscopy or high-speed cameras. What makes this new MPS different, is the simplified manufacturing process and the integrated sensors. Both improvements were accomplished with multi-material 3D printing. The researchers designed six “inks” that enable integration of sensors. The researchers successfully 3D printed a heart-on-a-chip with integrated sensors. They then used the heart-on-a-chip in various studies, including drug responses.  The integrated sensors enable continuous data collection, allowing scientists to study gradual changes over longer periods of time. Read the research published in Nature Materials or watch this video to learn more:         Photo and video credit: Wyss Institute for Biologically Inspired Engineering at Harvard University

Els

Els

 

Overcome Hair Loss with 3D Printing

Significant thinning or loss of hair can have a detrimental impact on the individual’s overall quality of life. Men and women with unhealthy hair often suffer from emotional issues and low self-esteem. The condition may also be indicative of an underlying medical problem. As per the American Hair Loss Association, two-thirds of American men experience some hair loss by the age of 35 and about 80 percent of them have significant thinning of hair by the age of 50. Approximately half of women over the age of 50 also suffer from serious hair loss. Apart from genetics and lifestyle, certain medications and infections can also contribute to the condition. You will find a variety of hair loss treatments in the market today ranging from herbal products to surgical interventions. However, none of these solutions have succeeded in producing dramatic results in a consistent manner. Researchers are, therefore, looking at three-dimensional (3D) medical printing and bioprinting to find products that really work, and their efforts seem to be paying off. 3D Printing Technology to Create Cranial and Hair Implants AdviHair, a subsidiary of London-based AdviCorp PlC, has developed a unique set of cranial prosthetics known as the CNC Hair Replacement System. The company uses 3D printing technology to create implants that conform to the patient’s scalp measurement and skin color. The product can help conceal partial or full scalp baldness associated with Alopecia. Once the prosthetic scalp is placed in position, it behaves like regular hair. You can swim, wash and style it the way you want. The product is expected to benefit more than 6.8 million Americans suffering from Alopecia, an autoimmune disorder that occurs when the patient’s immune system destroys his own hair follicles. The prosthetics are ideal for individuals who cannot undergo transplantation or other Alopecia treatments. Cosmetic giant L’ Oreal has collaborated with French bioprinting company Poietis to print hair follicles that will enhance their understanding of hair biology. The process involves creation of a digital map that indicates the exact position of the living cells and other tissue fragments. The digital map is used to generate instructions for the printing process. A pulsing laser bounces off a mirror through a lens and knocks one micro-droplet of the bio-ink into its position. Approximately 10,000 such droplets are deposited each second. L’Oreal is hoping to use this technology to create products that will treat and prevent hair loss at a realistic price. Improved 3D Printing Software for Hair Implants Although 3D printed cranial prosthetics and hair implants are gaining popularity, many of them take several hours to print. Researchers at Massachusetts Institute of Technology’s Media Lab are, therefore, working on a software platform called Cilllia that allows users to print hair-like structures within minutes. Additionally, researchers at the institute are looking beyond the aesthetics to explore other major functions of the follicles including adhesion, sensing, thermal protection and actuation. Hair loss can be stressful and overwhelming, and the treatments can be expensive. Many patients experience poor results in spite of their best efforts. Scientists are now using 3D printing to overcome the drawbacks associated with conventional treatments, and their recent success is offering hope to the millions of hair loss sufferers across the globe.

mattjohnson

mattjohnson

 

Atlas and Axis, 3D PDF

Hello My recent anatomy projects forced me to start importing my 3d models into 3d pdf documents. So I'll share with you some of my findings. The positive things about 3d pdf's are: 1. You can import a big sized 3d model and compress it into a small 3d pdf. 40 Mb stl model is converted into 750 Kb pdf. 2. You can run the 3d pdf on every computer with the recent versions of Adobe Acrobat Reader. Which means literally EVERY computer. 3. You can rotate, pan, zoom in and zoom out 3d models in the 3d pdf. You can add some simple animations like spinning, sequence animations and explosion of multi component models. 4. You can add colors to the models and to create a 3d scene. 5. You can upload it on a website and it can be viewed in the browser (if Adobe Acrobat Reader is installed). The negative things are: 1. Adobe Reader is a buggy 3d viewer. If you import a big model (bigger than 50 Mb) and your computer is business class (core I3 or I5, 4 Gb ram, integrated video card), you'll experience some nasty lag and the animation will look terrible. On the same computer regular 3d viewer will do the trick much better. 2. You can experience some difficulties with multi component models. During the rotation, some of the components will disappear, others will change their color. Also the model navigation toolbar is somewhat hard to control. 3. The transparent and wireframe polygon are not as good as in the regular 3d viewers. The conclusion: If you want to demonstrate your models to a large audience, to sent it via email and to observe them on every computer, 3d pdf is your format. For a presentation it's better to use a regular 3d viewer, even the portable ones will do the trick. But if the performance is not the goal, 3d pdf's  are a good alternative. Here is a model of atlas and axis as 3d pfg: https://www.dropbox.com/s/2gm7occq5ur50um/vertebra.pdf?dl=0 Best regards, Peter  

valchanov

valchanov

 

3D Printed Batteries Are Edible with Many Medical Device Applications

Implantable medical devices help diagnose and treat serious health conditions ranging from anatomical abnormalities to cardiovascular illnesses and kidney diseases. Commonly used devices include implantable cardioverter defibrillators, pacemakers, intra-uterine devices, spine crews, hip implants, metal screws, and artificial knees. Recent years have seen a significant increase in the use of such implants, which has led to the creation of several innovative products with improved function. Batteries play a crucial role in the successful operation of certain implantable devices. Most products rely on lithium cells that are powerful and easy to use. These electrochemical power sources can, however, lead to toxic side effects. Some patients may also experience biocompatibility issues. Healthcare professionals, nonetheless, had limited options, at least until now. The 3D Printed Battery Researchers at Carnegie Mellon University are aiming to overcome the drawbacks associated with traditional batteries by developing biodegradable versions made from natural ingredients. They have developed a prototype battery that can provide 5 milliWatts of power for up to 18 hours. This energy is enough to deliver medications slowly over a span of several hours or to detect the growth of pathogenic bacteria within the body.     The battery is made from melanin pigment found in skin, hair and nails. The pigment protects the body by absorbing ultraviolet light and toxic free radicals. It also has the ability to bind to metallic ions and can therefore, transform into the perfect battery material. While melanin can form either the anodic or the cathodic terminal of the battery, magnesium oxide is used as the second terminal and the GI fluid comprises the electrolyte. The materials are housed in a three-dimensional (3D) printed capsule made from polylactic acid, or PLA.   A 3D printer allows researchers to deposit the desired materials on a substrate in a specific pattern. It was invented in the 1980s to create engineering prototypes. Soon, researchers began using 3D printers in the field of medicine to improve patient outcomes. The technology helps customize the shape and the size of the outer capsule as per the needs of the consumer. The 3D printed capsule maintains the structural integrity of the battery and allows it to glide smoothly through the device. The capsule can dissolve quickly once it completes the essential functions. Other natural components within the battery can also degrade without producing any toxic side effects. The Future Currently, most ingestible and degradable probes and drug delivery systems remain in the body for about 20 hours. Although melanin batteries are less powerful when compared to their lithium counterparts, researchers believe that they could work very well with devices that remain in the body for only a few hours. The new battery is in the initial stages of development and will need to undergo extensive clinical testing before actual use. Nonetheless, it is a step in the right direction. Eventually, it may be possible to create more powerful versions of edible batteries that can support all types of medical devices, irrespective of their duration of use.

mattjohnson

mattjohnson

 

How to Share, Sell, Organize, and Reprocess Automatically Generated 3D Printable Medical STL Models on Embodi3D

Please note that any references to “Imag3D” in this tutorial should be replaced with “democratiz3D”   In this tutorial we will discuss how to share, sell, organize, and reprocess 3D printable medical models you make using the free online democratiz3D service from embodi3D. democratiz3D is a powerful tool that automatically converts a medical CT scan into a 3D printable file in minutes with minimal user input. It is no longer necessary to master complicated desktop software and spend hours manually segmenting to create a 3D printable model. Learn how to make high quality medical 3D models with democratiz3D by following my introductory guide to creating medical 3D printing files and my more advanced 3D printing file processing tutorial. Once you create your medical masterpiece, you can share, sell, organize, or tweak your model to make it perfect. This tutorial will show you how.         Resubmit your CT Scan for Reprocessing into Bone STL If you are trying to learn the basics of how to convert CT scans into 3D printable STL models, please see my earlier tutorials on basic creation of 3D printable models and more advanced multiprocessing. If you are not 100% satisfied with the quality of your STL model, you can resubmit the input scan file for repeat processing. To do this, go to the page for your input NRRD file. IMPORTANT: this is the NRRD file you originally uploaded to the website, NOT the STL file that was generated for you by the online service. Since both the original NRRD file and the processed STL file have similar titles, you can tell the difference by noting that the NRRD file you uploaded won't have any thumbnails, Figure 1. In most cases, the processed file will have the word "processed" appended to the file name.   Figure 1: Choose the original NRRD file, not the generated STL file.   You can find your files underneath your profile, as shown in Figure 2. That will show you your most recent activity, including recently uploaded files.   Figure 2: Finding your files under your profile.   If you uploaded the file long ago or contribute a lot of content to the site, your uploaded NRRD file may not be among the first content item shown. You can search specifically for your files by clicking on See My Activity under your Profile, and selecting Files from the left hand now bar, as shown in Figures 3 and 4.     Figure 3: Showing all your activity.  
Figure 4: Showing the files you own.   Once you have found your original NRRD file, open the file page and select File Actions on the lower left-hand corner, as shown in Figure 5. Choose Edit Details as shown in Figure 6.   Figure 5: File Actions – start making changes to your file   Figure 6: Edit Details   Scroll down until you reach the democratiz3D Processing section. Make sure that the democratiz3D Processing slider is turned ON. Then, make whatever adjustments you want to the processing parameters Threshold and Quality, as shown in Figure 7. Threshold is the value in Hounsfield units to use when performing the initial segmentation.   Quality is a measure of the number of polygons in the output mesh. Low quality is quick to process and generates a small output file. Low quality is suitable for small and geometrically simple structures, such as a patella or single bone. High quality takes longer to process and produces a very large output file, sometimes with millions of polygons. This is useful for very large structures or complex anatomy, such as a model of an entire spine where you wish to capture every crack and crevice of the spine. Medium quality is a good balance and suitable in most cases.   Figure 7: Changing the processing parameters.   When you're happy with your parameter choices, click Save. The file will now be submitted for reprocessing. In 5 to 15 minutes you should receive an email saying that your file is ready. From this NRRD file, an entirely new STL file will be created using your updated parameters and saved under your account.   Sharing your 3D Printing File on embodi3D.com Sharing your file with the embodi3D community is easy. You can quickly share the file by toggling the privacy setting on the file page underneath the File Information box on the lower right, as shown in Figure 8. If this setting says "Shared," then your file is visible and available for download by registered members of the community. If you wish to have more detailed control over how your file is shared, you can edit your file details by clicking on the File Actions button on the lower left-hand side of the file page, also shown in Figure 8. Click on the Edit Details menu item. This will bring you to the file editing page which will allow you to change the Privacy setting (shared versus private), License Type (several Creative Commons and a generic paid file license are available), and file Type (free versus paid). These are shown in detail in Figure 9. Click Save to save your settings.   Figure 8: Quick sharing your file, and the File Actions button   Figure 9: Setting the file type, privacy, and license type for your file.     Sell your Biomedical 3D Printing File and Generate Income If you would like to sell your file and charge a fee for each download, you may do so by making your file a Paid File. If you have a specialized model that there is some demand for, you can generate income by selling your file in the marketplace. From the Edit Details page under File Actions, as shown in Figure 8, scroll down until you see Type. Choose Paid for the Type. Choose the price you wish to sell your file for in the Price field. This is in US dollars. Buyers will use PayPal to purchase the file where they can pay with Paypal funds or credit card. Make sure that the privacy setting is set to Shared. If you list your file for sale but keep it private and invisible to members, you won't sell anything. Finally, make sure you choose an appropriate license for users who will download your file. The General Paid File License is appropriate and most instances, but you have the option to include a customized license if you wish. This is shown in Figure 10.   Figure 10: Configuring settings to sell your file   The General Paid File License contains provisions appropriate for most sellers. It tells the purchaser of your file that they can download your file and create a single 3D print, but they can't resell your file or make more than one print without paying you additional license fees. All purchasers must agree to the license prior to download. If you wish to have your own customized license terms, you can select customized license and specify your terms in the description of the file.   Organize your file by moving it to a new category   If you share your file, you should move the file into an appropriate file category to allow people to find it easily. This is quite simple to do. From the file page, select File Actions and choose the Move item, as shown in Figure 11. You will be able to choose any of the file categories. Choose the one that best fits your particular file.  
Figure 11: Moving your file to a new category.
That's it! Now you can share your amazing 3D printable medical models with the world.

Dr. Mike

Dr. Mike

 

How to Convert Multiple 3D Printable Bone Model STL Files from a CT Scan

Please note that any references to “Imag3D” in this tutorial has been replaced with “democratiz3D”   In this tutorial you will learn how to create multiple 3D printable bone models simultaneously using the free online CT scan to bone STL converter, democratiz3D. We will use the free desktop program Slicer to convert our CT scan in DICOM format to NRRD format. We will also make a small section of the CT scan into its own NRRD file to create a second stand-alone model. The NRRD files will then be uploaded to the free democratiz3D online service to be converted into 3D printable STL models.   If you haven't already, please see the tutorial A Ridiculously Easy Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes, which provides a good overview of the democratiz3D service.   You should download the file pack that accompanies this tutorial. This contains an anonymized DICOM data set that will allow you to follow along with the tutorial.   >>> DOWNLOAD THE TUTORIAL FILE PACK <<<         Step 1: Register for an Embodi3D account
 
If you haven't already done so, you'll need to register for an embodi3D account. Registration is free and only takes a minute. Once you are registered you'll receive a confirmatory email that verifies you are the owner of the registered email account. Click the link in the email to activate your account. The democratiz3D service will use this email account to send you notifications when your files are ready for download.   Step 2: Create NRRD Files from DICOM with Slicer   Open Slicer, which can be downloaded for free from www.slicer.org. Take the folder that contains your DICOM scan files and drag and drop it onto the slicer window, as shown in Figure 1. If you downloaded the tutorial file pack, a complete DICOM data set is included. Click OK when asked to load the study into the DICOM database. Click Copy when asked if you want to copy the images into the local database directory. Remember, this only works with CT scans. MRIs cannot be converted at this time.   Figure 1: Dragging and dropping the DICOM folder onto the Slicer application. This will load the CT scan.   A NRRD file that encompasses the entire scan can easily be created by clicking the save button at this point. Before we do that however, we are going to create a second NRRD file that only contains the lumbar spine, which will allow us to create a second 3D printable bone model of the lumbar spine. Open the CT scan by clicking on the Show DICOM Browser button, selecting the scan and series within the scan, and clicking the Load button. The CT scan will then load within the multipanel viewer.   From the drop-down menu at the top left of the Slicer window, select All Modules and then Crop Volume, as shown in Figure 2. You will now want to create a Region Of Interest (ROI) to encompass the smaller volume we want to make. Turn on the ROI visibility button and then under the Input ROI drop-down menu, select "Create new AnnotationROI," As shown in Figure 3.   Figure 2: Choosing the Crop Volume module   Figure 3: Turn on ROI visibility and Create a new AnnotationROI under the Input ROI drop-down menu.   A small cube will then be displayed in the blue volume window. This represents the sub volume that will be made. In its default position, the cube may not overlay the body, and may need to be dragged downward. Grab a control point on the cube and drag it downward (inferiorly) as shown in Figure 4.
Figure 4: Grab the sub volume ROI and drag it downwards until it overlaps with the body.   Next, use the control points on the volume box to position the volume box over the portion of the scan you wish to be included in the small 3D printable model, as shown in Figure 5. Figure 5: Adjusting the control points on the crop volume box.   Once you have the box position where you want it, initiate the volume crop by clicking the Crop! button, as shown in Figure 6. Figure 6: The Crop! button   You have now have two scan volumes that can be 3D printed. The first is the entire scan, and the second is the smaller sub volume that contains only the lumbar spine. We are now going to save those individual volumes as NRRD files. Click the Save button in the upper left-hand corner. In the Save Scene window, uncheck all items that do not have NRRD as the file format, as shown in Figure 7. Only NRRD file should be checked. Be sure to specify the directory that you want each file to be saved in.   Figure 7: The Save Scene window   Your NRRD files should now be saved in the directory you specified.   Step 3: Upload your NRRD files and Convert to STL Files Using the Free democratiz3D Service   Launch your web browser and go to www.embodi3d.com. If you haven't already register for a account. Registration is free and only takes a minute. Click on the democratiz3D navigation item and select Launch App, as shown in Figure 8.   Figure 8: launching the democratiz3D application.   Drag-and-drop both of your NRRD files onto the upload panel. Fill in the required fields, including a title, short description, privacy setting (private versus shared), and license type. You must agree to the terms of use. Please note that even though license type is a required field, it only matters if the file is shared. If you keep the file private and thus not available to other members on the site, they will not see it nor be able to download it.   Be sure to turn on the democratiz3D Processing slider! If you don't turn this on your file will not be processed but will just be saved in your account on the website. It should be green when turned on. Once you turn on democratiz3D Processing, you'll be presented with some basic processing options, as shown in Figure 9. Leave the default operation as "CT NRRD to Bone STL," which is the operation that creates a basic bone model from a CT scan in NRRD format. Threshold is the Hounsfield attenuation to use for selecting the bones. The default value of 150 is good for most applications, but if you have a specialized model you wish to create, you can adjust this value. Quality denotes the number of polygons in your output file. High-quality may take longer to process and produce larger files. These are more appropriate for very large or detailed structures, such as an entire spinal column. Low quality is best for small structures that are geometrically simple, such as a patella. Medium quality is balanced, and is appropriate for most circumstances.   Figure 9: The democratiz3D File Processing Parameters.   Once you are satisfied with your processing parameters, click submit. Both of your nrrd files will be processed in two separate bone STL files, as shown in Figure 10. The process takes 10 to 20 minutes and you will receive an email notifying you that your files are ready. Please note, the stl processing will finish first followed by the images. Click on the thumbnails for each model to access the file for download or click the title.   Figure 10:  Two files have been processed simultaneously and are ready for download   Step 4: CT scan conversion is complete your STL bone model files are ready for 3D Printing That's it! Both of your bone models are ready for 3D printing. I hope you enjoyed this tutorial. Please use the democratiz3D service and  SHARE the files you create with the community by changing their status from private or shared. Thank you very much and happy 3D printing!

Dr. Mike

Dr. Mike

 

The Benefits of Additive Manufacturing Applies to 3D Printed Pills and Medication

In August 2015, the U.S. Food and Drug Administration (FDA) approved the first three-dimensional (3D) printed drug for commercial use when it allowed Pennsylvania-based Aprecia Pharmaceuticals to manufacture and market its anti-epileptic pill Spritam. The company relied on additive printing technology to create a rapidly dissolving pill that could be consumed with very little water. One of the main goals was to benefit patients who are unable to swallow medications, especially during an epileptic fit.

The licensed ZipDose technology used by Aprecia Pharmaceuticals combines formulation and material science with additive printing technology. The process involves deposition a thin layer of the powdered medicine on a substrate followed by the addition of a liquid to bind the particles into porous layer. The process is repeated multiple times to create a pill of the desired size and concentration. The success of Spritam has encouraged Aprecia Pharmaceuticals to use ZipDose technology to develop medications for other serious illnesses as well.   Dosage – Additive printing allows pharma companies to print drugs at specific dosages. Consequently, the patients do not have to suffer from poor prognosis associated with low-dose medications or consume high doses of drugs that can lead to unwanted side effects. As 3D printing technology becomes more prevalent in the pharmaceutical world, doctors can request for a specific dose of the drug instead of choosing from the available options. Solubility – Although rapidly disintegrating, porous pills have been in use for several years, they usually provide lower doses of the active ingredient. Three-dimensional printing technology has allowed Aprecia Pharmaceuticals to add up to 1,000 mg of the potent drug into one Spritam pill while retaining its solubility. This can benefit a large section of the population including young children, elderly, and patients suffering from complex neurological disorders. Compatible shape – Additive printing also helps produce pills in a variety of shapes and sizes, as per the needs of the consumer. Drug companies can produce small batches of the drug based on specific demand. Distribution of Production and Distribution – Unlike large machines, 3D printers are easy to setup and operate. The manufacturer can shift the production of the drug to a location that is closer to the consumer and thereby, lower transportation and distribution costs and reduce wait times for patients with potentially life-threatening conditions. Simplify Research and Development - 3D printing can also simplify research and development of new medications by making the process more efficient and cost-effective. Potential compounds can be printed in the laboratory and tested on 3D printed organs and cell lines for immediate results.
Recent developments in additive printing have forced most drug companies to sit up and take notice. They are investing millions of dollars in the technology to speed up drug development. While the time to replace medication prescriptions with printer algorithms is not yet here, 3D printing is bound to have a huge impact on the way companies develop and manufacture drugs in the near future.   Sources: http://www.computerworld.com/article/3048823/3d-printing/this-is-the-first-3d-printed-drug-to-win-fda-approval.html https://www.asme.org/engineering-topics/articles/manufacturing-design/3dprinted-drugs-does-future-hold http://www.npr.org/sections/thetwo-way/2015/08/04/429341196/your-pill-is-printing-fda-approves-first-3d-printed-drug

mattjohnson

mattjohnson

 

Three-Dimensional Printers Changing Hospitals for Good

The three-dimensional (3D) medical printing and bioprinting industry is evolving at a rapid pace as 3D printers continue to move beyond research labs into commercial manufacturing facilities and hospitals. The printers are being used to create anatomical models, customized implants and even body parts that help treat, manage and prevent complex illnesses and injuries. The technology has contributed to the success several challenging surgical interventions in the recent times.   Three-dimensional Printing Systems While scientists are using 3D printers for a variety of purposes, most physicians are relying on them to create patient-specific models of targeted organs and tissues. Healthcare professionals obtain accurate dimensions of the patient’s body parts from radiological images and feed the information into a computer to print exact replicas of the organs. These models help the surgeons assess the abnormality with precision and practice the surgery before the actual procedure.

Several consumer-friendly 3D printing systems have been created to meet these needs. Belgium-based Materialise offers Mimics inPrint system that allows physicians to directly import patient images from hospital PACS and use them for 3D printing. The product comes with DICOM compatibility that supports all types of imaging machines. The semi-automated segmentation and editing tools within the printer’s software system ensure error-free printing and enhanced communication. Materialise sets up the entire system and trains the hospital staff to operate it efficiently.

Stratasys Inc. also offers additive printing technology to hospitals across the globe. It has the widest variety of materials ranging from clear, rubberlike and biocompatible photopolymers to rigid and flexible composite materials in over 360,000 colors. The Medical Innovation Series from Stratsys has been created for physicians, medical device designers, clinical educators and other professionals in the healthcare industry.
  Success Stories Twelve National Health System (NHS) hospitals in the United Kingdom are relying on Stratsys printers to create models that allow surgeons to analyze patients’ condition, test implants and practice surgical interventions for better outcomes. Most popular 3D models at NHS hospitals include jaw bones for facial reconstruction surgeries, hip models for hip replacements, forearms for repairing deformed bones, and cranial plastics for fixing holes in a person’s skull.

Doctors Without Borders, the Italian humanitarian organization, is also using 3D printed replicas of hospital models to setup new ventures in remote areas of the world. The technology allows physicians to have a realistic experience and thereby, improve patient care.

Several other healthcare facilities are also using additive printing technology for increased efficiency. Physicians at Hong Kong’s Queen Elizabeth Hospital used 3D printing technology to help a 77-year-old woman suffering from two damaged valves. The patient had already undergone three open heart surgeries and needed a complex fourth intervention. The 3D printed model helped the doctors complete the surgery in just four hours. In another case, surgeons at Children’s Hospital in Colorado and engineers at Mighty Oak Medical created a 3D model of a patient’s spine to rehearse the surgery. The physicians also used additive printing technology to print customized brackets to treat the patient’s scoliosis.

These success stories are inspiring other hospitals to install 3D printers at their facilities. They would, however, require expertise to handle the printer and tools to eventually use the 3D model for clinical purposes. Several facilities are incorporating 3D printing training programs to build knowledge within the institution and to lower the lead times for the actual procedure. While the initial investment may appear significant, most experts agree that 3D printing technology can be a game changer as it can help physicians improve clinical outcomes and reduce costs associated with complicated surgical interventions.

mattjohnson

mattjohnson

 

A Ridiculously Easy Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes

Please note the democratiz3D service was previously named "Imag3D" In this tutorial you will learn how to quickly and easily make 3D printable bone models from medical CT scans using the free online service democratiz3D®. The method described here requires no prior knowledge of medical imaging or 3D printing software. Creation of your first model can be completed in as little as 10 minutes.   You can download the files used in this tutorial by clicking on this link. You must have a free Embodi3D member account to do so. If you don't have an account, registration is free and takes a minute. It is worth the time to register so you can follow along with the tutorial and use the democratiz3D service.   >> DOWNLOAD TUTORIAL FILES AND FOLLOW ALONG << Both video and written tutorials are included in this page.           Before we start you'll need to have a copy of a CT scan. If you are interested in 3D printing your own CT scan, you can go to the radiology department of the hospital or clinic that did the scan and ask for the scan to be put on a CD or DVD for you. Figures 1 and 2 show the radiology department at my hospital, called Image Management, and the CDs that they give out. Most radiology departments will have you sign a written release and give you a CD or DVD for free or with a small processing fee. If you are a doctor or other healthcare provider and want to 3D print a model for a patient, the radiology department can also help you. There are multiple online repositories of anonymized CT scans for research that are also available.     Figure 1: The radiology department window at my hospital.       Figure 2: An example of what a DVD containing a CT scan looks like. This looks like a standard CD or DVD.       Step 1: Register for an Embodi3D account   If you haven't already done so, you'll need to register for an embodi3d account. Registration is free and only takes a minute. Once you are registered you'll receive a confirmatory email that verifies you are the owner of the registered email account. Click the link in the email to activate your account. The democratiz3D service will use this email account to send you notifications when your files are ready for download.   Step 2: Create an NRRD file with Slicer If you haven't already done so, go to slicer.org and download Slicer for your operating system. Slicer is a free software program for medical imaging research. It also has the ability to save medical imaging scans in a variety of formats, which is what we will use it for in this tutorial. Next, launch Slicer. Insert your CD or DVD containing the CT scan into your computer and open the CD with File Explorer or equivalent file browsing application for your operating system. You should find a folder that contains numerous DICOM files in it, as shown in Figure 3. Drag-and-drop the entire DICOM folder onto the Slicer welcome page, as shown in Figure 4. Click OK when asked to load the study into the DICOM database. Click Copy when asked if you want to copy the images into the local database directory.     Figure 3: A typical DICOM data set contains numerous individual DICOM files.     Figure 4: Dragging and dropping the DICOM folder onto the Slicer application. This will load the CT scan.   Once Slicer has finished loading the study, click the save icon in the upper left-hand corner as shown in Figure 5. One of the files in the list will be of type NRRD. make sure that this file is checked and all other files are unchecked. click on the directory button for the NRRD file and select an appropriate directory to save the file. then click Save, as shown in Figure 6.     Figure 5: The Save button     Figure 6: The Save File box   The NRRD file is much better for uploading then DICOM. Instead of having multiple files in a DICOM data set, the NRRD file encapsulates the entire study in a single file. Also, identifiable patient information is removed from the NRRD file. The file is thus anonymized. This is important when sending information over the Internet because we do not want identifiable patient information transmitted.   Step 3: Upload the NRRD file to Embodi3D   Now go to www.embodi3d.com, click on the democratiz3D navigation menu and select Launch App, as shown in Figure 7. Drag and drop your NRRD file where indicated. While NRRD file is uploading, fill in the "File Name" and "About This File" fields, as shown in Figure 8.     Figure 7: Launching the democratiz3D application     Figure 8: Uploading the NRRD file and entering basic information To complete basic information about your NRRD file. Do you want it to be private or do you want to share it with the community? Click on the Private File button if the former. If you are planning on sharing it, do you want it to be a free or a paid (licensed) file? Click the appropriate setting. Also select the License Type. If you are keeping the file private, these settings don't matter as the file will remain private. Make sure you accepted the Terms of Use, as shown in Figure 9.     Figure 9: Basic information fields about your uploaded NRRD file   Next, turn on democratiz3D Processing by selecting the slider under democratiz3D Processing. Make sure the operation CT NRRD to Bone STL is selected. Leave the default threshold of 150 in place. Choose an appropriate quality. Low quality produces small files quickly but the output resolution is low. Medium quality is good for most applications and produces a relatively good file that is not too large. High quality takes the longest to process and produces large output files. Bear in mind that if you upload a low quality NRRD file don't expect the high quality setting to produce a stellar bone model. Medium quality is good enough for most applications. If you wish, you have the option to specify whether you want your output file to be Private or Shared. If you're not sure, click Private. You can always change the visibility of the file later. If you're happy with your settings, click Save & Submit Files. This is shown in Figure 10.     Figure 10: Entering the democratiz3D Processing parameters.       Step 4: Review Your Completed Bone Model After about 10 to 20 minutes you should receive an email informing you that your file is ready for download. The actual processing time may vary depending on the size and complexity of the file and the load on the processing servers. Click on the link within the email. If you are already on the embodied site, you can access your file by going to your profile. Click your account in the upper right-hand corner and select Profile, as shown in Figure 11.     Figure 11: Finding your profile.   Your processed file will have the same name as the uploaded NRRD file, except it will end in "– processed". Renders of your new 3D model will be automatically generated within about 6 to 10 minutes. From your new model page you can click "Download this file" to download. If you wish to share your file with the community, you can toggle the privacy setting by clicking Privacy in the lower right-hand corner. You can edit your file or move it from one category to another under the File Actions button on the lower left. These are shown in Figure 12.     Figure 12: Downloading, sharing, and editing your new 3D printable model.   If you wish to sell your new file, you can change your selling settings under File Actions, Edit Details. Set the file type to be Paid, and specify a price. Please note that your file must be shared in order for other people to see it. This is shown in Figure 13. If you are going to sell your file, be sure you select General Paid File License from the License Type field, or specify your own customized license. For more information about selling files, click here.     Figure 13: Making your new file available for sale on the Embodi3D marketplace.     That's it! Now you can create your own 3D printable bone models in minutes for free and share or sell them with the click of a button.If you want to download the STL file created in this tutorial, you can download it here. Happy 3D printing!  

Dr. Mike

Dr. Mike

 

How 3D Printing is Changing Drug Discovery and Testing

Advances in science and technology are helping pharmaceutical companies and biotech giants to come up with novel molecules that may help treat serious and life-threatening conditions such as cancer, heart disease, and Alzheimer’s disease. However, bringing a new drug to the market can get complex and exhaustive. While most companies pass through the initial stages of drug development with ease, they face a lot of challenges during pre-clinical and clinical trials. Recent numbers reveal that only one in 5,000 drugs become accessible to patients. The biopharmaceutical industry spends over $31.3 billion on research and development each year. They also face a lot of ethical questions related to animal testing. Nonetheless, this scenario may soon change as additive printing technology becomes more accessible and dependable.   Additive printing, also known as three-dimensional (3D) printing, involves deposition of desired materials on substrates to obtain 3D objects with specific dimensions and characteristics. Many different types of 3D printers are available in the market. Some machines help the user print mechanical and non-living objects. Others can print living tissues and cells when relevant biomaterials are added in controlled environments. Researchers across the globe have already succeeded in printing complex tissue fragments and even small organs such as ears using 3D printers.   3D Printed Systems for Drug Testing Organovo, a leader in 3D printing technology, has created multicellular, dynamic and functional 3D human tissue models for research and pre-clinical testing. As per the company’s website, the printed tissue will remain viable in vitro for a significant period of time while exhibiting all the structural and functional features of the actual tissue. Pharmaceutical companies can use these fragments to study the impact of new drugs on human cells and to predict the final outcome with greater accuracy. Organovo claims that its exVive3D will help researchers “assess biochemical, genomic, proteomic, and unique histologic endpoints.” Nano3D BioSciences, a Texas-based startup, has collaborated with AstraZeneca and LC Sciences to develop a cell-based assay system to assess the effects of a panel of vasodilating and vasoconstricting compounds. The company hopes that the assay will soon become a standard in toxicity testing and in the development of cardiovascular drugs.      Similarly, a Canadian company, Aspect Biosystems, allows researchers to create customized tissue fragments for drug testing. The researchers will place specific cells in a hydrogel and print tissue fragments that are allowed to grow in an incubator until they achieve the desired dimensions. The components will resemble the target tissue in structure and function.   Researchers at University of California, San Diego, have printed tissue fragments that closely mimic the human liver. According to Shaochen Chen, a NanoEngineering professor at the University, most companies spend 12 years and about $1.8 billion to create one FDA-approved drug. Their 3D printed liver tissue can help companies to perform pilot studies with minimal effort instead of waiting for animal testing or clinical trials, and thereby save millions of dollars.   Benefits Apart from making pre-clinical trials more accessible and efficacious, 3D printed tissues also help drug companies overcome ethical issues associated with animal testing. Most researchers agree that animal testing is expensive, time-consuming and often inhumane. The animals require a lot of care, and this limits the number of tests that can be performed at a time. Additionally, results obtained from animal testing may not correlate with actual results in humans. The 3D printed tissue fragments help overcome such obstacles and may eventually allow drug companies to simplify research and development. In the long run, it may also help reduce costs and make therapeutics more accessible and effective for everyone.    Sources: http://thenextweb.com/insider/2016/03/29/3d-printing-changes-pharmaceutical-world-forever/#gref http://eandt.theiet.org/news/2016/aug/3d-bioprinting.cfm    

mattjohnson

mattjohnson

 

How BioBots is Shaping the Future of Medical 3D Printing and Bioprinting

The three-dimensional (3D) medical printing and bioprinting market has exploded in the last decade with the invention of several new printers that can print everything from anatomical models to living cells. Each new machine has contributed in its own way to the success of this industry. However, only a few of them have impacted the field of medicine the way BioBot 1 has done in the recent years.

BioBots, a Philadelphia-based startup, hopes to use 3D printing technology to cure diseases, eliminate organ transplantation wait times, reverse climate change, and promote life on other planets. Their BioBot 1 desktop 3D printer is capable of printing live tissues from human cells. The low-cost machine is making bioprinting technology accessible to everyone from major universities to small research labs and is thereby, helping transform medicine and biology.
  The History of BioBiots The BioBots printer began as a dorm room project for two of its co-founders who were biology and computer science students at the University of Pennsylvania. Their initial prototype won a university competition and a $50,000 grant through the Dreamit Health program. The team began building smaller, cheaper and more efficient printers and is currently targeting biotech and pharma majors that spend millions of dollars on clinical research. The printer may help the companies generate specific cells lines and tissue fragments to test their therapeutics.   Unique Features of the BioBots Printer The popularity of the BioBots printer is not without a reason. The machine comes with several novel features and a small footprint. It can essentially fit into most bio-safety hoods and allows the researchers to work in a sterile environment with ease. The printer uses standard petri dishes and 96-well plates to simplify the printing process. The user can upload designs, choose biomaterials and eventually print the tissue fragments with minimal effort.

The BioBots 1 printer uses visible blue light to cure biomaterials quickly without damaging the cells. It includes a compressed air pneumatic system with a pressure range of 0 to 10 PSI that accommodates a variety of viscous materials and helps achieve specific start and stop points. The linear rails guarantee 10-micron precision. The printer also has two heated extruder heads to achieve temperatures between room temperature to 120 degrees. The Bio-Ink BioBots 1 printer also differs from its rivals in the type of bioink it uses. The support material maintains the structural integrity of the cells during the printing process and prevents their degradation after the printing is complete. The user also opts for a scaffold or a matrix gel prior to adding the cells and printing the final tissue fragments. BioBots offers a large selection of products for its printers including support bioinks, sacrificial bioinks, matrix base reagents, matrix ECM proteins, matrix print enhancers, and curing bioinks. The company has also created a bioink open source allowing researchers to improve the technology further. Potential Uses of BioBots Printers Although BioBots is currently pitching its product to companies and research institutes involved in drug development, most experts are hopeful that the use of this printer will expand further to benefit patients waiting for organ transplants. Researchers at Drexel University are using the BioBots 1 to print bone tissue while University of Michigan professors are using it to print nerve tissue. Physicians may soon be able to print compatible body parts with lower risk of rejection prior to transplantation surgeries for greater success.

BioBots 1 printer definitely holds a competitive edge due to its small foot print, ease of use, wide selection of bioinks, and lower price. The company is investing millions of dollars on improving the performance of the machine, and if recent developments are an indication, the BioBots is bound to play an important role in diagnoses, treatment and prevention of complex diseases in the near future.

mattjohnson

mattjohnson

 

How to create an NRRD file from a DICOM Medical Imaging Data Set

NRRD is a file format for storing and visualizing medical image data. Its main benefit over DICOM, the standard file format for medical imaging, is that NRRD files are anonymized and contain no sensitive patient information. Furthermore NRRD files can store a medical scan in a single file, whereas DICOM data sets are usually comprised of a directory or directories that contain dozens if not hundreds of individual files. NRRD is thus a good file for transferring medical scan data while protecting patient privacy. This tutorial will teach you how to create an NRRD file from a DICOM data set generated from a medical scan, such as a CT, MRI, ultrasound, or x-rays.   To complete this tutorial you will need a CD or DVD with your medical imaging scan, or a downloaded DICOM data set from one of many online repositories. If you had a medical scan at a hospital or clinic you can usually obtain a CD or DVD from the radiology department after signing a waiver and paying a small copying fee.   Step 1: Download Slicer   Slicer is a free software program for medical imaging. It can be downloaded from the www.slicer.org. Once on the Slicer homepage, click on the Download link as shown in Figure 1.   Figure 1   Slicer is available for Windows, Mac, and Linux. Choose your operating system and download the latest stable release as shown in Figure 2.   Figure 2: Download Slicer   Step 2: Copy the DICOM files into Slicer.   Insert your CD or DVD containing your medical scan data into your CD or DVD drive, or open the folder containing your DICOM files if you have a downloaded data set. If you navigate into the folder directory, you will notice that there are usually multiple DICOM files in one or more directories, as shown in Figure 3. Navigate to the highest level folder containing all the DICOM files. Figure 3: There are many DICOM files in a study   Open Slicer. The welcome screen will show, as demonstrated in Figure 4. Left click on the folder that contains the DICOM files and drop it onto the Welcome panel in Slicer. Slicer will ask you if you want to load the DICOM files into the DICOM database, as shown in Figure 5. Click OK Slicer will then ask you if you want to copy the files or merely add links. Click Copy as shown in Figure 6. Figure 4: Drag and drop the DICOM folder onto the Slicer Welcome window.   Figures 5 and 6   After working for a minute or two, Slicer will tell you that the DICOM import was successful, as shown in Figure 7. Click OK Figure 7   Step 3: Open the Medical Scan in Slicer.   At this point you should see a window called the DICOM Browser, as shown in Figure 8. The browser has three panels, which show the patient information, study information, and the individual series within each study. If you close the DICOM Browser and need to open it again, you can do so under the Modules menu, as shown in Figure 9. Figure 8: DICOM Browser   Figure 9: Finding the DICOM browser   Each series in a medical imaging scan is comprised of a stack of images that together make a volume. This volume can be used to make the NRRD file. Modern CT and MRI scans typically have multiple series and different orientations that were collected using different techniques. These multiple views of the same structures allow the doctors reading the scan to have the best chance of making the correct diagnosis. A detailed explanation of the different types of CT and MRI series is beyond the scope of this article, but will be covered in a future tutorial.   Click on the single patient, study, and a series of interest. Click the Load button as shown in Figure 8. The series will then begin to load as shown in Figure 10. Figure 10: The study is loading   Step 4: Save the Imaging Data in NRRD Format Once the series loads you will see the imaging data displayed in the Slicer windows. Click the Save button on the upper left-hand corner, as shown in Figure 11. Figure 11: Click the Save button   The Save Scene dialog box will then appear. Two or more rows may be shown. Put a checkmark next to the row that has a name that ends in ".nrrd". Uncheck all other rows. Click the directory button for the nrrd file and specify the directory to save the file into. Then click the save button, as shown in Figure 12. Figure 12: Check the NRRD file and specify save directory.   The NRRD file will now be saved in the directory you specified!
 

Dr. Mike

Dr. Mike

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