1 pointThis tutorial is based on course I taught at the 2018 RSNA meeting in Chicago, Illinois. It is shared here free to the public. In this tutorial, we walk though how to convert a CT scan of the face into a 3D printable file, ready to be sent to a 3D printer. The patient had a gunshot wound to the face. We use only free or open-source software and services for this tutorial. There are two parts to this tutorial: Part 1: How to use free desktop software to create your model Part 2: Use embodi3D's free democratiz3D service to automatically create your model Key Takeaway from this Tutorial: You can make high quality 3D printable models from medical imaging scans using FREE software and services, and it is surprisingly EASY. A note on the FDA (for USA people): There is a lot of confusion about whether expensive, FDA-approved software must be used for medically-related 3D printing in the United States. The FDA recently clarified its stance on the issue.* If you are not using these models for patient-care purposes, this does not concern you. If you have questions please see the FDA website. If you are a DOCTOR, you can use whatever software you think is appropriate for your circumstances under your practice of medicine. If you are a COMPANY, selling 3D printed models for diagnostic use, you need FDA-approved software. If you are designing implants or surgical cutting guides, those are medical devices. Seek FDA feedback. *Kiarashi, N. FDA Current Practices and Regulations, FDA/CDRH-RSNA SIG Meeting on 3D Printed Patient- Specific Anatomic Models. Available at https://www.fda.gov/downloads/MedicalDevices/NewsEvents/WorkshopsConferences/UCM575723.pdf Accessed 11/1/2017. Part 1: Using Desktop software 3D Slicer and Meshmixer Step 1: Download the scan file and required software To start, download the starting CT scan file at the link below. Also, install 3D Slicer (slicer.org) and Meshmixer (meshmixer.com). Step 2: Open 3D Slicer Open Slicer. Drag and drop the scan file gunshot to face.nrrd onto the slicer window. The scan should open in a 4 panel view as shown below in Figure 1. Figure 1: The 4 up view. If your view does not look like this, you can set the 4 up view to display by clicking Four-Up from the View menu, as shown in Figure 2 Figure 2: Choosing the four-up view Step 3: Learning to control the interface Slicer has basic interface controls. Try them out and become accustomed to how the interface works. Note how the patient has injuries from gunshot wound to the face. Left mouse button – Window/Level Right mouse button – Zoom Scroll wheel – Scroll through stack Middle mouse button -- Pan Step 4: Blur the image The CT scan was created using a bone reconstruction kernel. Basically this is an image-enhancement algorithm that makes edges more prominent, which makes detection of fractures easier to see by the human eye. While making fracture detection easier, this algorithm does unnaturally alter the image and makes it appear more "speckled" Figure 3: Noisy, "speckled" appearance of the scan on close up view To fix this issue, we will slightly blur the image. Select Gaussian Blur Image Filter as shown below in Figure 4 Figure 4: Choosing the Gaussian Blur Image Filter Set up the Gaussian Blur parameters. Set Sigma = 1.0. Set the input volume to be Gunshot to face. Create a new output volume called "Gaussian volume" as shown in Figure 5. Figure 5: Setting up the Gaussian parameters When ready, click Apply, as shown in Figure 6. You will notice that the scan becomes slightly blurred. Figure 6: Click Apply to start the Gaussian Blur Image filter. Step 5: Create a 3D model using Grayscale Model Maker Open the Grayscale Model Maker Module as shown below in Figure 7. Figure 7: Opening the Grayscale Model Maker Set up the Grayscale Model Maker parameters. Select the Gaussian volume as the input volume, as shown in Figure 8. Figure 8: Choosing the input volume in Grayscale Model Maker Next, set the output geometry to be a new model called "gunshot model." Set the other parameters: Threshold = 200, smooth 15, Decimate 0.5, Split normals unchecked as shown in Figure 9. Figure 9: Grayscale Model maker parameters When done, click Apply. A new model should be created and will be shown in the upper right hand panel, as shown in Figure 10. Figure 10: The new model Step 6: Save the model as an STL file To start saving the model, click the save button in the upper left of the Slicer window as shown in Figure 11. Figure 11: The save button Be sure that only the 3D model, gunshot model.vtk is selected. Uncheck everything else, as shown in Figure 12. Figure 12: The Save dialog. Check the vtk file Make sure the format of the 3D model is STL as shown in Figure 13. Specify the folder to save into, as shown in Figure 14. Figure 13: Specify the file type Figure 14: Specify the folder to save into within the Save dialog. Step 7: Open the file in Meshmixer for cleanup Open Meshmixer. Drag and drop the newly created STL file on the meshmixer window. The file will open and the model will be displayed as in Figure 15. Figure 15: open the STL file in Meshmixer Get accustomed to the Meshmixer interface as shown in Figure 16. A 3 button mouse is very helpful. Figure 16: Controlling the Meshmixer user interface Choose the Select tool. In is the arrow button along the left of the window. Figure 17: The select tool Click on a portion of the model. The selected portion will turn orange, as shown in Figure 18. Figure 18: Selected areas turn orange. Expand the small selected area to all mesh connected to it. Use Select->Modify->Expand to Connected, or hit the E key. The entire model should turn orange. See Figure 19. Figure 19: Expanding the selection to all connected mesh. Next, Invert the selection so that only disconneced, unwanted mesh is selected. Do this with Select->Modify->Invert, or hit the I key as shown in Figure 20. Figure 20: Inverting the selection At this point, only the unwanted, disconnected mesh should be selected in orange. Delete the unwanted mesh using Select->Edit->Discard, or use the X or DELETE key as shown in Figure 21. At this point, only the desired mesh should remain. Figure 21: Deleting unwanted mesh. Step 8: Run the Inspector tool The Inspector tool will automatically fix most errors in the model mesh. To open it, choose Analysis->Inspector as shown in Figure 22. Figure 22: The Inspector tool The Inspector will identify all of the errors in the mesh. To automatically correct these mesh errors, click Auto Repair All as shown in Figure 23. Figure 23: Auto Repairing using Inspector The Inspector will usually fix all or most errors. In this case however, there is a large hole at the edge of the model where the border of the scan zone was. The Inspector doesn't know how to close it. This is shown in Figure 24. Figure 24: The inspect could not fix 1 mesh error Step 9: Close the remaining hole with manual bridges Using the select tool, select a zone of mesh near the open edge. The Select tool is opened with the arrow button along the left. Choose a brush size -- 40 is good -- as shown in Figure 25. Figure 25: Choosing the select tool The mesh should turn orange when selected, as shown in Figure 26. Figure 26: Selected mesh turns orange. Next, rotate the model and select a zone of mesh opposite the edge from the first selected zone, as shown in Figure 27. Figure 27: Selecting mesh opposite the defect. Once both edges are selected, create a bridge of mesh spanning the two selected areas using the Bridge operation: Select->Edit->Bridge, or CTRL-B, as shown in Figure 28. Figure 28: The bridge tool There should now be a bridge of orange mesh spanning the gap. Click Accept, as shown in Figure 29. Figure 29: The new bridge. Be sure to click Accept. Next, repeat the bridge on the opposite side of the skull. Be sure to deselect the previously selected mesh before working on the opposite side, as shown in Figure 30. Figure 30: Creating a second bridge on the opposite side. Step 10: Rerun the Inspector Rerun the Inspector tool, as shown in Figure 31. Now with the bridges to "help" Meshmixer to know how to fill in the hole, it should succeed. If it fails, create more bridges and try again. Figure 31: Rerun the Inspector tool Next, export your file to STL. ' Figure 32: Export to STL Step 11: 3D print your file! Your STL file is now ready to be sent to the 3D printer of your choice. Figure 33 shows the model after printing. Figure 33: The final print Part 2: Using the democratiz3D service on embodi3d.com democratiz3D automatically converts scans to 3D printable models. It automates the mesh cleanup process and saves time. The service is free for general bone model creation. Step 1: Register Register for a free embodi3D account. The process takes only a minute. You need an account for your processed files to be saved to. Step 2: Upload the NRRD source scan to democratiz3D. From anywhere in the site, click democratiz3D-> Launch App Figure 34: Launching the democratiz3D app. Fill out basic information about your file. That information will be copied to your generated STL file, as shown in Figure 35. Figure 35: Entering basic file information Make sure democratiz3D processing is on. Choose an operation to convert your model. Set threshold to 200, as shown in Figure 36. Figure 36: Operation, threshold, and quality parameters. Click Submit! In 10 to 15 minutes your model should be done. You will receive an email notification. The completed model file will be saved under your account. Download the file and send it to your printer of choice! Figure 37; The final democratiz3D file, ready for download. That's it! I hope this tutorial was helpful to you. If you liked it, please rate it positively. If you want to learn more about democratiz3D, Meshmixer, or Slicer, please see our tutorials page. It has a lot of wonderful resources. Happy 3D printing!
1 pointIf you are planning on using the democratiz3D service to automatically convert a medical scan to a 3D printable STL model, or you just happen to be working with medical scans for another reason, it is important to know if you are working with a CT (Computed Tomography or CAT) or MRI (Magnetic Resonance Imaging) scan. In this tutorial I'll show you how to quickly and easily tell the difference between a CT and MRI. I am a board-certified radiologist, and spent years mastering the subtleties of radiology physics for my board examinations and clinical practice. My goal here is not to bore you with unnecessary detail, although I am capable of that, but rather to give you a quick, easy, and practical way to understand the difference between CT and MRI if you are a non-medical person. Interested in Medical 3D Printing? Here are some resources: Free downloads of hundreds of 3D printable medical models. Automatically generate your own 3D printable medical models from CT scans. Have a question? Post a question or comment in the medical imaging forum. A Brief Overview of How CT and MRI Works For both CT (left) and MRI (right) scans you will lie on a moving table and be put into a circular machine that looks like a big doughnut. The table will move your body into the doughnut hole. The scan will then be performed. You may or may not get IV contrast through an IV. The machines look very similar but the scan pictures are totally different! CT and CAT Scans are the Same A CT scan, from Computed Tomography, and a CAT scan from Computed Axial Tomography are the same thing. CT scans are based on x-rays. A CT scanner is basically a rotating x-ray machine that takes sequential x-ray pictures of your body as it spins around. A computer then takes the data from the individual images, combines that with the known angle and position of the image at the time of exposure, and re-creates a three-dimensional representation of the body. Because CT scans are based on x-rays, bones are white and air is black on a CT scan just as it is on an x-ray as shown in Figure 1 below. Modern CT scanners are very fast, and usually the scan is performed in less than five minutes. Figure 1: A standard chest x-ray. Note that bones are white and air is black. Miscle and fat are shades of gray. CT scans are based on x-ray so body structures have the same color as they don on an x-ray. How does MRI Work? MRI uses a totally different mechanism to generate an image. MRI images are made using hydrogen atoms in your body and magnets. Yes, super strong magnets. Hydrogen is present in water, fat, protein, and most of the "soft tissue" structures of the body. The doughnut of an MRI does not house a rotating x-ray machine as it does in a CT scanner. Rather, it houses a superconducting electromagnet, basically a super strong magnet. The hydrogen atoms in your body line up with the magnetic field. Don't worry, this is perfectly safe and you won't feel anything. A radio transmitter, yes just like an FM radio station transmitter, will send some radio waves into your body, which will knock some of the hydrogen atoms out of alignment. As the hydrogen nuclei return back to their baseline position they emit a signal that can be measured and used to generate an image. MRI Pulse Sequences Differ Among Manufacturers The frequency, intensity, and timing of the radio waves used to excite the hydrogen atoms, called a "pulse sequence," can be modified so that only certain hydrogen atoms are excited and emit a signal. For example, when using a Short Tau Inversion Recovery (STIR) pulse sequence hydrogen atoms attached to fat molecules are turned off. When using a Fluid Attenuation Inversion Recovery (FLAIR) pulse sequence, hydrogen atoms attached to water molecules are turned off. Because there are so many variables that can be tweaked there are literally hundreds if not thousands of ways that pulse sequences can be constructed, each generating a slightly different type of image. To further complicate the matter, medical scanner manufacturers develop their own custom flavors of pulse sequences and give them specific brand names. So a balanced gradient echo pulse sequence is called True FISP on a Siemens scanner, FIESTA on a GE scanner, Balanced FFE on Philips, BASG on Hitachi, and True SSFP on Toshiba machines. Here is a list of pulse sequence names from various MRI manufacturers. This Radiographics article gives more detail about MRI physics if you want to get into the nitty-gritty. Figure 2: Examples of MRI images from the same patient. From left to right, T1, T2, FLAIR, and T1 post-contrast images of the brain in a patient with a right frontal lobe brain tumor. Note that tissue types (fat, water, blood vessels) can appear differently depending on the pulse sequence and presence of IV contrast. How to Tell the Difference Between a CT Scan and an MRI Scan? A Step by Step Guide Step 1: Read the Radiologist's Report The easiest way to tell what kind of a scan you had is to read the radiologist's report. All reports began with a formal title that will say what kind of scan you had, what body part was imaged, and whether IV contrast was used, for example "MRI brain with and without IV contrast," or "CT abdomen and pelvis without contrast." Step 2: Remember Your Experience in the MRI or CT (CAT) Scanner Were you on the scanner table for less than 10 minutes? If so you probably had a CT scan as MRIs take much longer. Did you have to wear earmuffs to protect your hearing from loud banging during the scan? If so, that was an MRI as the shifting magnetic fields cause the internal components of the machine to make noise. Did you have to drink lots of nasty flavored liquid a few hours before the scan? If so, this is oral contrast and is almost always for a CT. How to tell the difference between CT and MRI by looking at the pictures If you don't have access to the radiology report and don't remember the experience in the scanner because the scan was A) not done on you, or you were to drunk/high/sedated to remember, then you may have to figure out what kind of scan you had by looking at the pictures. This can be complicated, but don't fear I'll show you how to figure it out in this section. First, you need to get a copy of your scan. You can usually get this from the radiology or imaging department at the hospital or clinic where you had the scan performed. Typically these come on a CD or DVD. The disc may already have a program that will allow you to view the scan. If it doesn't, you'll have to download a program capable of reading DICOM files, such as 3D Slicer. Open your scan according to the instructions of your specific program. You may notice that your scan is composed of several sets of images, called series. Each series contains a stack of images. For CT scans these are usually images in different planes (axial, coronal, and sagittal) or before and after administration of IV contrast. For MRI each series is usually a different pulse sequence, which may also be before or after IV contrast. Step 3: Does the medical imaging software program tell you what kind of scan you have? Most imaging software programs will tell you what kind of scan you have under a field called "modality." The picture below shows a screen capture from 3D Slicer. Looking at the Modality column makes it pretty obvious that this is a CT scan. Figure 3: A screen capture from the 3D Slicer program shows the kind of scan under the modality column. Step 4: Can you see the CAT scan or MRI table the patient is laying on? If you can see the table that the patient is laying on or a brace that their head or other body part is secured in, you probably have a CT scan. MRI tables and braces are designed of materials that don't give off a signal in the MRI machine, so they are invisible. CT scan tables absorb some of the x-ray photons used to make the picture, so they are visible on the scan. Figure 4: A CT scan (left) and MRI (right) that show the patient table visible on the CT but not the MRI. Step 5: Is fat or water white? MRI usually shows fat and water as white. In MRI scans the fat underneath the skin or reservoirs of water in the body can be either white or dark in appearance, depending on the pulse sequence. For CT however, fat and water are almost never white. Look for fat just underneath the skin in almost any part of the body. Structures that contained mostly water include the cerebrospinal fluid around the spinal cord in the spinal canal and around the brain, the vitreous humor inside the eyeballs, bile within the gallbladder and biliary tree of the liver, urine within the bladder and collecting systems of the kidneys, and in some abnormal states such as pleural fluid in the thorax and ascites in the abdomen. It should be noted that water-containing structures can be made to look white on CT scans by intentional mixing of contrast in the structures in highly specialized scans, such as in a CT urogram or CT myelogram. But in general if either fat or fluid in the body looks white, you are dealing with an MRI. Step 6: Is the bone black? CT never shows bones as black. If you can see bony structures on your scan and they are black or dark gray in coloration, you are dealing with an MRI. On CT scans the bone is always white because the calcium blocks (attenuates) the x-ray photons. The calcium does not emit a signal in MRI scans, and thus appears dark. Bone marrow can be made to also appear dark on certain MRI pulse sequences, such as STIR sequences. If your scan shows dark bones and bone marrow, you are dealing with an MRI. A question I am often asked is "If bones are white on CT scans, if I see white bones can I assume it is a CT?" Unfortunately not. The calcium in bones does not emit signal on MRI and thus appears black. However, many bones also contain bone marrow which has a great deal of fat. Certain MRI sequences like T1 and T2 depict fat as bright white, and thus bone marrow-containing bone will look white on the scans. An expert can look carefully at the bone and discriminate between the calcium containing cortical bone and fat containing medullary bone, but this is beyond what a layperson will notice without specialized training. Self Test: Examples of CT and MRI Scans Here are some examples for you to test your newfound knowledge. Example 1 Figure 5A: A mystery scan of the brain Look at the scan above. Can you see the table that the patient is laying on? No, so this is probably an MRI. Let's not be hasty in our judgment and find further evidence to confirm our suspicion. Is the cerebrospinal fluid surrounding the brain and in the ventricles of the brain white? No, on this scan the CSF appears black. Both CT scans and MRIs can have dark appearing CSF, so this doesn't help us. Is the skin and thin layer of subcutaneous fat on the scalp white? Yes it is. That means this is an MRI. Well, if this is an MRI than the bones of the skull, the calvarium, should be dark, right? Yes, and indeed the calvarium is as shown in Figure 5B. You can see the black egg shaped oval around the brain, which is the calcium containing skull. The only portion of the skull that is white is in the frontal area where fat containing bone marrow is present between two thin layers of calcium containing bony cortex. This is an MRI. Figure 5B: The mystery scan is a T1 spoiled gradient echo MRI image of the brain. Incidentally this person has a brain tumor involving the left frontal lobe. Example 2 Figure 6A: Another mystery scan of the brain Look at the scan above. Let's go through our process to determine if this is a CT or MRI. First of all, can you see the table the patient is lying on or brace? Yes you can, there is a U-shaped brace keeping the head in position for the scan. We can conclude that this is a CT scan. Let's investigate further to confirm our conclusion. Is fat or water white? If either is white, then this is an MRI. In this scan we can see both fat underneath the skin of the cheeks which appears dark gray to black. Additionally, the material in the eyeball is a dark gray, immediately behind the relatively white appearing lenses of the eye. Finally, the cerebrospinal fluid surrounding the brainstem appears gray. This is not clearly an MRI, which further confirms our suspicion that it is a CT. If indeed this is a CT, then the bones of the skull should be white, and indeed they are. You can see the bright white shaped skull surrounding the brain. You can even see part of the cheekbones, the zygomatic arch, extending forward just outside the eyes. This is a CT scan. Figure 6B: The mystery scan is a CT brain without IV contrast. Example 3 Figure 7A: A mystery scan of the abdomen In this example we see an image through the upper abdomen depicting multiple intra-abdominal organs. Let's use our methodology to try and figure out what kind of scan this is. First of all, can you see the table that the patient is laying on? Yes you can. That means we are dealing with the CT. Let's go ahead and look for some additional evidence to confirm our suspicion. Do the bones appear white? Yes they do. You can see the white colored thoracic vertebrae in the center of the image, and multiple ribs are present, also white. If this is indeed a CT scan than any water-containing structures should not be white, and indeed they are not. In this image there are three water-containing structures. The spinal canal contains cerebrospinal fluid (CSF). The pickle shaped gallbladder can be seen just underneath the liver. Also, this patient has a large (and benign) left kidney cyst. All of these structures appear a dark gray. Also, the fat underneath the skin is a dark gray color. This is not in MRI. It is a CT. Figure 7B: The mystery scan is a CT of the abdomen with IV contrast Example 4 Figure 8A: A mystery scan of the left thigh Identifying this scan is challenging. Let's first look for the presence of the table. We don't see one but the image may have been trimmed to exclude it, or the image area may just not be big enough to see the table. We can't be sure a table is in present but just outside the image. Is the fat under the skin or any fluid-filled structures white? If so, this would indicate it is an MRI. The large white colored structure in the middle of the picture is a tumor. The fat underneath the skin is not white, it is dark gray in color. Also, the picture is through the mid thigh and there are no normal water containing structures in this area, so we can't use this to help us. Well, if this is a CT scan than the bone should be white. Is it? The answer is no. We can see a dark donut-shaped structure just to the right of the large white tumor. This is the femur bone, the major bone of the thigh and it is black. This cannot be a CT. It must be an MRI. This example is tricky because a fat suppression pulse sequence was used to turn the normally white colored fat a dark gray. Additionally no normal water containing structures are present on this image. The large tumor in the mid thigh is lighting up like a lightbulb and can be confusing and distracting. But, the presence of black colored bone is a dead giveaway. Figure 8B: The mystery scan is a contrast-enhanced T2 fat-suppressed MRI Conclusion: Now You Can Determine is a Scan is CT or MRI This tutorial outlines a simple process that anybody can use to identify whether a scan is a CT or MRI. The democratiz3D service on this website can be used to convert any CT scan into a 3D printable bone model. Soon, a feature will be added that will allow you to convert a brain MRI into a 3D printable model. Additional features will be forthcoming. The service is free and easy to use, but you do need to tell it what kind of scan your uploading. Hopefully this tutorial will help you identify your scan. If you'd like to learn more about the democratiz3D service click here. Thank you very much and I hope you found this tutorial to be helpful. Nothing in this article should be considered medical advice. If you have a medical question, ask your doctor.
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