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Found 24 results

  1. Version 1.0.0

    42 downloads

    Source Head and Neck CT scan in NRRD file format for the Radiological Society of North America (RSNA) Annual Meeting 2017 course on Open-Source and Freeware Medical 3D Printing, RCA12 and RCA21, November 26 and 27, 2017. Be sure to view the full tutorial that uses this file here. https://meeting.rsna.org/program/index.cfm Search for "3D Printing Hands-on with Open Source Software: Introduction (Hands-on)"

    Free

  2. Version 1.0.0

    2 downloads

    dental tutorial source file

    Free

  3. Version 1.0.0

    7 downloads

    Vertebral column This 3D model was created from the file STS_036 A 3D printable STL file model created from this scan can be found here.

    Free

  4. Version 1.0.0

    5 downloads

    Left ribs This 3D model was created from the file STS_036 A 3D printable STL file model created from this scan can be found here.

    Free

  5. Version 1.0.0

    1 download

    Right ribs This 3D model was created from the file STS_036. A 3D printable STL file model created from this scan can be found here.

    Free

  6. Version 1.0.0

    0 downloads

    L5 A 3D printable STL file model created from this scan can be found here.

    Free

  7. L4 Lumbar Vertebra CT

    Version 1.0.0

    2 downloads

    L4 A 3D printable STL file model created from this scan can be found here.

    Free

  8. Version 1.0.0

    2 downloads

    The lumbar spine represents the mid-lower segment of the vertebral column and is composed of five adjacent vertebrae. They are convex anteriorly to form a lumbar lordosis. The lumbar spine facet joints allows limited movements and rotation. Each lumbar vertebra is formed of: A body: which is kidney shaped and is convex anteriorly while flattened posteriorly, pedicles and lamina, transverse processes, articular processes and a spinous process. This model shows the whole vertebral body with related articulations of the lower level vertebra. This 3D model was created from the file STS_036. A 3D printable STL file model created from this scan can be found here.

    Free

  9. L2 Lumbar CT scan

    Version 1.0.0

    1 download

    Second lumbar vertebra A 3D printable STL file model created from this scan can be found here.

    Free

  10. L1 Lumbar CT scan

    Version 1.0.0

    3 downloads

    L1 vertebral body This 3D model was created from the file STS_036. A 3D printable STL file model created from this scan can be found here.

    Free

  11. Version 1.0.0

    5 downloads

    Pelvic Bones 3D Printable STL File Converted From CT Scan This 3D model was created from the file STS_036. A 3D printable STL file model created from this scan can be found here.

    Free

  12. Version 1.0.0

    0 downloads

    Left Groin Leiomyosarcoma 3D Printable STL File Converted From CT Scan This 3D model was created from the file STS_036 A 3D printable STL file model created from this scan can be found here.

    Free

  13. Version 1.0.0

    11 downloads

    Left Knee Joint 3D Printable STL File Converted From CT Scan This 3D model was created from the file STS_045 A 3D printable STL file model created from this scan can be found here.

    Free

  14. Version 1.0.0

    13 downloads

    Mandible & Maxilla bones 3D Printable STL File Converted From CT Scan This 3D model was created from the file STS_044. A 3D printable STL file model created from this scan can be found here.

    Free

  15. Version 1.0.0

    2 downloads

    Dorsal (Thoracic) Spine 3D Printable STL File Converted From CT Scan This 3D model was created from the file STS_044. A 3D printable STL file model created from this scan can be found here.

    Free

  16. Cervical Spine

    Version 1.0.0

    1 download

    This 3D model was created from the file STS_044. A 3D printable STL file model created from this scan can be found here.

    Free

  17. Version 1.0.0

    3 downloads

    This 3D model was created from the file STS_045

    Free

  18. 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.
  19. 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!
  20. Occasionally files uploaded to the democratiz3D service for conversion to STL will not process correctly. What should you do if this happens? Usually these failure are due to one of two items: 1) There is some problem with the uploaded file, or 2) The uploaded file is simply massive (i.e. head to toe thin cut CT). If you encounter a problem with processing of your file, the first thing to do it check the quality of your input file. See my earlier tutorial, Choosing the Best Medical Imaging Scan to Create a 3D Printed Medical Model, if you want more details. 1) Check the modality. Did you upload an MRI when the operation calls for a CT? 2) Check for artifacts. This will often cause the model to have obvious deformities. The most common is beam hardening from dental fillings, as shown below. Normal teeth without fillings are on the left, and teeth with metal dental fillings are shown on the right. Unfortunately, you can't make an STL file from data that isn't there. If you scan has lots of artifact, you can either choose another scan or go through the laborious process of fixing the artifacts manually after the model is created. 3) Reconstruction kernel. This refers to the edge enhancement or sharpening algorithm that was applied to the scan images after they were acquired on the scanner. These are often done on dedicated bone or lung CT scans to enhance the contrast as make it easier for the radiologist to see subtle findings, like hairline fractures. Which the edge enhancement algorithm (or sharp kernel) as shown on the left below makes the edges easier to see, it also results in a speckled or noisy appearance of the tissue. This can confuse the algorithm because some very high intensity spots may look like bone. If your file is failing and you are using a sharp kernel series from you scan, consider using a different series that has a smooth kernel, such as shown on the right below. If you must stick with the sharp kernel, increase the threshold level to reduce the amount of "sand" in your output file and increase the changes of a successful processing job. Hope this helps, Dr. Mike
  21. Version 1.0.0

    47 downloads

    This STL file of a highly detailed dental scan shows the bony anatomy of the maxilla, mandible and facial structures in great detail. This model was created using the Imag3D service. incisix, H, 150

    Free

  22. 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!
  23. Version 1.0.0

    363 downloads

    Supporting files for the democratiz3D tutorial A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes which allows you to follow along with the tutorial. Included is an anonymized chest abdomen pelvis CT in both DICOM and NRRD formats.

    Free

  24. 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!