User Manual: Easy Medical 3D Printing
Create Medical Models Automatically
For democratiz3D version 1.1, 6/16/2018
User Manual Navigation
- Getting Started
- Choosing a Scan
- Creating an NRRD file from a CT scan in DICOM format
- Step 1 - Uploading your file to democratiz3D – Starting a conversion
- Step 2 – Add screenshots
- Step 3 – File Information about the Uploaded scan file
- Turn Processing On
Democratiz3D® is an automated online service for the creation of 3D printable models from medical scans for purposes of medical 3D printing. The service takes uploaded medical CT scans in the NRRD file format and automatically converts them into a 3D printable model in the STL file format, based on the parameters provided by the user. STL is a file format that can be sent to almost any 3D printer. Before using the service, users must convert their CT scans from the DICOM format into the NRRD format, a relatively easy process that is described in detail here . Users have the option to share their uploaded CT scan or the generated 3D printable STL model with the embodi3D® community. Most features of the democratiz3D service are free, and the vast majority of users will find that the free services are adequate. A few advanced features are only available to paying members.
This user manual provides detailed steps for processing medical images for medical 3D printing. See our Quick Start Guide for abbreviated instructions. To use the democratiz3D service you need to log into your embodi3D account. If you do not have an account yet, you can click on the registration link to register, or the Sign Up button on the top of any embodi3D.com webpage. You will need a validated email address to register. Please be sure to check your email after signing up to activate your account. Registration is quick and free.
Choosing a CT Scan
To create a good 3D printable model, you need to start with a high quality medical scan. If you start off with a low-quality scan, your 3D printable model will also be low-quality. At this time, the democratiz3D service only accepts CT scans. MRIs will not process successfully. If you are not sure whether the scan you have is a CT or MRI, this tutorial will help you tell the difference.
A CT scan (left) and an MRI scan (right) of the brain. Make sure you have the correct type of scan for your operation! Currently democratiz3D only accepts CTs.
There are many factors that can impact the quality of a CT scan and thus its suitability for medical model creation. For a detailed explanation of how to determine scan quality, please see the tutorial Choosing the Best Medical Imaging Scan to Create a 3D Printed Medical Model.
Many hospitals will create CT scans with a default slice thickness of 5 mm. In general this is too thick for good 3D model creation. 2.5 mm should be considered the maximum acceptable slice thickness for most uses. 1.25 mm is typically good. For specialized applications where high detail is required, such as coronary artery CT or dental CT, even thinner slices, such as 0.75 mm, will be best. If you are not sure how thick the slices are for your scan, you can open your scan in 3D Slicer (available for free at slicer.org), and look in the Volumes module under Volume Information. This will show you the X, Y, and Z (slice thickness) resolution of your scan.
Using 3D Slicer to determine the slick thickness (Z image spacing) of a CT scan in the Volumes module.
Effect of slice thickness on scan quality. The scan on the left has thick slices and there is a jagged appearance of structures along the Z axis (head to toe). Note how rough the top of the liver appears. The scan on the right has much thinner slices and appears much smoother. The scan on the left will result in a poor 3D printed model.
Metal implants can cause streak artifact in CT scans. This is most common in the teeth due to fillings, in the back due to spinal fusion rods, and in the hips due to artificial hip implants. The metal blocks x-ray photons from passing, resulting in a star-like pattern centered around the metal. Streak artifact due to metal can be very difficult to remove from a 3D printed model without extensive manual processing. Choose a starting CT scan that is as free from metal artifact as possible. If you have to use a CT scan with lots of metal artifact, be prepared to spend a lot of time manually removing it from the model, or expect that your final model will have spiky metal artifact in it.
Effect of metal dental fillings on a CT scan. The scan on the left has no metal fillings. The scan on the right has metal fillings that result in a starlike streak pattern. Without manual editing, a 3D printed model will have spike-like structures originating from the metal.
After acquisition, many CT scanners will apply an edge enhancement algorithm to pictures before saving them as DICOM images. This is most commonly used in CT scans looking for detail at the edge of anatomic structures, such as scans designed to look for fractures in bones, or subtle lung patterns. Dental and facial CT scans and lung CT scans almost always have edge enhancement, also called sharp kernel, applied to them. Edge enhancement has the side effect of adding a lot of imaging noise to the picture, as represented by a speckled background. Starting with version 0.93 (released 3/30/2017), democratiz3D has much better handling of edge enhanced CT scans, and can now process both regular and edge enhanced CT scans with high reliability.
Effective edge enhancement on image quality. The image on the left has an edge-enhanced sharp kernel applied to it. The edges of the bones are more clearly seen but there is a speckled appearance to the background. The image on the right has no edge enhanced algorithm applied (smooth kernel) and has a much smoother background, although the edges are less well defined. Democratiz3D can now process both types of the scans with high success rates.
Most medical scans are saved in the DICOM format. DICOM is unsuitable for online processing because a single scan is often saved in a folder with hundreds of individual files. Furthermore, DICOM files contain patient identifiable information, which should be protected and kept private. Because of these limitations, democratiz3D only accepts files in the NRRD file format. With NRRD, an entire scan can be saved in a single file. Furthermore, the NRRD file is anonymized, with no patient identifiable information. NRRD files can be transferred on the Internet without any fear of accidental exposure of private patient information.
Creating an NRRD file from a DICOM medical scan is quite easy and takes just a few minutes. Here is a tutorial that explains how to do it using a free software program.
Step 1: Uploading your file to democratiz3D – Starting a conversion
To begin converting your CT scan in NRRD file format into a 3D printable model, you must first launch the democratiz3D service. From any webpage on the embodi3D.com site, click on the democratiz3D menu item and choose "Launch App."
To start uploading your NRRD file, drag-and-drop your NRRD file onto the drag and drop field or use the Choose Files button to navigate to and select the file on your computer that you wish to upload. Then click the Save & Submit Files button and your scan file will start to upload.
Step 2 – Add screenshots
If you are uploading a scan in NRRD format for democratiz3D processing, thumbnails of your scan will automatically be generated upon submission. However, you also have the option to upload your own images to be attached to the scan file via the Add screenshots field. Drag-and-drop or use the Choose Files button to navigate to and select images on your computer that you wish to attach.
Step 3 – File Information about the UPLOADED NRRD scan file
This section of the upload form pertains to the NRRD scan file that is being uploaded. Give the file a name and a text description in the appropriate fields. You also have the option to enter in appropriate keyword tags. If you want your file to be easily found by other members, it is advantageous to make the file name, file description, and tags as descriptive as possible. Information entered in the About This File field will be copied over to the processed file.
Choose a file type for your scan file. The default Type is Free, which means you and other embodi3D members can download your file for free. Even if you make your file Free, other members will not be able to see or download the file unless you mark it as Shared (see next section). The Associate with product(s) choice is rarely used and is only needed for complex subscription-based files. This is not needed for typical users.
If you wish to make your scan available for download for a fee, choose the Paid option. You will then be asked to set a download price in US dollars. Members who wish to download your file for their own use will have to pay the specified fee before downloading. Any funds that you earn will be stored as a credit in your embodi3D account, and will be disbursed to you per embodi3D policy. Payment is handled by a third-party processor. For more information on how to sell your file, see the tutorial How to Share, Sell, Organize, and Reprocess Automatically Generated 3D Printable Medical STL Models on Embodi3D.
Use the privacy setting to set the visibility of your scan file. Private Files are visible only by you. Even if the file is set as a Paid File for sale, if the privacy is set to Private it will not be visible to anybody and you will not get any sales.
If you wish to share the file with the community and allow other people to download and use it, choose the "Share this File" option. The embodi3D community is built around sharing, so it is highly recommended that you share your files.
Choose a license type for your uploaded file. This really only matters for Shared Files. If your file is set to Private, then nobody will be downloading your file and the license will not be necessary. You can choose from one of the standard Creative Commons license types if you wish to share your file for free. If you are selling your file, you can choose to use the General Paid File License provided as a convenience for you by embodi3D, or you can specify your own customized license. The text of your customized license can be pasted into the About this file field above so that any user downloading the file will see and have to agree to your license.
If you are uploading a new version of an existing file on the embodi3D website, you can enter a numerical version number here. The default is 1.0.0.
When this toggle is green, you will be notified when someone has posted a comment on your file page. This only applies to shared files.
Step 4 – Democratiz3D Processing: Enter file information about the GENERATED STL file
Step 4 of the upload form is where you specify how you would like your uploaded scan file to be converted into a 3D printable model. All parameters that influence the output of your 3D model are specified in this section.
Leave to toggle green (on) or your 3D model will not be generated.
The operation dictates what kind of 3D model will be generated from your source scan. Currently there are six operations available:
- CT NRRD to Bone STL (Free) – This is the standard bone creation operation. It converts a CT scan in NRRD file format into an STL file of the bones contained within the scan. Performs moderate amount of smoothing on the bone to reduce artifact from the source scan and improve appearance. Appropriate for bones of the extremities and body, and large models. To learn how to create an NRRD file from a DICOM data set, read this tutorial.
- CT NRRD to Bone STL Detailed (Free) - Same as the standard CT NRRD to Bone STL operation except there is less smoothing, so more detail is visible. More scan artifact may show in the model as a result. Appropriate for bony structures that have complex geometry and need to show detail, such as the spine.
- CT NRRD to Bone STL Very Detailed (Premium) - Highest detailed bone creation operation that uses minimal smoothing, thus preserving the maximum amount of detail. Appropriate for large models that require high detail. Works best with High or Ultra quality levels. Available to premium members, or general members on a Pay or Share basis.
- CT NRRD to Dental STL (Premium) – Bone creation operation specialized for dental and maxillofacial models. Uses minimal smoothing, thus preserving the maximum amount of detail. Works best with High or Ultra quality levels. Available to premium members, or general members on a Pay or Share basis.
- CT NRRD to Muscle STL (Free) - Converts a CT scan in NRRD format and extracts soft tissue (e.g. muscles) to a 3D model in STL file format. If IV contrast was administered in the CT scan, then enhancing organs and vessels may also be included. Excellent for showing muscular anatomy of the extremities. Here is a tutorial on creation of muscle and skin files.
- CT NRRD to Skin STL (Free) - Converts a CT scan in NRRD to an STL model showing the skin surface. Useful for creating sculptures based on real human anatomy, and face masks. Learn more about creation of muscle and skin files.
Threshold value in Hounsfield units with which to create the surface. This is automatically adjusted based on the operation you have selected, however you have the ability to modify the threshold value for your specific needs. Recommended for advanced users only.
Choose the polygon density of the generated 3D model. Low, Medium, and High are free to all members. Ultra is available to Premium members, and general members on a Pay or Share basis - if you share your processed file with the embodi3D community, all Premium services are free. However, if you wish to keep your processed file private when using Premium services, you can download your file after paying a one-time fee or when signing up for a subscription. You can always view the thumbnails of your processed file for free before deciding whether to download it.
- Low quality models (Free) are quick to generate but have fewer polygons with moderate loss of detail. Generated STL models have a low polygon count (approximately 20,000) and file size is relatively small (approximately 1 MB). Low quality is a good choice for testing files for convertibility. They are usually generated in a few minutes, not including thumbnail images.
- Medium quality models (Free) have an intermediate number of polygons (about 140,000) with mild loss of detail. Files are of intermediate size (approximately 6 MB) and conversions are fast, typically taking 5 to 10 minutes. Medium quality is best for models with simple geometry where fine detail is not important, such as long bones (femur, humerus)
- High quality models (Free) have many polygons (approximately 650,000) and are large files (approximately 30 MB). They take longer to generate (15 to 20 minutes). They have a high level of detail, clearly showing 1 to 2 mm structures. High quality is appropriate for all but the most demanding anatomic modeling applications.
- Ultra quality models (Premium) offers the highest level of polygon density (approximately 3 million) and generates very large files (approximately 140 MB). They take a long time to generate (about one hour) and ensure the highest level of detail with millimeter and sub- millimeter sized structures often depicted. Ultra quality is best for applications that require the highest level of detail and precision. It works best with Very Detailed Bone and Dental operations. High resolution source scans are needed to get the most from this operation. Available to premium members. Regular members have access to it for free via the Pay or Share program.
Comparison of different quality levels on a dental CT.
Type of Processed File(s)
Essentially the same as File Type in Part 3 of the form, except this applies to the STL file that will be generated. Specify if you want the file to be Free for download by others or you wish to sell it as a Paid File. Just as with the equivalent field in Part 3, your generated STL file will only be viewable, downloadable, or purchasable if you make the file shared. For more information on how to sell your files, see the tutorial How to Share, Sell, Organize, and Reprocess Automatically Generated 3D Printable Medical STL Models on Embodi3D.
Privacy of Processed File(s)
The same as the Privacy setting in Part 3 of the form, except this applies to the generated STL file. Specify if you want to keep the file Private and viewable only by you, or if you want the file to be Shared and viewable by the public.
License type of Processed File(s)
The same as License Type of Source File(s) in Part 3 of the form, except it applies to the generated STL file. Choose a license type for STL file under which people can download the file. This really only matters for Shared Files, as private files will not be visible by the public and there will be no downloads. Choose from one of the standard Creative Commons license types if you wish to share your file for free. If you are selling your file, you can choose to use the General Paid File License provided as a convenience for you by embodi3D, or you can specify your own customized license. The text of your customized license can be pasted into the About This File field in Part 3 so that any user downloading the file will see and have to agree to your license.
Category of Processed File(s)
Choose a Downloads category for your generated STL file. If you are going to be sharing the file, it will be most helpful to place it in the appropriate category to allow others to easily find it.
When the form is completed to your liking, click on the Save and Submit Files button. Your uploaded NRRD file will then be submitted for processing. You will see a notification on the estimated time it will take to convert the file. When the job is done and your STL model is ready for inspection and download, you will receive an email notification.
Downloading your generated STL 3D medical model files
There are two ways you can access your 3D model after it has been created by the democratiz3D service:
1) When processing is completed and your file is ready to download, you will receive an email with a link that will take you to the file download page.
2) Alternatively, you can access your file directly by viewing a list of files associated with your account. To do this, click on your username at the top right of any embodi3D screen and choose the My Files menu item.
Once you have opened your model download page, you can inspect the automatically generated thumbnails. If you are happy, you can download the file by clicking on the download button.
If you are a regular member and are using a Premium Operation or Quality level, you will also see a message alerting you that payment may be required to download your file. We offer both a Premium Membership and a Pay or Share program to give everyone access to the Premium services - if you share your processed file with the embodi3D community, all Premium Services are free. If you use Premium Services to process your file and wish to keep your processed file private, you have various payment options to download your file: you can pay a one-time fee to download your file, or you can become a Premium Member with a monthly or annual subscription.
Premium Members have unlimited access to Premium Services and have full control over their files, including downloading, editing, and marking them private. You can view the thumbnails of your processed file for free before deciding whether to download it. Premium subscribers have full control over the files they generate with premium features, and can download freely without being shown the choices below. If you are satisfied with your thumbnails, click Unlock to proceed. If you are not happy with your thumbnails, you can convert your NRRD file again using different processing parameters. You may also want to confirm that your CT scan is of sufficient quality for medical 3D printing.
Choose one of the options to unlock your file. If you wish to keep your file private, you can
1) become an monthly or annual subscriber
2) pay a one-time fee to download this file
If you permanently share your file, it is free to download to you and the embodi3D community. Should you later decide to make this file private, you will have to pay the one-time download fee. You can learn more about these options and pricing here.
Batch processing of medical scans
Democratiz3D can accept multiple NRRD source files for converting multiple STL medical models simultaneously. To enable batch processing, simply drag-and-drop multiple NRRD files onto the file upload pane in Part 1 of the democratiz3D® form. Then, fill out the form as usual, including the processing parameters. Each individual NRRD file will be processed using the same specified parameters and will generate a separate STL model file. For more information about batch processing, you can read this tutorial.
You can resubmit an NRRD file that you have already uploaded for conversion into an STL file. This can be convenient if you want to compare the outcome of different processing parameters, such as Operation or Quality levels. Locate the file you wish to process again in My Files, under your Profile.
Once the file page opens, select File Actions, Edit Details.
A page similar to the one you completed when you uploaded and processed your NRRD file will load (Steps 3 above). Complete the various fields. Ensure you give it a different name and a description that allows you to distinguish it from the previous processed file(s).
If you wish to convert your file to an STL file, you need to turn processing on by clicking on the slider until it is green. This will bring up the processing parameter input fields as in Step 4 above.
Complete all fields, accept the terms and save. Then wait for the email notification that your file has been processed.