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

large.57fc815d6d130_entrypic.pngPlease 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.

 

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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.

 

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Figure 2: Choosing the Crop Volume module

 

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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.

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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.

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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.

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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.

 

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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.

 

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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.

 

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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.

 

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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!


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