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

Entry posted by Dr. Mike · - 6,778 views

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!

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I am new to the use of 3DSLICER 

Please can you advise if the SLICER program can be used to convert ultrasound DICOM files to a CAD (.STL) as is possible I see with CT scans etc?


Thank you


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On 7/6/2017 at 4:19 PM, Peter3D said:


I am new to the use of 3DSLICER 

Please can you advise if the SLICER program can be used to convert ultrasound DICOM files to a CAD (.STL) as is possible I see with CT scans etc?


Thank you



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yes , it is very easy in 3D slicer.

after loading data as described above, go to1)  volume rendering >select process 

                                                                            2) segmentation >export as> save>see for different format


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