Slicing Scientific Data

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I've covered scientific software in previous articles that either analyzes image information or actually generates image data for further analysis. In this article, I introduce a tool that you can use to analyze images generated as part of medical diagnostic work.

In several diagnostic medical tests, complex three-dimensional images are generated that need to be visualized and analyzed. This is where 3D Slicer steps into the workflow. 3D Slicer is a very powerful tool for dissecting, analyzing and visualizing this type of complex 3D imaging data. It is fully open source, and it's available not only on Linux, but also on Windows and Mac OS X.

It's also built as a core program with a plugin architecture. This means you can add extra functionality to do completely new analysis.

Although 3D Slicer was written to handle medical images, the development team has been very careful to say that the software has not been approved for clinical use and shouldn't be used for diagnostic work. It's intended to be a research tool—hence its open-source license and plugin architecture, which aid in working with newly created algorithms and developing the next-generation tools that will be incorporated into diagnostic software.

Installation involves downloading a file directly from the project website. For Linux, this file is a gzipped tarball. You can select between a stable release or a nightly release. Once you download the tarball, you can unpack it with the command:


tar xvzf Slicer-4.6.2-linux.amd64.tar.gz

This unpacks everything into a subdirectory named Slicer-4.6.2-linux-amd64. Of course, the 4.6.2 portion will be different if you download a different version.

Once you have everything untarred, you can run it with:


./Slicer-4.6.2-linux-amd64/Slicer

When it starts, you end up with an empty project (Figure 1).

Figure 1. When you first start 3D Slicer, you get a display of an empty project, ready to start your work.

If you're trying to learn how to use 3D Slicer, you may not have any data to work with at first. Luckily, there is a button on the main window that allows you to download sample data. When you click it, you get a list of potential sample data sets available for download.

For this article's example, click the Download MRHead button and use the related data set (Figure 2).

Figure 2. Several sample data sets are available for you to learn with, such as this head MRI data.

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Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.