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Frequently Asked Questions (By Category)


Tell me about the Utah Torso Dataset

  • Date: Feb 2006
  • Author: Rob MacLeod

First, the original source of the geometry was MRI, as you have read. However, our interest in the bone data came later and they were not visible enough in the MRI to extract from there. Instead, we acquired standardized rib and spine geometry and fit them to the torso model.

With that said, there is considerable variation among patients with regard to heart shape and even location. Some hearts are long and relatively narrow while others sit higher and are larger in a transverse slice. The variation you have spotted between the textbook and the Utah torso is, I believe, well within that normal range of variation.

Finally, gating to the R wave does not ensure systole in the images of the heart for a couple reasons. The first reason is that electrical and mechanical systole are not aligned in time. Each cell of the heart experiences a delay between electrical and mechanical excitation, up to 200 ms in fact.. The result is that the R wave occurs during end diastole of the mechanical cycle, i.e., well before mechanical systole. Even more important, using the R wave to gate the image acquisition does not mean that all images have to be captured at the time of the peak of the R wave; rather the peak of the R wave provides a common reference so that acquisitions from different beats can capture the same phase of the heart cycle. The actual acquisition moment can be offset from the time of the R wave using a simple delay, i.e., each acquisition can occur with the same delay from that peak of the R wave.

I hope that with this information you can see that the Utah torso geometry can, indeed, be trusted to represent reasonably the geometry of an adult human torso. Just as with the visible human data, this is only one specific case and there are simply not enough data available to begin to create a true atlas that specifies the ranges of normal anatomy of the entire torso. There are atlases like this of the brain but I don't know of any other organ system that has received enough attention to begin to quantify anatomical variation.

Network Files (SRN)

How to use relative pathname support in SCIRun network files?

  • Date: Jan 2007
  • Author: Jeroen Stinstra

The relative path support in the SCIRun network fields assumes the following: The SCIRun network files are located at a fixed relative location from the data. It was designed so one create a repository in one's home directory with data files and networks in the same relative positions that can be easiy copied to another directory (another home directory for instance).

How to activate it: in the user's home directory there is a file called: .scirunrc

edit the line:


When this variable is set all filenames are exported in a relative fashion. Hence everyone that wants to export to the repository should have this set in the .scirunrc filename. Users who only check out files do not need to have this one set. SCIRun by default reads both files with absolute paths and with relative paths.

To convert files: Set the variable in the .scirunrc file. Then load up each network and save the files. This will export all the files in a relative format. After that check in the files and everything should work.


What is a generic CMake command line for building SCIRun?

  • Date: Jan, '07
  • Author: J. Davison de St. Germain

The SCIRun directory (that has the src subdirectory), has a bin directory. In the bin directory, run this command:

cmake ../src

Some other regularly used cmake variables are:

      CMAKE_BUILD_TYPE=Debug (or "Release")


What is the difference between BioPSE and SCIRun?

  • Date: 12/05/07
  • Author: J. Davison de St. Germain

BioPSE is a package that extends the base functionality of the SCIRun problem solving environment (PSE) for investigating bio-electric systems. When you go to download BioPSE, you will actually be downloading SCIRun and the BioPSE package.

What does "application failed to start because Core_Containers.dll was not found" mean?

  • Date: 1/30/07
  • Author: J. Davison de St. Germain

This will only appear on a Windows version of SCIRun. It means that your library path has not been set correctly. To fix this, follow these steps:

  1. Right click properties on "My Computer"
  2. Select the "Advanced" tab, and then press the "Environment Variables" button.
  3. Under "System Variables", select "Path" and edit it.
  4. Make sure that <path_to_scirun>/lib/<Release|Debug> and <path_to_thirdparty>/bin are in the path. (Double check to make sure that the path is correct.)
  5. If you change the path, you will probably have to re-open any application you open SCIRun from. I.e., if you run it inside of MS Visual Studio, you'll have to restart it; or if you double-click on an icon that's in a folder, you'll have to restart the folder.


How do I get BioImage? Where is BioImage located?

  • Date: 12/05/07
  • Author: J. Davison de St. Germain

BioImage is a PowerApp built on top of the SCIRun Dataflow system (and will be downloaded and built automatically when you go to download/build SCIRun/BioPSE). (Technically, BioImage is just a wrapper script on top of the SCIRun executable.) Under the Windows OS, the BioImage executable (script) is located in your binary directory in the Release (or Debug) subdirectory and is named BioImage.bat. (Note, in that same directory you will also see scirun.exe (the SCIRun executable).) On Mac OSX and Linux systems, both "scirun" and "BioImage" exist at the top level of your binary directory.

How do I segment data with BioImage?

  • Date: 12/05/07
  • Author: J. Davison de St. Germain

BioImage is designed only to visualize volumetric data sets, not to segment them. If you are interested in segmenting data, please look at the SCI Institutes Seg3D application.

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