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[SCIRUN-USERS] Re: problem with BioImage.bat

Chronological Thread 
  • From: Rob MacLeod <>
  • To: Raja Yalamanchili <>
  • Cc: Rob MacLeod <>,
  • Subject: [SCIRUN-USERS] Re: problem with BioImage.bat
  • Date: Wed, 25 Mar 2009 21:53:31 -0600

Hi again Raja,

A little more response as I left out some of your questions.  

PowerApps like BioImage and Biotensor are actually an interface wrapper around a SCIRun network, an approach which has pros and cons.  We have found over a few years worth of experience that the cons won and so we do not make powerapps like this any more.  Instead, we identify interesting needs and write standalone applications that may or may not make use of pieces of SCIRun.   These applications are open source but are not really design for user level modification or extension.   However, if you need to segment image data, visualize surface based time signals, volume render large volume data sets, etc., then these are great solutions!

SCIRun exists still and continues to improve as a very general purpose and powerful problem solving environment and it is here that you might want to investigate possibilities for adding your own algorithms to make something customized for your needs.  There are many sample networks included with SCIRun and they are meant to show how to construct dataflow applications using SCIRun.  SCIRun also has a MATLAB module that allows you to send data from SCIRun to MATLAB, execute some MATLAB code, and then pull the results back into SCIRUn for additional processing.  In this way, it becomes quite simple to experiment with additional functionality or ideas but make use of all the existing visualization and simulation capabilities built into SCIRun. 

The documentation is never as detailed as we would like but it does contain some instruction on how to use SCIRun.  The materials from our recent set of courses is also available and provides some more examples and ideas.  Of course, the best solution is to attend one of our courses, something we might repeat in the late summer of fall depending on the outcome of our upcoming grant renewal!

Here are some links to get you started:

and  (the titles of the sessions are links to the slides from each)

Hope this clarifies things and please feel free to get back to us with more questions.


We don't really support BioImage any more and you will get better functionality from ImageVis3D, a smaller, standalone application for volume visualization.  

Best regards,


On Mar 25, 2009, at 5:52 PM, Raja Yalamanchili wrote:


I'm new to SCIRun so i have few questions regarding its usage

BioImage.bat problem:

I downloaded SCIRun_4.1_20090320_win32.exe and i'm trying to see how the BioImage works.I tried to run the BioImage.bat file but it didn't work. It is giving the following error:
"The system cannot find the path specified"
I tried to change the paths in the batch file to appropriate path but no luck.

Is there any step i'm missing here ?

New power applications and modules:

I read that we can create new power applications is it possible to create new module also, like implementing a new algorithm which might require creating a new module.

Is it possible to separate the power applications as a separate executable and use it with other applications like matlab?

thanks and regards,
Raja Yalamanchili.(Phani)
Research Assistant, Computational Biomedicine Lab (
Dept. of Computer Science, University of Houston
235 Philip Guthrie Hoffman Hall (PGH)
Houston, TX 77204-3010
Tel: (281) 684-0195

Rob MacLeod, PhD
Associate Professor of Bioengineering and Internal Medicine
University of Utah
Scientific Computing and Imaging (SCI) Institute
72 South Central Campus Drive
Salt Lake City, Utah 84112
Phone: (801) 585 7596
Fax: (801) 585-6513

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