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Re: [SCIRUN-USERS] heart simulations and datasets for SCIRun

Chronological Thread 
  • From: Jess Tate <>
  • To: " List" <>
  • Cc:
  • Subject: Re: [SCIRUN-USERS] heart simulations and datasets for SCIRun
  • Date: Tue, 16 Feb 2016 12:54:35 -0700

Hi Nawar,

There isn't really a standard geometry for the heart or torso, though there are some geometries that are commonly used.  You can checkout what we have in the SCIRunData directory (on the scirun 4 download page  You can also checkout the edgar database, which has a few data sets for general use (  Most of these examples already have segmentations or meshes generated from medical imaging.  

Segmenting a geometry from a medical image scan can be done in many different ways.  We have a tool, Seg3D, which is built for doing segmentations such as these.  There are some tutorials (look in user documentation) and data examples which can be found at  

It sounds like you are working on doing a fwd/Inv problem.  We have  a toolkit that will provide several examples of such in our forward inverse toolkit in SCIRun.  It comes downloaded in SCIRun 4.  You can load example networks in the toolkit menu on the main SCIRun window.  You can download the SCIRun 5 version from the  There is a tutorial describing this toolkit in the user documentation tab on that page.


On Feb 16, 2016, at 10:01 AM, Elizabeth Jurrus <> wrote:

Just forwarding this question onto our mailing list.
- liz

-------- Forwarded Message --------

I've just started my phd study on source imaging of the heart. I wanted to ask how you conduct segmentation, meshing and lead field calculation in SCIRun. Additionally I wanted to ask if there is a standard (averaged) 3D MRI of the heart and torso. Where can I download this kind of MRI?

Many thanks and Best regards,

M.Sc. Nawar Habboush
Department of Medical Psychology and Medical Sociology,
Schleswig-Holstein University Hospital (UK-SH),
Campus Kiel,
Schwanenweg 20,
24105 Kiel, Germany

Tel.: +49 431 597-8742 | Fax: -8745
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