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Re: [SCIRUN-USERS] Issue in SCIrun

Chronological Thread 
  • From: Jess <>
  • To: "Boyett, Benjamin Travis" <>
  • Cc:
  • Subject: Re: [SCIRUN-USERS] Issue in SCIrun
  • Date: Wed, 22 Feb 2017 11:15:10 -0700

Hi Ben,

I’ve had a look at your segmentation. It looks like you do not have a
background torso tissue layer, but that that tissue is set to the same as the
air (outside the torso). There needs to be a layer that incorporates all the
rest of the tissue in the torso that you do not specifically segment out. We
usually set this layer to a conductivity of ~0.2 S/m. If you do not have
this layer, you will encounter problems because the air will be set to 0 S/m,
which will then insulate the heart and not allow any of the generated field
to reach the heart.

I’m not sure what problems you are experiencing with your pad placement, but
one of the problems you may be having is that you moved the Segmentation
space in the placement network, but I don’t see that same transformation in
the FEM network. There are two solutions to this. The simplest is to save
transformed segmentation a load that geometry into the FEM network. The
other option is to save the transform only, which is the blue output port on
the EditMeshBoundingBox, then load that transform into the FEM network and
use TransformMeshWithTransform to apply it to the segmentation. The second
option is useful if you want to keep the nrrd file as is, or if you want to
keep the nrrd format and you apply a rotation. SCIRun should handle nrrd
files that are not oriented on the x,y,z, axes, but other software may not.

I hope that helps.


> On Feb 18, 2017, at 3:35 PM, Boyett, Benjamin Travis
> <> wrote:
> Hello!
> I have recently been on contact with someone at the help desk, but
> that correspondence as somewhat stopped so I was hoping I could get
> some questions answered. I am working with SCIrun to model external
> defibrillation, using a four pad set up instead of a typical 2 pad
> one. In the program where I am making the pads, I am having an issue
> clipping the field of the electrode to the torso. In this case, I am
> not using the given torso-defib, I am using an imported .nrrd file of
> my own. I am also having an issue with implementing it into my main
> FEM analysis program, but I think it is due to the pads not being
> configured correctly. My .nnrd is only 4 sections, with 1 being the
> spine and ribs, 2 being the skin, 3 being the lungs, and 4 being the
> heart. I'll attach my programs to this email for reference. Any advice
> about the clipping would be great!
> Thanks,
> Ben Boyett
> <SixMonthSegmentation.nrrd><babypads.srn><FEManalysis.srn>
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