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Re: [SCIRUN-USERS] View MR-image and dipole location

Chronological Thread 
  • From: David Weinstein <>
  • To:
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  • Subject: Re: [SCIRUN-USERS] View MR-image and dipole location
  • Date: Wed, 11 Feb 2004 10:35:07 -0700

Hi Christopher,

I'd be happy to help you with this. I just need additional clarification on this component:

I would like to make a rendering
of the surface of the volume and make a cutout to show the superior
temporal lobes (auditory cortex).

Do you want to render the scalp and cortex, and then just cut-away a wedge-shaped portion of the scalp surface to reveal the temporal lobe of the cortex? And if so, do you want the cortical surface to be semi-transparent, or perhaps rendered in wire-frame? --otherwise, there's a chance the dipole could be "hidden" if it's sub-cortical. And then there's the question to determine the surfaces -- are you planning on finding the scalp and/or cortical surface via isovalues?

Alternatively, we could use volume rendering instead, assuming you have a powerful enough graphics card (e.g. NVidia GeForce 3). For volume rendering we could cut a wedge out of the whole head -- then the challenge is choosing the transfer function to pull out those features of the volume that should appear (similar to picking the isovalues, above).

Any additional information you could give me regarding what you want this visualization to look like (and what type of graphics card you'll be using) would help me as I'm building this net for you.


David Weinstein
SCIRun Project Coordinator
SCI Institute, University of Utah

On Feb 11, 2004, at 6:20 AM, Christopher Joseph Bailey wrote:

Dear List,

I appologise in advance for trying to take a shortcut, but...

I have two MR-images of subjects we had in an MEG experiment. We used
proprietary software (xfit, Neuromag, Finland) to fit dipoles to their
MEG responses at a few timepoints. Now we want to show these individual
subject responses on their MR's, and I would like to use SCIRun. My
problem is zero experience (appart from the tutorial) on it's use and
would really appreciate some help.

I have the MR image in Analyze format (can of course convert to
whatever) that I would like to read in. I would like to make a rendering
of the surface of the volume and make a cutout to show the superior
temporal lobes (auditory cortex). Then I would like to show one or two
dipoles (as standard dot-arrow objects) "nicely" placed within the
cutouts. The MR- and dipole coordinate systems have been aligned.

Could anyone out there share a net I could modify for my purposes or
otherwise get me started? I was unable to find help "Googling" on the
web. In the future, I plan to get more familiar with BioPSE.

Any help much appreciated,

Christopher Bailey
-- Research Assistant (MSc)
Center for Functionally Integrative Neuroscience (CFIN)
Bygning 30
Århus Sygehus
DK-8000, Århus C

phn: +45 89 49 43 78
fax: +45 89 49 44 00

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