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Re: [SCIRUN-USERS] Problems setting contact voltage on DBS lead


Chronological Thread 
  • From: Andrew Janson <jansonap@gmail.com>
  • To: jess <jess@sci.utah.edu>
  • Cc: "Gorman, Sydney N." <gorman.sydney@mayo.edu>, scirun-users@sci.utah.edu
  • Subject: Re: [SCIRUN-USERS] Problems setting contact voltage on DBS lead
  • Date: Wed, 26 Feb 2020 10:21:29 -0700
Hi Sydney,

To expand on Jess' answer, the other common reasons that do not produce a valid solution are not setting Dirichlet boundary conditions in "ApplyFEMVoltageSource" (if you are using "ApplyFEMCurrentSource" make sure the Source model is set to "sources and sinks") and make sure "SolveLinearSystem" has converged (Click the "i" on the module to see how many iterations it needed to converge, you may need to increase the maximum iterations in the module). I remember Grayson Goss emailed me last summer about DBS simulations in SCIRun and he had a network called "DBS In A Box". This is a bit less complex than the network from my paper but covers the necessary modules to simulate DBS for both voltage and current-controlled stimulation. This network is a part of our BrainStimulator toolkit which you can download directly through SCIRun in the "Toolkit" tab or here (https://github.com/SCIInstitute/BrainStimulator). Once downloaded, extract the zip file and look in the "Networks" folder and set your Path under "Windows>>Preferences" to the extracted BrainStimulator folder.

Thanks,
Andrew

On Tue, Feb 25, 2020 at 4:51 PM jess <jess@sci.utah.edu> wrote:
Hi Sydney,

There are a few reasons that there would be zeros in your solution.  The most common is that the voltages are not set properly.  To calculate the potential field from known electrodes (boundary conditions) the field need to be the set voltages only at the desired locations and nan everywhere else.  You can test this using clipfieldbyfunction and using 'isfinite(DATA);’ in the parser.  Other things to check include the conductivities (cannot be 0 or too high), and the error on the solvelinearsystem module (which should be 10e-6 or lower). 

cheers,
Jess





> On Feb 25, 2020, at 10:57 AM, gorman.sydney@mayo.edu wrote:
>
> Hello!
>
> I'm attempting to model the electric field produced by a DBS electrode using a
> voltage controlled model. I'm basing most of my current Sci Run environment
> off of the example published in "Targeting Neuronal Fiber Tracts for Deep
> Brain Stimulation Therapy Using Interactive, Patient-Specific Models.",
> however, the results of the linear system seem to be zero regardless of the
> voltage I have set. I was wondering if anyone had run into a similar problem,
> or if there is something obvious I am missing. I can send a picture of my
> workstation if that would be helpful!
>
> Thank you so much!
>
> Sydney Hillan
>
>
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