[Homer-users] AtlasViewer Help for Prefrontal Cortex NIRS Headband

[Michael Cannizzaro]

Dear Meryem,

Thank you so very much, your suggestions were extremely helpful. After many hours of work yesterday and today, I have made a lot of progress and think I am quite close (see figures & .sd file below).  These are what I imagined in terms of placement and localization, but I would like to fine tune a bit and continue to get stuck (unexpected results) when I try to tweak the model. 

First, I would like the #4 source optode to be more centered in the surrounding detector field, like the #1 source is on the other side. 

Second, I feel that the connecting lines are a good fit for some source detector pairs (black lines) but others are not as good. Do you have any suggestions as to small fine tuning type adjustments that will not distort the model but create closer pairings?






At this point the dynamics and physics of the system are still somewhat mysterious to me. I often find that small  and symmetrical changes can produce very distorted and unexpected results. So, any help from you or the users group is very much appreciated!

Thanks,

MIKE

Michael S. Cannizzaro, Ph.D., CCC-SLP

Associate Professor 

University of Vermont 
Department of Communication Sciences & Disorders - Graduate Program Coordinator
Undergraduate Neuroscience Program
401 Pomeroy Hall
489 Main Street
Burlington, VT 05405

1-802-656-9725

michael.cannizzaro at uvm.edu

http://www.uvm.edu/cmsi/ 




On Oct 28, 2013, at 4:44 PM, Meryem Ayse Yucel <mayucel at nmr.mgh.harvard.edu> wrote:

> Hi Mike,
> 
> I'd suggest the following:
> 
> 1) Use more springs including the midlines connecting your optodes.
> 2) Make your springs elastic by right clicking them (they appear dashed)
> 3) Choose your anchor points more sparse
> 
> Hope this helps.
> 
> Meryem
> 
>> Hi List,
>> 
>> I am new to the AtlasViewer so sorry if this is a rudimentary question or
>> I am overlooking a fundamental step.
>> 
>> I am trying to make a probe for my Biopac fNIR headband that has 4 sources
>> and 10 detectors in a very simple rectangular grid (example included
>> below). Fp1 and Fp2 are to align horizontally to the midway point between
>> the sources and lower row of detectors. I have made an SD file that I
>> believe matches this set up exactly using real measurements from the
>> headband and the center of each optode. When I add the springs, everything
>> looks just like the schematic, however when I register the probes to the
>> surface, it is a blob of jumbled points without any resemblance to the
>> rectangular shape. It is also no where near where I expect it to be on the
>> prefrontal cortex. I have also included the .SD file if that helps. Any
>> support is appreciated and thanks.
>> 
>> MIKE
>> 
>> 
>> Michael S. Cannizzaro, Ph.D., CCC-SLP
>> 
>> Associate Professor
>> 
>> University of Vermont
>> Department of Communication Sciences & Disorders - Graduate Program
>> Coordinator
>> Undergraduate Neuroscience Program
>> 401 Pomeroy Hall
>> 489 Main Street
>> Burlington, VT 05405
>> 
>> 1-802-656-9725
>> 
>> michael.cannizzaro at uvm.edu
>> 
>> http://www.uvm.edu/cmsi/
>> 
>> 
>> 
>> 
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