[Homer-users] AtlasViewer - visualizing recorded NIRS data

[David Boas]

Let us know if you make progress updating AtlasViewer to display data. It is something we’ve started working on and would be happy to discuss.




> On Apr 20, 2015, at 9:40 PM, pankaj gupta <pankajkmrgupta at gmail.com> wrote:
> 
> Thanks Meryem and David, got it.
> Though I will try to modify Homer code to be able to plot averaged trial data - hope its not very complex.
> 
> Sure David, please post it on the mailing list once the Tutorial is available.
> 
> 
> Regards
> Pankaj
> 
> On Tue, Apr 21, 2015 at 3:45 AM, David Boas <dboas at nmr.mgh.harvard.edu <mailto:dboas at nmr.mgh.harvard.edu>> wrote:
> A tutorial on how to use AtlasViewer is about to be published in Neurophotonics and will be freely available.
> 
> We will post the link to the paper here once it is available.
> 
> David
> 
> 
> 
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> <image001.jpg>
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>> On Apr 20, 2015, at 12:02 PM, Meryem Ayse Yucel <mayucel at nmr.mgh.harvard.edu <mailto:mayucel at nmr.mgh.harvard.edu>> wrote:
>> 
>> Hi Pankaj,
>> 
>> Please see my responses interleaved.
>> 
>> Meryem
>> 
>>> Hi Homer-users,
>>> I am trying to get used to AtlasViewer. I have followed all the tutorial
>>> videos on youtube and listed on tutorial page of Homer website.
>>> Is there a way to visualise the actual recorded NIRS data over the Atlas ?
>>> Some SPM or conditional comparison ?
>> 
>> The current version of AtlasViewer does not have this option, however that
>> is in our to do list.
>> 
>>> 
>>> As of now, please correct me if I am wrong, AtlasViewer can visualise the
>>> optode, channel locations and compute and display sensitivity profiles for
>>> channel locations.
>> 
>> That is correct. You can also evaluate probe fabrication error and
>> inter-subject probe placement variability.
>> 
>>> 
>>> Again, I find very little details as to what is sensitivity profile of a
>>> channel ?
>> 
>> It is the sensitivity of the channel to absorption changes. Sensitivity
>> matrix (A) transforms the absorption change in each voxel to a measurement
>> change (eg optical density change). Or in other words, it will give us the
>> information of how much absorption change has taken place if we observe
>> this much optical density change at a specific source detector couple,
>> because the optical density changes we observe is actually an integration
>> of absorption changes over a volume (the tissue under the source and
>> detector where the photon travel takes place). This A matrix can be
>> obtained by performing Monte Carlo simulations of photon migration from or
>> to each optode.
>> 
>> 
>>> 
>>> I appreciate efforts of the developers in making Homer and AtlasViewer
>>> tools. Your response to my queries would really be appreciated.
>>> 
>>> Kind regards
>>> Pankaj
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>> 
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