[Homer-users] AtlasViewer - visualizing recorded NIRS data

[pankaj gupta]

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>
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
>
>
>
>
> .
> .
> .
>
>
> http://brain.kenes.com/
>
> *Society for fNIRS*
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>
> On Apr 20, 2015, at 12:02 PM, Meryem Ayse Yucel <
> 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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