[Homer-users] AtlasViewer - visualizing recorded NIRS data

Tue Apr 21 10:35:35 EDT 2015

Let’s move this discussion to private emails.

We’ll then let the rest of the homer community know once we made some progress.

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> On Apr 21, 2015, at 8:53 AM, Pankaj Gupta <beckman16 at gmail.com> wrote:
> 
> Ok David, to begin with, I am editing homer2/PACKAGES/AtlasViewerGUI/ForwardModel/genSensitivityProfile.m file.
> 
> My idea is to-
> 1) load HRF data saved from Homer2
> 2) Adot(meas_ch, n_vertices, n_wave) contains sensitivity profile of 'meas_ch'.
> 3) Obtain percentage sensitivity of each vertices - sensitivity(i) / max(sensitivity). 
> 4) Multiply percentage sensitivity of each vertex with OxyHb, DeOxyHb and TotalHb values from HRF data (possibly scale these results) to obtain a updated Adot matrix that reflects HRF of NIRS data.
> 
> How does it sound ?
> 
> Also, If I checkout AtlasViewer from developer site, would it have some of the new functionalists related to displaying NIRS data ?
> 
> 
> Kind regards
> Pankaj
> 
> On Tue, Apr 21, 2015 at 12:43 PM, David Boas <dboas at nmr.mgh.harvard.edu <mailto:dboas at nmr.mgh.harvard.edu>> wrote:
> 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 <mailto: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
>> 
>> 
>> 
>> 
>> .
>> .
>> .
>> 
>> <image001.jpg>
>> 
>> http://brain.kenes.com/ <http://brain.kenes.com/>
>> 
>> Society for fNIRS
>> Make sure you get the monthly news letter
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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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