[Homer-users] AtlasViewer - visualizing recorded NIRS data

[Pankaj Gupta]

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>
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>
> 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>
> 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/
>>
>> *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> 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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