[Homer-users] AtlasViewer - visualizing recorded NIRS data

Tue Apr 21 03:11:06 EDT 2015

Hi everyone!

A few years ago I coded part of the (not yet) HOMER2 atlas viewer tool and I was able to display my fNIRS data on the atlas cortical surface.
You can find a few details here: http://emma.polimi.it/emma/events/vdp/attachments/paper_09_5_caffini.pdf

Ciao!
Matteo

From: homer-users-bounces at nmr.mgh.harvard.edu [mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of pankaj gupta
Sent: 21 April 2015 03:40
To: homer-users at nmr.mgh.harvard.edu
Subject: Re: [Homer-users] AtlasViewer - visualizing recorded NIRS data

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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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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