[Homer-users] Questions about AtlasViewer on short separation channels and image reconstruction

[Jörn M. Horschig]

Dear Homer developers and users,

We would be grateful if someone could shed light on below questions. Also partial answers are more than welcome.

With best regards,
Jörn

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Jörn M. Horschig, PhD, Software Engineer & Project Leader NeuroGuard XS
Artinis Medical Systems  |  +31 481 350 980 
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-----Original Message-----
From: homer-users-bounces at nmr.mgh.harvard.edu [mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of saskia at artinis.com
Sent: Friday, November 17, 2017 12:04
To: homer-users at nmr.mgh.harvard.edu
Subject: [Homer-users] Questions about AtlasViewer on short separation channels and image reconstruction

Dear Homer and AtlasViewer users,

I am Saskia Kruitwagen and I am doing my masters internship at Artinis Medical Systems. I am preforming NIRS measurements with a probe which includes short separation channels.
For the data processing and analysis, I am using Homer and AtlasViewer, which are fantastics tools for analyzing fNIRS data. However, I have a few questions about AtlasViewer:

1.	I have a question about the processing step involving the short 
separation channels. I can do this in Homer, using enAdaptiveSS or a GLM filter. However, in AtlasViewer there is also an option ‘short separation threshold’. Therefore, I was wondering, when to should I do the processing step with the short separation channels: in Homer or in AtlasViewer?
What is AtlasViewer exactely doing with the short separation channels? 
In AtlasViewer, I can set a ‘short separation threshold’ when I do image reconstruction. However, this option gives me errors when this value is nonzero. So, is this option even working?

2.	The second question is about image reconstruction in AtlasViewer. For 
the image reconstruction I have to specify an alpha value. This is the regularization parameter. The default value is 1000. In Custo et al. 
(2010) I looked up how to calculate alpha. They give a formula (following formula 3) how to calculate a tau, based on the sensitivity matrix. To my understanding alpha in AtlasViewer is the same parameter as tau squared in Custo et al. Is this correct? When I use the formula in Custo et al, alpha is 10, which is much lower than the default of 1000. Is this a sensible value?

3.	My third question is about image reconstruction as well. In the 
ImageRecon window I can either choose ‘brain only’ or ‘ brain and scalp’. For this second option, I need the file “fw/Adot_scalp.mat”. 
Since I apparently do not have this file, AtlasViewer gives me an error. 
How can I obtain this data file? And what is the difference between both options?

4.	Next, when AtlasViewer has calculated the image matrix, with certain 
thresholds, these values are stored and cannot be changed initially set. 
The calculation dialog does not open a second time. If I want to change the thresholds, how can I perform this calculation again?

5.	What is the unit and scale of the resolution images? In Aasted et al. 
it says, “a linear scale in millimeter” for the localization error, but does that hold as well for the resolution profile? It seems to me that the scale is flipped, because resolution has the lowest values where I have a very dense probe profile.

6.	My last question is: how can I obtain the MNI coordinates of my 
activation map?

It would be nice if someone could help me out?

Best regards,

Saskia Kruitwagen
Master student Biomedical Engineering, UT Twente, The Netherlands _______________________________________________
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