[Homer-users] Questions about AtlasViewer on short separation channels and image reconstruction
saskia at artinis.com
saskia at artinis.com
Fri Nov 17 06:03:47 EST 2017
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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