[Homer-users] AtlasViewer

[Moulton, Theresa (NIH/CC/RMD) [F]]

Hello Homer users,

Many thanks to David for the helpful tutorials and beneficial features of AtlasViewer. 

One problem that I was having initially was that after running the Monte Carlo simulations and generating the sensitivity profiles in AtlasViewer, they were not being displayed. I figured out that it was because my probe design did not include a connection between source 1 and detector 1 (the default S-D pair), so in the displaySensitivity.m was returning early and not enabling the text box to change channels. Updating the sensitivity.Ch value in initSensitivity.m solved this problem for me. Although I've been looking at this issue from my limited viewpoint, it appears that setting the default to [0 0] could be a solution to work for any probe design.

I was hoping to also ask for some feedback from the group. I'm having another problem with either the Monte Carlo simulations outside of Matlab or the genSensitivityProfile.m function, and I was wondering if anyone in the user group might have some advice... In 2 probe designs that I've tried so far, I have found one or more channels where the generated sensitivity profiles (Adot and sensitivity.Adot) returns NaN. I can individually see the profiles of all other channels in AtlasViewer, but no sensitivity is displayed for those with a Nan value (makes sense), and setting the channel to [0 0] as shown in the tutorial will also not display anything since having NaN in the sum returns NaN throughout. In one probe design this is a short-separation (1 cm) channel, but in the other probe it is a longer separation of 3 cm. Has anyone seen this before, or have a suggestion for the source of this problem?

Thanks in advance,
Theresa


Theresa Sukal Moulton, DPT, PhD
Post-doctoral Fellow
Functional & Applied Biomechanics Section
Rehabilitation Medicine Department
National Institutes of Health Clinical Center


-----Original Message-----
From: David Boas [mailto:dboas at nmr.mgh.harvard.edu] 
Sent: Saturday, August 31, 2013 12:21 PM
To: homer-users at nmr.mgh.harvard.edu
Subject: [Homer-users] AtlasViewer

I've posted some new tutorials to show how to register digitized points to an atlas in AtlasViewer and then how to run the Monte Carlo forward model to calculate the measurement sensitivity profiles. You can see these tutorials at http://homer-fnirs.org/documentation/

You can also find links to download the files so that you can duplicate what is shown in the tutorials.

Make sure you have the latest developers version of homer to run AtlasViewer. We are trying to create an executable of AtlasViewer for those who don't have matlab.

Let me know what else you need tutorials on for AtlasViewer and I will try to make a video.

David

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