[Homer-users] Atlas Viewer: Probe Registration

[David Boas]

I don’t fully understand your problem. The optode locations are projected on to the brain surface. This is why they disappear when you make the head opacity equal to 1. MNI coordinates are not defined outside of the brain, as far as I know. Further, to facilitate comparison with fMRI studies, it is useful to know the brain coordinate associated with the fNIRS data channel, rather than the scalp coordinate.

 

I am probably misunderstanding your question. Please clarify if I’ve got it wrong.

 

Thanks,

David

 

 

 

 

 

From: <homer-users-bounces at nmr.mgh.harvard.edu> on behalf of Christine Hucke <Hucke at ifado.de>
Reply-To: <homer-users at nmr.mgh.harvard.edu>
Date: Thursday, February 23, 2017 at 8:51 AM
To: "homer-users at nmr.mgh.harvard.edu" <homer-users at nmr.mgh.harvard.edu>
Subject: [Homer-users] Atlas Viewer: Probe Registration

 

Dear Homer users,

 

I recently designed my first probe using Atlas Viewer and until today I didn’t notice any problems. However, I was trying to use the MNI coordinates for further analyses and somehow they seemed to be too close to the brain thus beneath the surface of the standard head. 

I assumed it was a compatibility problem as I was trying to use those coordinates in another program. So I tried to trace back the error and discovered that the problem already occurred in AtlasViewer. I couldn’t see it right away as I was using the default head opacity of 0.7 but it became quite clear when I increased the opacity to 1 (see screenshots in attachment).

 

Does anyone else have the same problem and/or solution? Maybe it’s also due to my parameters that I’ve set during the probe design. 

 

I am happy for any help.

 

Best

Christine

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