[Homer-users] AtlasViewer registration

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

Hi Homer users,

I'm writing to ask for some feedback about an issue I've encountered when using AtlasViewer to register digitized points to the Atlas.

We have digitized the location of the optodes on our probe, as well as Nz, Iz, Ar, and Al using reflective markers on the Vicon system, so the markers are definitively 'floating' above the head of the participant, in a similar way to the use of other systems discussed in the AtlasViewer training video. Attached is a word document showing screen shots of the different steps within AtlasViewer, as well as my digpts.txt file. When AtlasViewer initializes, we can see the markers, but no view of the brain - I'm guessing because the origin of the two coordinate systems are appreciably different. When I register the points to the Atlas via the Tool menu, there is a very nice looking approximation of where the probe should be - it is symmetrical, matches the shape of the probe, and rests on the surface of the atlas skull. However, I also see that the Atlas reference points are all floating above the apparent surface of the Atlas skull.

When I take the next step to register the probe to the surface, I am left with optodes floating above the skull, and distorted compared to the real probe. I am able to project the individual optodes to the cortex, but not the channels (there is also a .nirs file in the folder that has the associated SD configuration for this probe). Although this step doesn't even seem relevant when the probe arrangement has changed so much.

Any suggestions about where I may be going wrong? Should I be taking into account an approximate offset between the center of the reflective marker and the surface of the skull already in the digpts file? I've played around with translating my digpts coordinate system so the origin was near the middle of the skull, but that did not change the results. The participant is an adult, of fairly average head size.

Thanks in advance for any suggestions you may have.

Kind regards,
Theresa



Theresa Sukal Moulton, DPT, PhD
Post-doctoral Fellow
Functional & Applied Biomechanics Section
Rehabilitation Medicine Department
National Institutes of Health Clinical Center
10 Center Drive, Room 1-1425

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