[Homer-users] AtlasViewer registration

[David Boas]

Theresa,
Thanks for sharing your digpts.txt file. I was able to register the 
atlas to the digpts and view the probe on the surface of the head. 
Register probe to surface worked well for me as did project to cortex. I 
don't have your SD information and so can't verify the behavior of 
project channels to cortex.

I do see that the 10-20 ref pts are floating above the head. This also 
confuses me. I have to check with Jay, but I suspect he applies some 
absolute offset projecting these ref points away from the center of the 
head so that they float a little bit above the surface of the head. 
Perhaps your dig pt units are not standard and thus his "absolute" 
offset causes the ref pts to appear floating away from the head. I need 
to check with Jay on this.

I didn't recreate the problem you indicated of the probe becoming 
distorted when you registered the probe. Perhaps send me your SD info 
(either sd file or nirs file) directly to me at 
dboas at nmr.mgh.harvard.edu and I can try again.

Thanks,
David



On 5/27/14, 4:56 PM, Moulton, Theresa (NIH/CC/RMD) [F] wrote:
>
> 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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> Homer-users mailing list
> Homer-users at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users

-- 
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