[Homer-users] AtlasViewer registration

Wed May 28 16:19:17 EDT 2014

Update....

Based on this feedback, I did update my developer's version again to the latest files. I didn't pay close enough attention to the files that had changed, but the registration of the probe to the surface does not distort the optodes arrangement as it had previously. The 10/20 ref points are still floating, but the optodes and reference  points look reasonable to the surface of the scalp, and the MNI coordinates make sense for the areas we are targeting.

Another thing that might be useful to others -- In my digpts.txt file, I discovered that I needed to artificially add in d9 through d16 - those are detectors that are not in our CW6 setup, but are modules that could be added. They are required placeholders in the SD file, but I wasn't accounting for them in the digpts because we don't collect 3D coordinates for them because they are not real. I copied the Cz position as the location of each of those detectors, and AtlasViewer was able to determine the configuration so I was able to view the measurement list and project the channels to the cortex (vs. just the optodes previously).

We look forward to trying to use these features with a subject-specific MRI vs the Colin atlas as mentioned in the last training - we'll watch the listserv when that documentation/update is available.

Many thanks,
Theresa

From: David Boas [mailto:dboas at nmr.mgh.harvard.edu]
Sent: Wednesday, May 28, 2014 9:22 AM
To: homer-users at nmr.mgh.harvard.edu
Subject: Re: [Homer-users] AtlasViewer registration

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<mailto: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

_______________________________________________

Homer-users mailing list

Homer-users at nmr.mgh.harvard.edu<mailto:Homer-users at nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users

--

==============================================================

fNIRS 2014 Conference in Montreal Oct 10-12, 2014

The conference is preceded by a one day educational workshop.

Abstract Deadline June 16, 2014

see http://fnirs2014.org for more details

==============================================================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20140528/ee335197/attachment.html 