[Homer-users] Atlas Viewer using 10-20

Tue Mar 25 20:09:47 EDT 2014

Hi Katherine,

Thanks for the description -- I was able to setup what appears to be the
developer's version (I've noticed several additional prompts that were not
there before).  I am still encountering the same error as before, where,
after defining the measurement list, adding dummy optodes (which works
now), and defining the reference points for 4 optodes (which also works
now), the "springs" do not show up (see attached screenshot) and the probe
is not localised over the locations I am trying to specify (see attached
screenshot).  Any inclining as to why this might be?

I wonder if another GoTo Meeting would be useful to hold.  In addition to
landmarking with 10-20, I understand that a 3D digitiser acquisition
component, EasyMapper, is under development.  In a different tutorial video
that demonstrates registering an atlas using 3D points (
http://www.youtube.com/watch?v=tAhSwiIUAZI), it seems that generating a
text file by converting from EasyMapper (.ezs) points is essential.  I have
Polhemus digitiser points from a revised version of PolGUI that are in a
similar format (i.e., with Nz, Ar, Lr, Iz & Cz, then optode locations).  It
appears however, that the only way to call these points into the GUI is
through converting from .ezs into a text file, and the option to register
probe to surface seems to become available only after this conversion -- is
this correct?

Thanks again for your help,
Drew

On Mon, Mar 24, 2014 at 8:57 AM, Perdue, Katherine <
Katherine.Perdue at childrens.harvard.edu> wrote:

>  Hi Drew,
>
>  You should be able to set up SmartCVS client to download the project
> without having a specific link if you set up the repository profile like:
>
>  Access method: pserver
> User name: anonymous
> Server name: orbit.nmr.mgh.harvard.edu
> Repository path: /cvsroot/homer
>
>   best,
>  Katherine
>
>
>  -------------
>  Katherine Perdue, PhD
>  Research Fellow in Pediatrics
>  Labs of Cognitive Neuroscience
>  Division of Developmental Medicine
>  Boston Children's Hospital
>  Office Phone: 857-218-5214
>
>  On Mar 24, 2014, at 10:05 AM, Drew Halliday <d.halliday at ucl.ac.uk>
>  wrote:
>
>  Hi David,
>
>  Thanks for your reply.  I was using the Matlab package, and not the
> developer's version.  I've located the Orbit page and downloaded a CVS
> client (SmartCVS).  I can't seem to find Homer 2 -- I see Homer and Homer
> 3, although 3 doesn't appear to have any files.  Have you got a link to the
> relevant files?  Admittedly, using a CVS client is not something I'm
> entirely familiar with.
>
>  Thanks again,
> Drew
>
>
> On Sat, Mar 22, 2014 at 4:59 PM, David Boas <dboas at nmr.mgh.harvard.edu>wrote:
>
>> Indeed, you are not able to change the dummy optode number. That is on
>> purpose. It is automatically set to a value and automatically handled. Is
>> there any particular reason you are finding that you need to change the
>> dummy optode number?
>>
>> Regarding the anchor points, it is strange that some anchor points are
>> not being accepted for you. Are you using the developers version of
>> atlasViewer that you get from CVS from orbit? Or are you using the released
>> package? The released package is out of date. If you are using that and
>> can't easily get the cvs version, then maybe we need to update the released
>> package. If you are using the cvs version, then email me directly and if I
>> can recreate the problem, then we can fix it.
>>
>> >From your screen shots, I don't really understand the problem of springs
>> not showing up.
>>
>> Maybe it is time to have another online GoToMeeting to go over
>> AtlasViewer.  Please let me know if you want that I set that up.
>>
>> Thanks,
>> David
>>
>>
>>
>>
>>
>>
>> On 3/21/14, 6:45 PM, Drew Halliday wrote:
>>
>>  Hi Homer2 Users,
>>
>>  I am using AtlasViewer GUI to register an array to the atlas, based on
>> 10-20 landmarks.  Although this is covered at the end of the March 4, 2013
>> training video (http://www.youtube.com/watch?v=a1jtsIEVHMY), several
>> steps remain unclear to me, and I am seeking clarification.  I have tried
>> this approach using both a UCL NTS system (and calling the separate SD
>> file), and a TechEn system (calling the .nirs file in its totality).
>>
>>  When adding springs after calling the SD file, I am unable to
>> manipulate the opt# variable under the Dummy Optodes menu.  I am able to
>> manipulate the x and y coordinates, but not the optode #.  I am also able
>> to define what I believe is the measurement list (i.e., the "Springs" menu,
>> with opt1, opt2 and length).  With the Anchor Points menu, I am able to
>> manipulate the opt# variable, but the ref pt variable will only tolerate
>> certain 10-20 points (e.g., F3 & F4, but not F1 or F2). The springs do not
>> show up like in the video, even after clicking add springs (see attached
>> screenshot).  All of these steps appear to have already been completed in
>> the training video.  Pushing through to the registration step, the probe
>> does appear in the GUI, but is not localised over the 10-20 reference
>> points I specify (see attached screenshot).
>>
>>  If anyone has thoughts regarding why the "springs" don't show up, and
>> why, after specifying 4, 10-20 anchor points the probe is not repositioned,
>> please let me know!
>>
>>  Thanks,
>>  Drew
>>
>>
>>
>>  --
>> Drew Halliday
>> Research Assistant
>> Medical Physics & Bioengineering
>> University College London
>>
>>
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>> Homer-users mailing listHomer-users at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
>>
>>
>>
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>
>
>  --
> Drew Halliday
> Research Assistant
> Medical Physics & Bioengineering
> University College London
> _______________________________________________
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>
>
> The information in this e-mail is intended only for the person to whom it
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> addressed. If you believe this e-mail was sent to you in error and the
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> HelpLine at
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> properly
> dispose of the e-mail.
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> is
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> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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>

-- 
Drew Halliday
Research Assistant
Medical Physics & Bioengineering
University College London
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