[Homer-users] Atlas Viewer using 10-20

Mon Mar 24 12:46:19 EDT 2014

Katherine
i think you sent this message to me by mistake
best
mari

Maria Angela Franceschini,
Associate Professor,
Harvard Medical School,
Massachusetts General Hospital
Athinoula A. Martinos Center for Biomedical Imaging
13th Street, Building 149
Charlestown, MA 02129
office: (617) 726-4024
fax: (617) 643-5136
mari at nmr.mgh.harvard.edu

On Mar 24, 2014, at 11:57 AM, Perdue, Katherine 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 The released package is out of date.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
>>> 
>>> 
>>> _______________________________________________
>>> 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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>> 
>> 
>> 
>> -- 
>> Drew Halliday
>> Research Assistant
>> Medical Physics & Bioengineering
>> University College London
>> _______________________________________________
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>> Homer-users at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
>> 
>> 
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and properly
>> dispose of the e-mail.
> 
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