[Homer-users] Atlas Viewer using 10-20

[Drew Halliday]

Hi Ted,

Your suggestion was indeed correct!  Whereas before I was trying to
manually adjust the values in the 1st of the 3 menus in Position Probe
(after clicking the Add Springs button), I now see that this is done
automatically when you click on 2 optodes (i.e., a "spring" is added, and
the distances are generated automatically).  The spring list is also
available upon loading the SD file in Matlab.

My sincerest thanks for all the collective advice.

Best wishes,
Drew


On Wed, Mar 26, 2014 at 4:59 AM, Huppert, Ted <huppertt at upmc.edu> wrote:

> The lack of springs on the GUI is probably the culprit.  I would suggest
> that it's not a matter of them just not showing up, but that they aren't
> being specified in the file for some reason.
>
> Note, the springs don't automatically add when you switch to the add
> springs page.  Just like adding measurement pairs, you have to manually add
> them.  If you click once it's a hard spring (fixed distance and solid line)
> if you double click it's a directional vector (dotted line and length is
> listed as "-1").  You have to click on the source and then detector (or
> vice versa) to add a spring.
>
> .  One way to check is if you save and load the probe.sd file into matlab
> (load using the "-MAT" flag) there should be a field called probe.sl (for
> spring list) which should have size <n x 3> where n is the number of
> springs.
>
> Assuming the spring list is empty, the question is why?  When you click on
> the source/detectors to add the springs, do the lines appear and go away or
> does something else happen?  I usually have the issue of accidentally
> adding too many springs and can't get them off.  I've never had the issue
> of them not appearing. When you first click on the source it should change
> fonts (does it?) and then when you click a second point it should draw a
> line (does it?).  Do the lines appear and then go away or never appear?
>
>
>
>
> Theodore Huppert, PhD
> Assistant Professor
> Dept of Radiology and Bioengineering
> University of Pittsburgh
> huppertt at upmc.edu<mailto:huppertt at upmc.edu>
>
> On Mar 26, 2014, at 4:53 AM, "Drew Halliday" <d.halliday at ucl.ac.uk<mailto:
> d.halliday at ucl.ac.uk>> wrote:
>
> 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<mailto:
> 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<http://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<tel:857-218-5214>
>
> On Mar 24, 2014, at 10:05 AM, Drew Halliday <d.halliday at ucl.ac.uk<mailto:
> 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
> <mailto: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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> --
> Drew Halliday
> Research Assistant
> Medical Physics & Bioengineering
> University College London
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> --
> Drew Halliday
> Research Assistant
> Medical Physics & Bioengineering
> University College London
> <Atlas-screenshot_1.png>
> <Atlas-screenshot_2.png>
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-- 
Drew Halliday
Research Assistant
Medical Physics & Bioengineering
University College London
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