Re: [Freesurfer] Tkregister2 / Tksurfer / Tkmedit Won't Open

Daniel,

Are you using your Mac to run recon-all? I'm curious about the run-times you are seeing. Others have had very long run times, which I cannot explain. I'd expect about 24 hour runtime, possible half that or less, on a current Macbook Pro.

Nick

On Tue, 2013-02-26 at 12:51 -0500, Daniel Cole wrote:

I was holing out on an analysis before rebooting but that seemed to do the trick! Thanks all!

Daniel

On Mon, Feb 25, 2013 at 5:58 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: have you rebooted since installing XQuartz? i've found a reboot is necessary to get Terminal to open up again.

    N.


    On Mon, 2013-02-25 at 17:07 -0500, Daniel Cole wrote:
    > Hi Zeke,
    > Thank you for the advice.  I have Mac OS X Version 10.7.5.
    > I checked to see if XQuartz is installed and it is.  I
    reinstalled it
    > to be sure but I'm still running into the same problems.  Do
    you (or
    > does anyone else) have other ideas about what could be
    causing this
    > issue?
    >
    > Thanks,
    > Daniel
    >
    >
    > On Thu, Feb 21, 2013 at 5:22 PM,
    <zkaufman@nmr.mgh.harvard.edu> wrote:
    >         Daniel,
    >
    >         What operating system are you on? If your using
    MacOS, you
    >         must have
    >         XQuartz installed in order to use the the
    >         Tkregister2/Tksurfer/Tkmedit
    >         tools. Check the Application->Utilities folder to
    see if its
    >         already
    >         installed. If not, you can download it from here:
    >
    >         http://xquartz.macosforge.org/landing/
    >
    >         If your are on Linux than I am sorry but someone
    else will
    >         have to chime
    >         in with a potential solution.
    >
    >         -Zeke
    >
    >
    >         > Hello freesurfers,
    >         > I just ran registration of my functional images
    and am
    >         trying to visualize
    >         > the registration for assessment.  However, when I
    use the
    >         commands
    >         > "tkregister-sess -s $SESSIONNAME -d
    $SESSIONDIRECTORY -fsd
    >         bold -funcstem
    >         > f"
    >         > or
    >         >
    >         > "tkregister2 --targ T1.mgz --fstarg --s $SUBJECTID
    --surf
    >         --mov
    >         > $FUNCTIONAL_MRI --reg $REG_DAT --plane sag
    --movbright
    >         $MYBRIGHTNESS"
    >         >
    >         > the command gets stuck on "Opening window
    SUBJECT01".
    >         >
    >         >
    >         > I've also tried just opening tksurfer and tkmedit
    but the
    >         terminal
    >         > produces
    >         > no output/windows opening and simply freezes.
    >         >
    >         > Any ideas to why this could be occurring?  I've
    let it sit
    >         at this stage
    >         > for multiple hours without anything popping up and
    without
    >         any errors.
    >         >
    >         >
    >         > Thanks!
    >         >
    >         > Daniel
    >         >
    >         >
    >         > --
    >         > Daniel Cole
    >         > University of Rochester
    >         > Brain and Cognitive Sciences
    >         > dcole10@u.rochester.edu
    >
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    > --
    > Daniel Cole
    > University of Rochester
    > Brain and Cognitive Sciences
    > dcole10@u.rochester.edu
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-- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10@u.rochester.edu