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,
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.-- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10@u.rochester.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.-- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10@u.rochester.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > 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. > > > > > > -- > Daniel Cole > University of Rochester > Brain and Cognitive Sciences > dcole10@u.rochester.edu > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10@u.rochester.edu
Yes I am running recon-all on a Mac. It is an office computer (so not a Macbook pro) and my runtimes are around 15-20 hours for each subject.
Daniel
On Tue, Feb 26, 2013 at 12:54 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
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 > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > 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. > > > > > > -- > Daniel Cole > University of Rochester > Brain and Cognitive Sciences > dcole10@u.rochester.edu > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10@u.rochester.edu
freesurfer@nmr.mgh.harvard.edu
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Daniel Cole -
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