I had a similar error when using CentOS on VirtualBox. The error came from an error in the OpenCL driver. Are you running a virtualmachine? If not i would advise trying a different graphics driver. As to the CentOS/Ubuntu choice. I would go with CentOS as it seems more stable/constant and is more easy to also install FSL.
Best regards Rune Frandsen MD Danish Center for Sleep Medicine. On Wed, Aug 28, 2013 at 5:18 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > JoJo, > > I have not tried to recreate your issues on machine running Ubuntu 13.04 > but have tried to run the commands on Ubuntu 12.04. To summarize: > > 1) Regarding your first issue... this is standard output to the terminal > on certain OS's including Ubuntu. I got it when I tested your command > but the tkmedit window still appeared. You may have to press enter after > receiving the "Couldn't create output file .xdebug_tkmeditReading > /usr/local/freesurfer/tktools/tkm_common.tcl" but this is a normal > warning message. > > 2) Change your command to the following: > tkmedit -segmentation $SUBJECTS_DIR/bert/mri/aseg.mgz \ > $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz > > 3) Again, I get the same warning, but the window still appears. Try > hitting enter after you get the warning message. > > -Zeke > > > On 08/23/2013 11:05 PM, JoJo wrote: > > Dear Freesurfer experts, > > I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I > > followed the commands in tutorial and got error message, listed as > > follows. (Nevertheless, FS can read in volume and surface from GUI.) > > Another question is, which one of Centos4 or Centos6 is more > > suitable for Ubuntu 13.04? > > 1. tkmedit bert orig.mgz > > Couldn't create output file .xdebug_tkmeditReading > > /usr/local/freesurfer/tktools/tkm_common.tcl > > 2. tkmedit -segmentation mri/aseg.mgz \ > > $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz > > Couldn't create output file > > > .xdebug_tkmeditmghRead(/usr/local/freesurfer/subjects/bert/mri/mri/aseg.mgz, > > -1): could not open file > > a window pop up: Error: loading segmentation mri/aseg.mgz > > Couldn't import the segmentation volume. Tkmedit couldn't read the > > segmentation specified. This could be because the segmentation volume > > wasn't a valid COR volume directory. > > (Note: In fact, I can load segmentation volume from window.) > > 3. tksurfer bert rh pial > > Couldn't create output file .xdebug_tksurfersubject is bert > > > > Thanks for your help, JoJo > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > 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. > > -- Rune Frandsen runefrand...@gmail.com
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