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.
