I Melissa, I had the same problem, I solved it this way:
in Xquartz go to preferences (cmd+,), and uncheck the first checkbox in the Security tab:
hope it helps! Gari
On 2012-09-13, at 16:19, Melissa Lancaster melissa.lancaster@my.rfums.org wrote:
Dr. Fischl,
Thanks so much. Unfortunately, I had closed the window. But here is what happened:
I set the environment: setenv FREESURFER_HOME /Applications/freesufer
However, after typing the next command: source $FREESURFER_HOME/SetUpFreeSurfer.csh I got the following error:
FREESURFER_HOME: Undefined variable.
I found an old post on the listserv with a similar problem, and directly copied the setenv command you had sent back to that user. I then got the source command to work, and the output was in line with what the installation website said I should get. Of note, at that time, I used a regular terminal window, I believe.
A friend told me to 'echo $FREESURFER_HOME' to see what the path is currently set at. When I do that, I get a blank space.
Thanks so much for the help!!!
-Missy
On Thu, Sep 13, 2012 at 8:12 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Missy,
yes, that sounds like at least part of your problem. What trouble did you have sourcing our env file? Can you send us the screen output?
Bruce On Wed, 12 Sep 2012, Melissa Lancaster wrote:
Hi again-
I should have added that I am using Mountain Lion. I have downloaded Quartz and when I work from an X11 window I get: tkmedit: command not found
I had difficulty with the source command when setting up the FREESURFER_HOME directory but eventually got it to work...not sure if this could have something to do with it.
Thanks again!!! -Missy
On Wed, Sep 12, 2012 at 10:46 PM, Melissa Lancaster melissa.lancaster@my.rfums.org wrote: Hi,
It seemed I had successful installed Freesufer, but when I went to run the tests I got errors with both tkmedit and tksurfer.
when typing <tkmedit bert orig.mgz> I got the following error:
Couldn't create output file .xdebug_tkmeditGLUT: Fatal Error in tkmedit.bin: could not open display:
when typing <tksurfer bert rh pial> I got the following error: GLUT: Fatal Error in tksurfer.bin: could not open display:
Any advice?
Thanks, Melissa
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-- Melissa A. Lancaster, M.S. Clinical Psychology Doctoral Student Rosalind Franklin University of Medicine and Science
-- Melissa A. Lancaster, M.S. Clinical Psychology Doctoral Student Rosalind Franklin University of Medicine and Science
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