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 r *egular 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.eduwrote:
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 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
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/**compliancelinehttp://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.
-- Melissa A. Lancaster, M.S. Clinical Psychology Doctoral Student Rosalind Franklin University of Medicine and Science
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
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.
-- 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
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.
Thanks Gari for the suggestion! I unchecked the "Authenticate connections" button in X11, and ran the setenv and source commands again, and everything seemed to work as it should.
[Melissas-iMac:/Applications] mlancaster% setenv FREESURFER_HOME /Applications/freesurfer [Melissas-iMac:/Applications] mlancaster% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni
*tkmedit and tksurfer appear toto work, but with tkmedit I got the following errors:*
[Melissas-iMac:/Applications/freesurfer/subjects] mlancaster% tkmedit bert orig.mgz Couldn't create output file .xdebug_tkmeditReading /Applications/freesurfer/tktools/tkm_common.tcl
*When I tried to test the cortical segmentation I got the following error:*
% tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt can't read "FREESURFER_HOME": no such variable % tksurfer bert rh pial Couldn't create output file .xdebug_tksurfersubject is bert hemi is rh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Applications/freesurfer/subjects surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=132934, faces=265864 surfer: single buffered window
*And the following errors with recon-all:*
% recon-all -s bert -autorecon1 ERROR: you do not have write permission to /Applications/freesurfer/subjects/bert child process exited abnormally % sudo recon-all -s bert -autorecon1 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/sudo) is setuid or setgid Password: FREESURFER_HOME: Undefined variable. child process exited abnormally
I dont understand why FREESURFER_HOME is not recognized. Thanks again to anyone for any suggestions!!
-Missy
On Fri, Sep 14, 2012 at 9:00 AM, Garikoitz Lerma Usabiaga < garikoitz@gmail.com> wrote:
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 r *egular 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 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
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/**compliancelinehttp://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.
-- 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
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.
freesurfer@nmr.mgh.harvard.edu
-
Garikoitz Lerma Usabiaga -
Melissa Lancaster