% 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 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
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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

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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