It certainly does seem like their are permissions issue. From your message below, the 'rm' and 'mv' command complained about inadequate permissions... and the recon-all.env command failed as well.

You've installed freesurfer on your Desktop folder, which is somewhat out of the ordinary, though not a problem in itself. Make sure you have adequate permissions to that folder. And get the recon-all command that you issued working (recon-all -s bert -autorecon1). Once that works the GUIs should work as well.

-Zeke

On 06/17/2014 05:36 PM, Jonathan Thomas O'Neil wrote:

Hello, I am having issue with running Tkmedit, tksurfer, qdec, and recon-all. Based on the error messages I am receiving, it appears that the program think I have permission issues. I have checked these and that does not appear to be the case. Here are the errors I am getting. Please let me know what I can do

*tkmedit: *mss169:Desktop jto929$ tkmedit bert orig.mgz

=================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu : : Now exiting...

*tksurfer: for tksurfer it seems to run, but then stops. a view appears on the screen, but then immediately disappears. *

s169:Desktop jto929$ tksurfer bert rh pial subject is bert hemi is rh surface is pial surfer: current subjects dir: /Users/jto929/Desktop/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/jto929/Desktop checking for nofix files in 'pial' Reading image info (/Users/jto929/Desktop/freesurfer/subjects/bert) Reading /Users/jto929/Desktop/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Users/jto929/Desktop/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=133299, faces=266594 surfer: single buffered window surfer: tkoInitWindow(bert) mss169:Desktop jto929$

*qdec: *mss169:Desktop jto929$ qdec Segmentation fault

recon-all

mss169:Desktop jto929$ recon-all -s bert -autorecon1 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/jto929/Desktop/freesurfer/subjects Actual FREESURFER_HOME /Users/jto929/Desktop/freesurfer rm: /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.cmd: Permission denied mv: rename /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env to /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env.bak: Permission denied /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env: Permission denied. /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env: Permission denied.

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