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.
_______________________________________________ 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.
