Hi Freesurfer gurus:
I recently installed 6.0.0 on MacOS 10.12 and recon-all is exiting with an error in mris_smooth. It looks like a library issue.
A prior post had the same issue and indicated uninstalling the whole distribution and re-installing 6.0.0 fresh (as opposed to installing over 5.3). I receive the same error however (pasted below).
Does anyone have any thoughts?
Thanks! Jared
#@# Smooth1 rh Thu Feb 16 16:47:23 EST 2017 /Users/jared/Desktop/fMRITest/test/scripts \n mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix \n Waiting for PID 11130 of (11130 11133) to complete... /Applications/freesurfer/bin/reconbatchjobs: line 81: 11130 Abort trap: 6 exec $JOB >> $LOG 2>&1 Waiting for PID 11133 of (11130 11133) to complete... /Applications/freesurfer/bin/reconbatchjobs: line 81: 11133 Abort trap: 6 exec $JOB >> $LOG 2>&1
mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
setting seed for random number generator to 1234 dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
setting seed for random number generator to 1234 dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
PIDs (11130 11133) completed and logs appended. Darwin Jareds-iMac.local 16.4.0 Darwin Kernel Version 16.4.0: Thu Dec 22 22:53:21 PST 2016; root:xnu-3789.41.3~3/RELEASE_X86_64 x86_64
recon-all -s test exited with ERRORS at Thu Feb 16 16:47:23 EST 2017
—
Jared M. Saletin, PhD
Assistant Professor of Psychiatry and Human Behavior Alpert Medical School of Brown University
E.P. Bradley Sleep Research Lab 300 Duncan Drive Providence, RI 02906
Email: jared_saletin@brown.edu Phone: 401-421-9440 Fax: 401-453-3578