On Feb 17, 2017, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:

Message: 30
Date: Fri, 17 Feb 2017 10:21:03 -0500
From: Z K <zkaufman@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra:
during mris_smooth. dyld: lazy symbol binding
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <c4e0438e-3a66-2e2e-038c-887ea392a948@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hello Jared,

Curious... Can you try processing this particular subject with a single 
thread and see what happens? If the problem persists let me know and I 
will take a look at the subject.

-Zeke

On 02/17/2017 08:28 AM, Jared Saletin wrote:

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 <mailto:jared_saletin@brown.edu>
Phone: 401-421-9440
Fax: 401-453-3578





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