Was the subject folder that fails ever uploaded? If not please upload and let me know when it's ready and I'll take a look. If it was already uploaded try reuploading as that area get cleared up occasionally. 

On Mar 1, 2017, at 5:17 PM, Mira Michelle Raman <mraman@stanford.edu> wrote:

HI,

 I had reported this issue a while ago and have been trying to track it down because it seems to be popping up in strange places on our El Capitan and Sierra machines.  

So I initially encountered the error

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from: /Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


dyld: Symbol not found: ___emutls_get_address

  Referenced from: /Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


when trying to run with  the -parallel flag for the same subject who finished fine through the traditional pipeline.  

I have since encountered it when running mri_deface and mri_info. The good news about that is they are really quick to run, unlike having to run the whole pipeline.


Here is an example, and it is repeatable on my machine for multiple input images (so hopefully the developers can reproduce)

 I can do something as simple as

mri_info cert01.nii from the command line as it works as usual.  I then put the same command in a very simple script (I tried bash and tsch)

#! /bin/bash -f
#
mri_info cert01.nii

and it fails with

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from: /Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib


dyld: Symbol not found: ___emutls_get_address

  Referenced from: /Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib

I then switch to Freesurfer 5.3 and run the same little script and it spits out the usual info.


Hopefully this can help in tracking down the problem, and creating a Sierra compatible  build, because we can't roll any of our newly ordered machines back to Yosemite anymore.


Sincerely,
Mira

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Z K <zkaufman@nmr.mgh.harvard.edu>
Sent: Monday, February 20, 2017 9:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding
 
Hello Jared,

Would it be possible to tar up the subject directory and upload it to our server so I can take a look?

 https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
top. Uploading Data. If you have been asked to send the FreeSurfer team a file, you can either send it via FTP or File Drop. Instructions for both are below.


-Zeke 

On Feb 20, 2017, at 2:47 PM, Jared Saletin <jared_saletin@brown.edu> wrote:

Dear Zeke,

Thanks for your reply. I can verify that recon-all completes without error on a single thread, but crashes on parallel.

I thought it may be hippocampus-subfield specific, but the same pattern remerges regardless of the subfield reconstruction.

Is there something in newer OS X that broke the libraries?

Thanks!
Jared

—

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



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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