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 -Zeke > On Feb 20, 2017, at 2:47 PM, Jared Saletin <jared_sale...@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_sale...@brown.edu > Phone: 401-421-9440 > Fax: 401-453-3578 > > > >> On Feb 17, 2017, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >> >> Message: 30 >> Date: Fri, 17 Feb 2017 10:21:03 -0500 >> From: Z K <zkauf...@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-887ea392a...@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_sale...@brown.edu <mailto:jared_sale...@brown.edu> >>> Phone: 401-421-9440 >>> Fax: 401-453-3578 >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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