The DYLD message does not appear on the 10.8.4 system. Both systems have homebrew (http://brew.sh) installed for handling linux dependencies, but that message only appears on the 10.8.5 system. Disabling homebrew does not resolve the error for me.
Best, Peter On Sep 17, 2013, at 2:40 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > Hello, > > Do you know if the following line: > > "dyld: DYLD_ environment variables being ignored because main executable > (/usr/bin/top) is setuid or setgid" > > from the log file you you've attached, also exists when you run the same case > on the machine running 10.8.4? I will update my Mac tonight to the most > recent version of OSX and attempt to duplicate the issue. I will keep you > updated. > > -Zeke > > On 09/17/2013 12:57 PM, Peter J. Molfese wrote: >> I updated my Mac OS X install to 10.8.5 late yesterday and now recon-all >> (FS 5.3) fails early in the processing pipeline (Talairach). I've attempted >> running the process with both my own data that works on Freesurfer 5.3 with >> 10.8.4 and receive the same error message. I have two identical computers, >> with only one updated to 10.8.5, which will make further testing >> straightforward. I attached the log below of the attempt to run the "bert" >> data with just one MRI. The error message is the same for other data. >> >> bugr output: >> --------------------------------------------------------------------- >> >> FREESURFER_HOME: /usr/local/freesurfer >> >> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 >> >> Kernel info: Darwin 12.5.0 x86_64 >> >> --------------------------------------------------------------------- >> Please include the following additional information in your report: >> >> 1) subject name - bert (and any other subject) >> 2) the entire command-line executed - recon-all -s bert -i >> /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T >> 3) the error message generated - see below >> 4) optionally include the subject's /script/recon-all.log >> >> See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> =============== BEGIN ERROR REPORT =================== >> >> recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz >> -all -3T >> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 >> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 >> INFO: SUBJECTS_DIR is /Volumes/MRIData/srtt/freesurfer >> Actual FREESURFER_HOME /usr/local/freesurfer >> Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 >> 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64 >> dyld: DYLD_ environment variables being ignored because main executable >> (/usr/bin/top) is setuid or setgid >> /Volumes/MRIData/srtt/freesurfer/bert >> \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz >> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz \n >> mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz >> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz... >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, 0, -1) >> k_ras = (0, 1, 0) >> writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz... >> #-------------------------------------------- >> #@# MotionCor Tue Sep 17 12:49:59 EDT 2013 >> Found 1 runs >> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz >> Checking for (invalid) multi-frame inputs... >> WARNING: only one run found. This is OK, but motion >> correction cannot be performed on one run, so I'll >> copy the run to rawavg and continue. >> \n cp /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz >> /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz \n >> /Volumes/MRIData/srtt/freesurfer/bert >> \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz >> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform \n >> mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz >> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz... >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, 0, -1) >> k_ras = (0, 1, 0) >> Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. >> Data is conformed to 1 mm size and 256 voxels for all directions >> changing data type from float to uchar (noscale = 0)... >> MRIchangeType: Building histogram >> writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz... >> \n mri_add_xform_to_header -c >> /Volumes/MRIData/srtt/freesurfer/bert/mri/transforms/talairach.xfm >> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz >> /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz \n >> INFO: extension is mgz >> #-------------------------------------------- >> #@# Talairach Tue Sep 17 12:50:13 EDT 2013 >> /Volumes/MRIData/srtt/freesurfer/bert/mri >> \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale >> --i orig.mgz --o orig_nu.mgz \n >> Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 >> 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64 >> >> recon-all -s bert exited with ERRORS at Tue Sep 17 12:50:20 EDT 2013 >> >> For more details, see the log file >> /Volumes/MRIData/srtt/freesurfer/bert/scripts/recon-all.log >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> _______________________________________________ >> 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. 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