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 > > _______________________________________________ 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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