Ok. Thanks for the info. But what dependancies were required to be installed (using homebrew)? Other than installing XQuartz, freesurfer should run on a clean system.
-Zeke On 09/17/2013 02:53 PM, Peter J. Molfese wrote: > 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. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
