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.
