I have dependencies for AFNI and the fBIRN QC tools. The dependencies get installed to /usr/local and I can disable the path extension to those binaries.
-Peter On Sep 17, 2013, at 3:01 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > 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
