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 zkaufman@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 zkaufman@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:
- subject name - bert (and any other subject)
- the entire command-line executed - recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T
- the error message generated - see below
- 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
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