Hi freesurfer experts,
I've recnetly upgraded to freesurfer 5.3 (lion) 64bit version on our Mac Pro
when I run trac-all -prep, I get the following error:
writing to /Studies/MJMRI/MJ0030/freesurfer/dmri/dwi_orig.nii.gz...
mri_probedicom --i /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1 >
/Studies/MJMRI/MJ0030/freesurfer/dmri/dcminfo.dat
Trace/BPT trap
Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7
16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Dec 6 11:20:50 CST 2013
I've included the trac-all.log and trac-all.error file
the trac-all log indicates in incompatible library version:
Reason: Incompatible library version: mri_probedicom requires version 10.0.0
or later, but libX11.6.dylib provides version 9.0.0
Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7
16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have reinstalled Xquartz and rebooted, but I still get the same error.
what else can I do?
system info:
mac pro 6-core intel Xeon
MAc OS 10.6.8 snowleopard
Jon
--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
Fri Dec 6 11:19:30 CST 2013
/Studies/MJMRI/MJ0030
/Applications/freesurfer/bin/trac-all
-c dmrirc_single_subject -prep
Subject freesurfer
SUBJECTS_DIR /Studies/MJMRI/MJ0030
FREESURFER_HOME /Applications/freesurfer
Actual FREESURFER_HOME /Applications/freesurfer
build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0
wieser
psy-blackbird.ad.uwm.edu
Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 2560
memorylocked unlimited
maxproc 266
PhysMem: 1343M wired, 1106M active, 2481M inactive, 4931M used, 19G free.
########################################
Program versions:
$Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $
mri_convert --all-info
ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-17:19:31-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: wieser Machine: psy-blackbird.ad.uwm.edu Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40200
FLIRT version 5.5
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-17:19:31-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: wieser Machine: psy-blackbird.ad.uwm.edu Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40200
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-17:19:31-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: wieser Machine: psy-blackbird.ad.uwm.edu Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40200
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-17:19:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: wieser Machine: psy-blackbird.ad.uwm.edu Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40200
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-17:19:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: wieser Machine: psy-blackbird.ad.uwm.edu Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40200
New invocation of trac-preproc
wieser
psy-blackbird.ad.uwm.edu
Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 2560
memorylocked unlimited
maxproc 266
PhysMem: 1344M wired, 1107M active, 2481M inactive, 4932M used, 19G free.
#-------------------------------------
/Applications/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Fri Dec 6 11:19:33 CST 2013
mri_convert /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1 /Studies/MJMRI/MJ0030/freesurfer/dmri/dwi_orig.nii.gz
mri_convert /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1 /Studies/MJMRI/MJ0030/freesurfer/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1...
Starting DICOMRead2()
dcmfile = /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1
dcmdir = /Studies/MJMRI/MJ0030//s1869
Ref Series No = 13
Found 3304 files, checking for dicoms
Found 3300 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 2
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 55
nslices = 60
ndcmfiles = 3300
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Studies/MJMRI/MJ0030/freesurfer/dmri/dwi_orig.nii.gz...
mri_probedicom --i /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1 > /Studies/MJMRI/MJ0030/freesurfer/dmri/dcminfo.dat
dyld: Library not loaded: /usr/X11/lib/libX11.6.dylib
Referenced from: /Applications/freesurfer/bin/mri_probedicom
Reason: Incompatible library version: mri_probedicom requires version 10.0.0 or later, but libX11.6.dylib provides version 9.0.0
Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Dec 6 11:20:50 CST 2013
------------------------------
SUBJECT freesurfer
DATE Fri Dec 6 11:20:50 CST 2013
USER wieser
HOST psy-blackbird.ad.uwm.edu
PROCESSOR x86_64
OS Darwin
Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
$Id: trac-preproc,v 1.17.2.8 2013/02/16 20:57:05 ayendiki Exp $
/Applications/freesurfer/bin/trac-preproc
PWD /Studies/MJMRI/MJ0030
CMD mri_probedicom --i /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1
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