This is really weird.
Can you please confirm that the file
/Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib
exists?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message -----
Sent: Tuesday, September 29, 2015 11:39:00 AM
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
Hi Eugenio,
Thanks for the response. I just tried that and it still didn't work (same error
message).
Subject Stamp: freesurfer-Darwin-OSX-dev-20150826
Current Stamp: freesurfer-Darwin-OSX-dev-20150826
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r-- 1 lab wheel 638418 Sep 29 08:37
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log
Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53
PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) left Tue Sep 29 08:39:10 PDT 2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left
\n
See log file:
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
dyld: Library not loaded: @rpath/libmwi18n.dylib
Referenced from:
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line
40: 90075 Trace/BPT trap: 5
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) right Tue Sep 29 08:39:10 PDT
2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right
\n
See log file:
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
dyld: Library not loaded: @rpath/libmwi18n.dylib
Referenced from:
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line
40: 90112 Trace/BPT trap: 5
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
Thanks,
Aarthi
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias
<e.igles...@bcbl.eu>
Sent: Monday, September 21, 2015 1:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
Hi Aarthi,
first of all, sorry for the late reply; you caught me on vacation.
Would you mind trying the following: please unset your DYLD_LIBRARY_PATH
environment variable, and the run the hippocampal subfield module. You can do
that as follows:
In bash:
unset DYLD_LIBRARY_PATH
In (t)csh:
unsetenv DYLD_LIBRARY_PATH
Let us know if this helps
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message -----
From: "Aarthi Padmanabhan" <aar...@stanford.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Saturday, September 19, 2015 9:32:55 AM
Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
Hi, I had posted this earlier and am still having issues.
Thank you,
I tried running the Hippocampal Segmentation using the Dev version, I get the
following error (running on a mac os x Yosemite):
I just downloaded the dev version a couple of days ago. Recon-all -all runs
fine, but it's unable to run the hippocampals segmentation component.
recon-all -s 15-03-07.1_3T2 -hippocampal-subfields-T1
Subject Stamp: freesurfer-Darwin-OSX-dev-20150826
Current Stamp: freesurfer-Darwin-OSX-dev-20150826
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r-- 1 lab wheel 605436 Sep 11 11:56
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/recon-all.log
Darwin DN2m1id7p.SUNet 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53
PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) left Fri Sep 11 11:57:14 PDT 2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects left
\n
See log file:
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:/Applications/freesurfer/lib/gcc/lib
dyld: Library not loaded: @rpath/libmwi18n.dylib
Referenced from:
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line
40: 6182 Trace/BPT trap: 5
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) right Fri Sep 11 11:57:15 PDT
2015
\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80
/Applications/freesurfer 15-03-07.1_3T2 /Applications/freesurfer/subjects right
\n
See log file:
/Applications/freesurfer/subjects/15-03-07.1_3T2/scripts/hippocampal-subfields-T1.log
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:/Applications/freesurfer/lib/gcc/lib
dyld: Library not loaded: @rpath/libmwi18n.dylib
Referenced from:
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
Reason: image not found
/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line
40: 6219 Trace/BPT trap: 5
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args
#------------------------------------------
Started at Fri Sep 11 11:57:12 PDT 2015
Ended at Fri Sep 11 11:57:15 PDT 2015
#@#%# recon-all-run-time-hours 0.001
recon-all -s 15-03-07.1_3T2 finished without error at Fri Sep 11 11:57:15 PDT
2015
done
Thank you,
Aarthi
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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