Hi Eugenio
the maci64 directory does not exist in /Applications/freesurfer/MCRv80/bin/
Should I reinstall freesurfer?
thanks!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Tuesday, September 29, 2015 10:43 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@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" aarthi@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
_______________________________________________ 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Eugenio,
Just following up on my message from last week. The file you asked me to look for does not exist and the folder it is supposed to be in also doesn't exist. Is this something I should install?
Thanks!
Aarthi
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Aarthi Padmanabhan aarthi@stanford.edu Sent: Thursday, October 1, 2015 9:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
Hi Eugenio
the maci64 directory does not exist in /Applications/freesurfer/MCRv80/bin/
Should I reinstall freesurfer?
thanks!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Tuesday, September 29, 2015 10:43 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Dev 6.0 Hippocampal Segmentation
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@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" aarthi@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
_______________________________________________ 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Aarthi Padmanabhan