Hi Eugenio the maci64 directory does not exist in /Applications/freesurfer/MCRv80/bin/
Should I reinstall freesurfer? thanks! ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.igles...@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-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 _______________________________________________ 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. 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