Hi Zeke,
process finished without error in 2h. Thanks, Stefano ----Messaggio originale---- Da: zkauf...@nmr.mgh.harvard.edu Data: 23-mar-2013 20.13 A: "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: hippo subfield It's not enough to simply put the zip file in the /Applications/freesurfer/bin directory,,, you must extract its contents to that directory. Just extract the zip file (anywhere on your machine will do). Then copy and paste the extracted files to /Application/freesurfer/bin -Zeke On Mar 22, 2013, at 7:00 PM, <std...@virgilio.it> wrote: > Hi Zeke, > > as you explain I have download the kvl.zip and put it in > /Application/freesurfer/bin. > > After rerunning I have: > > [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s > Diff01 -hippo-subfields > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > Actual FREESURFER_HOME /Applications/freesurfer > -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 > /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 > 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > #-------------------------------------------- > #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013 > \n mkdir -p > /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults > \n kvlSegmentHippocampalSubfields.sh Diff01 left > /Applications/freesurfer/subjects/subject_prova > /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n > Doing left side > meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz > compressionLookupTableFileName: > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt > boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz > subjectName: Diff01 > side: left > inputDirectory: /Applications/freesurfer/subjects/subject_prova > outputDirectory: > /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults > directory > /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 > already exists > directory > /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left > already exists > cd > /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left > cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz . > cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz . > cp -f > /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm > . > cp /Applications/freesurfer/data/GEMS/imageDump.mgz . > kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 > 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > dyld: Library not loaded: libITKCommon.3.16.dylib > Referenced from: /Applications/freesurfer/bin/kvlApplyTransform > Reason: image not found > /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: > 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 > 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > failed to do kvlApplyTransform imageDump.mgz > -0.9991 -0.0328 0.0258 144.0010 -0.0330 > 0.9994 -0.0086 2.6560 0.0255 0.0094 > 0.9996 -3.1939 > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 > 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > > recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET 2013 > > For more details, see the log file > /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > ----Messaggio originale---- > Da: zkauf...@nmr.mgh.harvard.edu > Data: 22-mar-2013 20.53 > A: <std...@virgilio.it>, <freesurfer@nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] hippo subfield > > Stefano, > > In order to fix this issue please follow these instruction exactly: > > 1) Download the file "kvl.zip" from this link: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ > > 2) Overwrite the existing kvl files in /Application/freesurfer/bin with > the files in kvl.zip > > I was able to replicate your issue and solve it using the steps above. > If these steps do not solve the issue for you, please respond with a the > exact error you receive. > > Hope this helps. > > -Zeke > > > > > > On 03/22/2013 12:00 PM, std...@virgilio.it wrote: > > I'm running: > > > > recon-all -s Diff02 -hippo-subfields > > > > with the following error. > > > > Thanks. > > > > > > Stefano > > > > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff02 > > Actual FREESURFER_HOME /Applications/freesurfer > > -rw-rw-r-- 1 Stefano wheel 499999 Mar 22 16:53 > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log > > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun > > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > > #-------------------------------------------- > > #@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013 > > \n mkdir -p > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > \n kvlSegmentHippocampalSubfields.sh Diff02 left > > /Applications/freesurfer/subjects/subject_prova/Diff02 > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > \n > > Doing left side > > meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz > > compressionLookupTableFileName: > > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt > > boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz > > subjectName: Diff02 > > side: left > > inputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02 > > outputDirectory: > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > directory > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 > > already exists > > directory > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > > already exists > > cd > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > > cp -f > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz . > > cp -f > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz . > > cp -f > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm > > . > > cp /Applications/freesurfer/data/GEMS/imageDump.mgz . > > kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 > > 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > > dyld: Library not loaded: libITKCommon.3.16.dylib > > Referenced from: /Applications/freesurfer/bin/kvlApplyTransform > > Reason: image not found > > /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: > > 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 > > -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 > > 0.9996 -3.1939 > > *failed to do kvlApplyTransform imageDump.mgz > > -0.9991 -0.0328 0.0258 144.0010 > > -0.0330 0.9994 -0.0086 2.6560 > > 0.0255 0.0094 0.9996 -3.1939* > > *Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun > > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64* > > * > > * > > *recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013* > > > > For more details, see the log file > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/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 > > > _______________________________________________ > 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 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.
