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, stdp82@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

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