Hello Luke,
A patch was released to fix this problem. In order to fix this issue please follow these instruction:
1) Download the file "kvl.zip" from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/kvl.zip
2) Overwrite the existing kvl files in your /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 let me know.
Hope this helps.
-Zeke
On 05/14/2013 02:41 PM, Lukas.Scheef@ukb.uni-bonn.de wrote:
Hi FreeSurfer Experts!
I try to run the hippocampus subfield reconstructions. Because I already run reconall -all on my subjects (without errors, all necessary manual edits were done) I try to reconstruct only the hippo-subfields:
recon-all -s my_subjects -hippo-subfields
The shell output is given below... Any ideas?
Best wishes,
Luke
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Users/lscheef/Desktop/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 lscheef staff 490363 May 14 20:08 /Users/lscheef/Desktop/subjects/p119/scripts/recon-all.log Darwin luke 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 Tue May 14 20:16:08 CEST 2013 \n mkdir -p /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh p119 left /Users/lscheef/Desktop/subjects /Users/lscheef/Desktop/subjects/p119/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: p119 side: left inputDirectory: /Users/lscheef/Desktop/subjects outputDirectory: /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults directory /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119 already exists directory /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119/left already exists cd /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119/left cp -f /Users/lscheef/Desktop/subjects/p119/mri/nu.mgz . cp -f /Users/lscheef/Desktop/subjects/p119/mri/aseg.mgz . cp -f /Users/lscheef/Desktop/subjects/p119/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: 89411 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 luke 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 p119 exited with ERRORS at Tue May 14 20:16:08 CEST 2013
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