[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: zkaufman@nmr.mgh.harvard.edu
Data: 22-mar-2013 20.53
A: <stdp82@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, 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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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