From command line I obtain:
Stefano% ldd kvlApplyTransformldd: Command not found. I do not know is useful, but I have done this analysis with the previous version with any problem.
Stefano
----Messaggio originale---- Da: iglesias@nmr.mgh.harvard.edu Data: 22-mar-2013 19.19 A: stdp82@virgilio.it Cc: koen@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield
Hi Stefano,
From the command line, type:
ldd kvlApplyTransform and send us the output that you get. Cheers, /Eugenio
On Fri, 2013-03-22 at 18:44 +0100, stdp82@virgilio.it wrote:
I'm sorry but, what's meaning "ldd kvlApplyTransform"? What's I should do more simply?
Stefano
----Messaggio originale---- Da: koen@nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield
Hi Stefano,
Can you do "ldd kvlApplyTransform" and send us the result?
Koen
On 3/22/13, stdp82@virgilio.it <stdp82@virgilio.it 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 \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName:
Diff02side:
leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp
-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 -3.1939dyld: 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
-3.1939failed 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 -3.1939Darwin 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.logTo 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
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
He's on a Mac, so the command would be:
otool -L kvlApplyTransform
and the output will be:
kvlApplyTransform: libITKCommon.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKIO.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKznz.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 52.0.0)
which is a little odd.
Stefano, I will get back to you while I debug the issue.
-Zeke
On 03/22/2013 02:39 PM, stdp82@virgilio.it wrote:
From command line I obtain:
Stefano% ldd kvlApplyTransform ldd: Command not found.
I do not know is useful, but I have done this analysis with the previous version with any problem.
Stefano
----Messaggio originale---- Da: iglesias@nmr.mgh.harvard.edu Data: 22-mar-2013 19.19 A: stdp82@virgilio.it Cc: koen@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield
Hi Stefano,
From the command line, type:
ldd kvlApplyTransform and send us the output that you get. Cheers, /Eugenio
On Fri, 2013-03-22 at 18:44 +0100, stdp82@virgilio.it wrote:
I'm sorry but, what's meaning "ldd kvlApplyTransform"? What's I should do more simply?
Stefano
----Messaggio originale---- Da: koen@nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield
Hi Stefano,
Can you do "ldd kvlApplyTransform" and send us the result?
Koen
On 3/22/13, stdp82@virgilio.it <stdp82@virgilio.it 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
\nDoing left sidemeshFileName:
/Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName:
/Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName:
/Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName:
Diff02side:
leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory:
/Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory
/Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02
already existsdirectory
/Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left
already existscd
/Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp
-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 -3.1939dyld: 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
-3.1939failed 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 -3.1939Darwin 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.logTo
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
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
--
Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
stdp82＠virgilio.it -
zkaufman＠nmr.mgh.harvard.edu