Hello Carl, I was unable to reproduce the error on a test data set using the same version of OSX. Any chance you would be able to provide me with your subject data?
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Thanks. -Zeke On 01/26/2016 09:55 AM, Carl Anderson wrote: > Hi Everyone, > > Subfields seems to fail to run when part of the recon-all -all command > line and also fails when run on its own (but gives no error). > > Here is the output and recon-all log attached: > > Thanks! > > Carl > > Fitting mesh to synthetic image from ASEG took 468.3773 seconds > > Transforming points > > Transforming points > > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > > Referenced from: > /Applications/freesurfer/bin//../lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/local/lib/libgcc_s.1.dylib > > > dyld: Symbol not found: ___emutls_get_address > > Referenced from: > /Applications/freesurfer/bin//../lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/local/lib/libgcc_s.1.dylib > > > /bin/bash: line 1: 22256 Trace/BPT trap: 5 > /Applications/freesurfer/bin//mri_convert tempT1.mgz T1resampled.mgz > -odt float -rt cubic -vs 0.33333 0.33333 0.33333 > /dev/null > > /Applications/freesurfer/bin//mri_convert tempT1.mgz T1resampled.mgz > -odt float -rt cubic -vs 0.33333 0.33333 0.33333 >/dev/null: > Trace/breakpoint trap > > mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, > -1): could not open file > > error reading from volume T1resampled.mgz > > threshold mask volume at 0.5 > > mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, > -1): could not open file > > /Applications/freesurfer/bin//mri_mask: could not read source volume > T1resampled.mgz > > /Applications/freesurfer/bin//mri_mask -T 0.5 T1resampled.mgz > asegModBinDilatedResampled.mgz T1resampled.mgz >/dev/null: Signal 124 > > mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, > -1): could not open file > > error reading from volume T1resampled.mgz > > mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/hippoMaskResampled.mgz, > -1): could not open file > > threshold mask volume at 0.5 > > mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, > -1): could not open file > > /Applications/freesurfer/bin//mri_mask: could not read source volume > T1resampled.mgz > > /Applications/freesurfer/bin//mri_mask -T 0.5 T1resampled.mgz > hippoMaskResampledDilated.mgz T1resampled.mgz >/dev/null: Signal 124 > > Error using kvlAtlas3D_Matlab > > /autofs/space/panamint_005/users/iglesias/software/MAC_ATLAS_3D/Atlas3D_131025/itkMGHImageIO.cxx:216: > > itk::ERROR: MGHImageIO(0x103507280): Can't find/open file: T1resampled.mgz > > > Error in kvlReadCroppedImage (line 11) > > > > > Error in segmentSubjectT1_autoEstimateAlveusML (line 605) > > > > > > > #------------------------------------------ > > > Started at Tue Jan 26 09:17:04 EST 2016 > > Ended at Tue Jan 26 09:34:33 EST 2016 > > #@#%# recon-all-run-time-hours 0.291 > > recon-all -s CAT104 finished without error at Tue Jan 26 09:34:33 EST 2016 > > > > > -- > <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> > Carl M. Anderson, Ph.D. (mail stop 204) > Assistant Professor of Psychiatry, > Harvard Medical School & > The Neuroimaging Center, > McLean Hospital 115 Mill St. Belmont, MA 02478 > Ph: 617-855-2972; Fax: 617-855-2770 > e-mail: remfr...@gmail.com <mailto:remfr...@gmail.com>; > carl_ander...@hms.harvard.edu <mailto:carl_ander...@hms.harvard.edu> > <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> > > > _______________________________________________ > 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.
