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: remfract@gmail.com mailto:remfract@gmail.com; carl_anderson@hms.harvard.edu mailto:carl_anderson@hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
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