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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