Dear LGI Experts,
I am attempting to run LGI using the freesurfer Dev Version (2017), and am
getting the following error:
[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
amaksimovskiy% recon-all -s SUBJ002 -localGI
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-dev-20171020-5567595
INFO: SUBJECTS_DIR is
/Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits
Actual FREESURFER_HOME /Applications/freesurfer
-rwx------ 1 amaksimovskiy staff 2449841 Oct 27 13:40
/Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/scripts/recon-all.log
Darwin arkadiysimac.mclean.harvard.edu 16.7.0 Darwin Kernel Version 16.7.0: Thu
Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer
Previous: /cm/shared/freesurfer
/Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/surf
#--------------------------------------------
#@# Local Gyrification Index lh Fri Oct 27 13:52:07 EDT 2017
\n mris_compute_lgi --i lh.pial \n
=================
rm -Rf
/Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mkdir -p
/Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mris_fill -c -r 1 lh.pial
/Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=================
reading surface from lh.pial...
freadInt: fread failed
conforming output volume
setting resolution for intermediate calculations to 1.0000
No such file or directory
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/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
Abort
ERROR: mris_fill -c -r 1 lh.pial
/Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
failed!
Darwin arkadiysimac.mclean.harvard.edu 16.7.0 Darwin Kernel Version 16.7.0: Thu
Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64
recon-all -s SUBJ002 exited with ERRORS at Fri Oct 27 13:52:08 EDT 2017
For more details, see the log file
/Volumeslab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits/SUBJ002/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I have not found anything similar to this issue in the archives, and wondering
if anyone might have suggestions.
Much appreciated,
Arkadiy
--
Arkadiy L. Maksimovskiy, Ph.D.
Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
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