Hi Arkadiy,

This might have to do with SIP, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-...

Andrew

On Oct 27, 2017, at 2:13 PM, Maksimovskiy, Arkadiy <AMAKSIMOVSKIY@mclean.harvard.edumailto:AMAKSIMOVSKIY@mclean.harvard.edu> wrote:

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.eduhttp://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.eduhttp://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer