[FieldTrip] ft_prepare_mesh ERROR

岡留敏樹 tokadome at neuro.med.kyushu-u.ac.jp
Tue Sep 25 09:13:03 CEST 2018

Hello fieldtrip experts, 
when trying to run ‘ft_prepare_mesh’ command from fieldtrip with MATLAB R2018a, I run into the error below.
I was preprocessing MRI date according with the paper ’Nature Protocol 2018; 13: 1699-1723. http://doi.org/10.1038/s41596-018-0009-6 <http://doi.org/10.1038/s41596-018-0009-6> ‘.
I’m running this on a iMac, macOS High Sierra 10.13.6, with fieldtrip-20180909, freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c. 
From past archives, I think this is because of SIP. So I disabled SIP of OSX, but I run into same errors.
I tried different subjects, which caused similar errors. 
Any ideas would be greatly appreciated, thank you! 

cfg = [];
cfg.method = ‘cortexhull’;
cfg.headshape = <path to freesurfer/surf/lh.pial>;
cfg.fshome = <path to freesurfer home directory>;
hull_lh = ft_prepare_mesh (cfg);


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

mris_fill -c -r 1 /Users/okadometoshiki/Desktop/SubjectUCI29/freesurfer/surf/lh.pial /private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq80000gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz: Aborted
reading filled volume...
gunzip: can't stat: /private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq80000gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz (/private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq80000gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz.gz): No such file or directory
ERROR: problem reading fname


Toshiki Okadome
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