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edickie / ciftify

The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
https://edickie.github.io/ciftify/
MIT License
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ciftify_recon_all fails with mris_convert #118

Closed aaron-barbieriaghib closed 5 years ago

aaron-barbieriaghib commented 5 years ago

Hi,

I'm trying to run ciftify_recon_all, and mris_convert is failing with returncode -6, even though when I run mris_convert manually from the command line, it works just fine. Here is the full error: 

cmd: mris_convert test_fs/derivatives/freesurfer/sub-10171/surf/lh.white /Users/aaron/test_outputs2/sub-10171/T1w/Native/sub-10171.L.white.native.surf.gii 
 Failed with returncode -6

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

Do you have any idea what might be causing this?

Best, Aaron

aaron-barbieriaghib commented 5 years ago

Turns out this is a known issue with FreeSurfer, and you need to disable SIP.

edickie commented 5 years ago

Thanks for figuring this out!