Hi Matt, this issue should be fixed in the freesurfer development version, but as a temporary fix to get things working in v6, I would suggest disabling SIP and rerunning:

http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/

 

best

Andrew

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <matt@grecsek.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, May 3, 2018 at 1:31 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] V6 Stable OSX software error - multistrip flag

 

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I'm using the following flags on my recon -all:  -mprage -time -multistrip -subcortseg

and getting the following errors at this section of the log file:

 

mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 5 T1.mgz brainmask_T1_PFH5.auto.mgz \n

\n mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 10 T1.mgz brainmask_T1_PFH10.auto.mgz \n

\n mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 20 T1.mgz brainmask_T1_PFH20.auto.mgz \n

\n mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 30 T1.mgz brainmask_T1_PFH30.auto.mgz \n

 

 mri_watershed -rusage /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 5 orig.mgz brainmask_orig_PFH5.auto.mgz

 

 

Mode:          Use the information of atlas (default parms, --help for details)

Mode:          Preflooding height manually specified

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

 

[... more of same ...]

 

WARNING: Some multi-skullstrip operations may have failed!

         Continuing multi-skullstrip with the others...

ERROR: failure in calculating best preflood height param.

Darwin Matthews-MacBook-Air.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64

 

recon-all -s mattmp exited with ERRORS at Thu May  3 12:57:24 EDT 2018

 

Attached is my log file for reference. Any suggestions appreciated.

 

Cheers,

 

-Matt

 

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