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-...
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
External Email - Use Caution 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