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Hi Andrew,

I installed the development version and everything ran correctly to completion as you suggested.

Thanks,

-Matt

On Mon, May 7, 2018 at 1:08 PM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

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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