External Email - Use Caution 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 <ahoo...@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-boun...@nmr.mgh.harvard.edu> on behalf of Matthew > Grecsek <m...@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 > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
