Thanks Tim and John, I previously ran mris_convert to turn my .mgz files into .giis and did not receive this error. I was actually able to fix it by disabling the System Integrity Protection that is on the newer Mac OSes. Someone on the Freesurfer forum pointed to this being an issue because it blocks libraries stored in /usr. The steps to follow are here: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
I appreciate your responses, and hope this will be helpful to others. Best, Kelly On Tue, Nov 28, 2017 at 10:47 AM, Harwell, John <[email protected]> wrote: > Tim and Kelly, > > This error probably occurs when wb_shortcuts runs ‘mris-convert’. A > solution for the “lazy symbol” errors is described at the end of these > FreeSurfer Release Notes: https://surfer.nmr.mgh.harvard.edu/fswiki/ > ReleaseNotes > > If your FreeSurfer installation is up to date, the release notes imply > that "source $FREESURFER_HOME/sources.sh” may be needed in the Mac version > of wb_shortcuts. > > Related link: https://mail.nmr.mgh.harvard.edu/pipermail// > freesurfer/2017-March/051087.html > > John Harwell > > On Nov 27, 2017, at 6:18 PM, Timothy Coalson <[email protected]> wrote: > > The wb_shortcuts command is actually just a bash script. However, it > calls other utilities, and that function specifically calls both > "mris_convert" and "wb_command". Since it is complaining about "libgomp" > which is involved in parallelization, it may in fact be an issue with > wb_command, as I don't know that we have tested it on the newest OS X. The > "lazy symbol binding" suggests that you might have to run a command that > actually uses parallelization to find out, however. The easiest command to > try this with may be "wb_command -signed-distance-to-surface" (run it with > any surfaces, and see if it crashes similarly). > > If it is in fact a problem with wb_command on the newest OS X, then you > could compile it yourself from source while we figure out how to manage the > OS version transition: > > https://github.com/Washington-University/workbench/tree/v1.2.3 > > Tim > > > On Mon, Nov 27, 2017 at 6:01 PM, Kelly Martin <[email protected]> > wrote: > >> Hi all, >> >> I am using wb_shortcuts to map from native individual Freesurfer space to >> cifti format. I successfully ran Freesurfer's recon-all on my subjects. I >> downloaded the standard_mesh_atlases, and intended to map the individual >> lh.white and lh.pial (converted to .gii) to the >> fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii. >> >> This is the command that I ran: >> >> wb_shortcuts -freesurfer-resample-prep >> $SUBJECTS_DIR/SPCh061/surf/lh.white.gii >> $SUBJECTS_DIR/SPCh061/surf/lh.pial.gii >> $SUBJECTS_DIR/SPCh061/surf/lh.sphere.reg.gii >> /Users/newportlab/Applications/workbench/standard_mesh_ >> atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii >> lh.midthickness.surf.gii SPCh061.lh.midthickness.32k_fs_LR.surf.gii >> lh.sphere.reg.surf.gii >> And this was the resulting error: >> >> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address >> >> Referenced from: /Users/newportlab/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: /Users/newportlab/Applications >> /freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib >> >> Expected in: /usr/lib/libSystem.B.dylib >> >> /Users/newportlab/Applications/workbench/bin_macosx64/wb_shortcuts: line >> 285: 22711 Abort trap: 6 >> I have tried installing and testing MacPorts, and running fs_update, with >> no success. Sierra has given Freesurfer users some grief, but since I have >> been able to run other Freesurfer commands successfully, I am wondering if >> it is something within the wb_shortcuts that is incompatible. Does anyone >> know of a work-around for this? >> >> Thank you! >> >> Kelly >> >> -- >> Kelly Martin >> Graduate Student >> Interdisciplinary Program in Neuroscience >> Georgetown University >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- Kelly Martin Graduate Student Interdisciplinary Program in Neuroscience Georgetown University _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
