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
