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]<mailto:[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]<mailto:[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]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
