Did you source the Freesurfer setup script? $> export FREESURFER_HOME=/Applications/freesurfer6 $> source $FREESURFER_HOME/SetUpFreeSurfer.sh
> Hello All, > > I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am > getting the following error when I run recon-all from freesurfer 6. > > Can you please suggest how to fix it ? > > Thank you, > > Ri > > ri@Magi [0] ~/ri/SampleDatasets$ export > FREESURFER_HOME= ;export > SUBJECTS_DIR=/Applications/freesurfer6/subjects;export > PATH=/Applications/freesurfer6/bin:$PATH;/Applications/freesurfer6/bin/recon-all > -s Dataset1-only-T1 -i Dataset1/MPRAGE.nii.gz -all > Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015 > Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015 > INFO: SUBJECTS_DIR is /Applications/freesurfer6/subjects > Actual FREESURFER_HOME /Applications/freesurfer6 > Darwin Magi.uphs.upenn.edu 14.4.0 Darwin Kernel Version 14.4.0: Thu May 28 > 11:35:04 PDT 2015; root:xnu-2782.30.5~1/RELEASE_X86_64 x86_64 > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_convert > Reason: image not found > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_convert > Reason: image not found > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_make_uchar > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_normalize > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_watershed > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_gcut > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_segment > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_label2label > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_em_register > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_ca_normalize > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_ca_register > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_ca_label > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_pretess > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_fill > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_tessellate > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_concatenate_lta > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_normalize_tp2 > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_smooth > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_inflate > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_curvature > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_sphere > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_fix_topology > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_topo_fixer > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_ca_label > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_euler_number > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_make_surfaces > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_register > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_volmask > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_anatomical_stats > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mrisp_paint > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_curvature_stats > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mris_calc > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_robust_register > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_robust_template > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_and > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_or > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_fuse_segmentations > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_segstats > Reason: image not found > Trace/BPT trap > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: > /Applications/freesurfer6/bin/mri_relabel_hypointensities > Reason: image not found > Trace/BPT trap > /Applications/freesurfer6/subjects/Dataset1-only-T1 > \n mri_convert /Users/iron/ri/SampleDatasets/Dataset1/MPRAGE.nii.gz > /Applications/freesurfer6/subjects/Dataset1-only-T1/mri/orig/001.mgz \n > dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib > Referenced from: /Applications/freesurfer6/bin/mri_convert > Reason: image not found > Trace/BPT trap > Darwin Magi.uphs.upenn.edu 14.4.0 Darwin Kernel Version 14.4.0: Thu May 28 > 11:35:04 PDT 2015; root:xnu-2782.30.5~1/RELEASE_X86_64 x86_64 > > recon-all -s Dataset1-only-T1 exited with ERRORS at Sat Dec 12 00:54:32 > EST 2015 > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list [email protected] 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. 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