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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer