Hi Barbara, It looks like there was a problem with a runtime library Freesurfer needs. Have a look at this similar issue:
https://www.mail-archive.com/[email protected]/msg40092.html I'd report your issue to the Freesurfer mailing list: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport Hopefully there is a fix that won't be too painful. Donna ________________________________ From: [email protected] <[email protected]> on behalf of Barbara Kreilkamp <[email protected]> Sent: Tuesday, May 31, 2016 3:36:30 AM To: [email protected] Subject: [SPAM] [HCP-Users] ERROR: mpr2mni305 failed in FreesurferPipelineBatch.sh Dear HCP experts, I am running freesurfer-Darwin-lion-stable-pub-v5.3.0 on MAC 10.10.5. Could you please help me with this error message? I think it relates to the library, this is what it states in talairach_avi.log. Running recon-all directly worked, but after that I am missing some files that are needed in PostFreesurferPipelineBatch.sh But I am unsure how to solve this issue. Any help is greatly appreciated, Thank you very much, Barbara #@# Talairach Sat May 28 14:18:53 CEST 2016 /Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 recon-all -s REF088c exited with ERRORS at Sat May 28 14:19:12 CEST 2016 For more details, see the log file /Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/scripts/recon-all.log To report a problem, see <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting talaraich_avi.log output /Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri /Applications/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 Sat May 28 13:27:28 CEST 2016 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from orig_nu.mgz... crypt_gkey = FSaWN44YqKOYA TR=8.21, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... crypt_gkey = FSaWN44YqKOYA Analyze Output Matrix -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -146.00000; 0.00000 -1.00000 0.00000 148.00000; 0.00000 0.00000 0.00000 1.00000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Sat May 28 13:27:29 CEST 2016 /Applications/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Sat May 28 13:27:30 2016 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib Referenced from: /Applications/freesurfer/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted _______________________________________________ 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
