Re: [HCP-Users] [SPAM] ERROR: mpr2mni305 failed in FreesurferPipelineBatch.sh

[Harms, Michael]

If running recon-all directly worked fine, that then suggests that something isn’t set up correctly in your environment when you go to run the HCP Pipeline scripts. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of "Dierker, Donna" <do...@wustl.edu> Date: Tuesday, May 31, 2016 at 9:30 AM To: Barbara Kreilkamp <bakk....@googlemail.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] [SPAM] ERROR: mpr2mni305 failed in FreesurferPipelineBatch.sh 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/freesurfer@nmr.mgh.harvard.edu/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: hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Barbara Kreilkamp <bakk....@googlemail.com> Sent: Tuesday, May 31, 2016 3:36:30 AM To: hcp-users@humanconnectome.org 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 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.datatypeoffset=70 value=2 hdr.dime.bitpixoffset=72 value=8 hdr.hist.orientoffset=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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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