Re: [Freesurfer] segmentHA_T1 error DYLD_LIBRARY_PATH - Freesurfer

13 Dec 2018


      External Email - Use Caution
Unless you turn off SIP, both DYLD_LIBRARY_PATH and DYLD_FALLBACK_LIBRARY_PATH are always ignored now at run time (since Mac OS 10.11, El-Capitan).I don't think you should need to set those in order to run Freesurfer 6.0.0 release binaries on a Mac if you are in the Freesurfer shell (download link to 6.0.0 .dmg file, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darw... recently built the latest development (dev) branch of Freesurfer on Mac OS 10.14 using the new cmake builld.&nbsp; You can do this using homebrew on a Mac with the gcc 5 compiler package.&nbsp; If you use the wrapper (makefile.wiki) from https://surfer.nmr.mgh.harvard.edu/fswiki/CMake, you can download and try to use the homebrew git project w/o having to install homebrew on your machine (and pollute /usr/local).&nbsp; But please beware that the dev branch has not been tested like the previous 6.0.0 release.- R.
On Dec 13, 2018, at 04:36, ts+ml@rcmd.org wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Without the full command line and error message it is hard to tell, but this may be an issue with the System Integrity Protection of Mac OS. Try turning it off and see whether that helps.TimOn December 13, 2018 at 10:05 AM Jaime Gomez &lt;borriquear@gmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi ,segmentHA_T1.sh of the dev version produces very often segmentationviolation errors.In the case I attach, it did the left hemisphere but when started theHippocampal Subfields processing (T1) right it terminates with SegmentationViolation Error.The computer where I'm running the script is a 16GBProductName: &nbsp;&nbsp;&nbsp;Mac OS XProductVersion: &nbsp;&nbsp;&nbsp;10.14.1BuildVersion: &nbsp;&nbsp;&nbsp;18B75Thanks_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer