External Email - Use Caution Could it be a solution to reinstall freesurfer? I tried to install a newer gcc version and now Matlab gave to me this error
-------------------------------------------------------------------------- ERROR: FreeSurfer environment FREESURFER_HOME is not defined. If you are outside the NMR-Martinos Center, please set this variable to the location where you installed FreeSurfer. If you are inside the NMR-Martinos Center, please source the standard environment. If you need to install FreeSurfer, go to: http://surfer.nmr.mgh.harvard.edu -------------------------------------------------------------------------- Attempting to use /Applications/freesurfer directory. using /Applications/freesurfer/subjects/10018/mri/aseg.mgz aseg volume to correct midline setting seed for random number generator to 1234 mris_ca_label: SUBJECTS_DIR not defined in environment No such file or directory mris_ca_label -aseg /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234 10018 lh /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Signal 124 ans = 252 Best, El jue., 14 mar. 2019 a las 18:59, Miguel Ángel Rivas Fernández (< miguelrivasf...@gmail.com>) escribió: > > Hello Douglas, > > Yes it works > > El jue., 14 mar. 2019 a las 18:51, Greve, Douglas N.,Ph.D. (< > dgr...@mgh.harvard.edu>) escribió: > >> It looks like the library is not set up properly. Does freesurfer work >> outside of matlab? >> >> On 3/14/19 1:46 PM, Miguel Ángel Rivas Fernández wrote: >> > >> > External Email - Use Caution >> > >> > >> > Dear Freesurfer devs, >> > >> > >> > Have you had occasion to review this error?. Could it be due to the >> > gcc version? >> > >> > Thank you very much for your help. >> > >> > >> > Best regards, >> > >> > El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández >> > (<miguelrivasf...@gmail.com <mailto:miguelrivasf...@gmail.com>>) >> escribió: >> > >> > >> > Dear Freesurfer experts, >> > >> > I am trying to run Freesurfer commands (eg. mri_ca_label) using >> > Matlab in a Mac computer (macOS High Sierra 10.13.6 version) >> > and I'm receiving the following error that I suspect are due to >> > library incompatibilities: >> > >> > >> > dyld: lazy symbol binding failed: Symbol not found: >> > ___emutls_get_address >> > Referenced from: >> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib >> > Expected in: /usr/lib/libSystem.B.dylib >> > >> > dyld: Symbol not found: ___emutls_get_address >> > Referenced from: >> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib >> > Expected in: /usr/lib/libSystem.B.dylib >> > >> > mris_ca_label -aseg >> > /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234 >> > 10018 lh >> > /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg >> > >> >> /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs >> > /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: >> Aborted >> > >> > ans = >> > >> > 134 >> > >> > >> > >> > I realized that this error has been previously reported >> > < >> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054961.html >> > >> > and, as Andrew said, one of the possible solutions could be to >> > disable the SIP (System Protection Integrity). I have disabled the >> > SIP following the instructions indicated here >> > < >> http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ >> > >> > but unfortunately Matlab continues giving the same error. >> > >> > >> > How could I solve this problem?. Any help would be appreciated. >> > >> > >> > Thanks in advance. >> > >> > Best, >> > >> > -- >> > *Miguel Ángel Rivas Fernández* >> > >> > >> > >> > -- >> > *Miguel Ángel Rivas Fernández* >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > *Miguel Ángel Rivas Fernández* > -- *Miguel Ángel Rivas Fernández*
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