External Email - Use Caution Hi
I can run the command through Matlab now (with FreeSurfer 6.0). Many thanks, Haiyang > On Nov 13, 2019, at 1:50 PM, fsbuild <fsbu...@contbay.com> wrote: > > Hello hj23, > > If you are running the 6.0.0 freesurfer Mac release, then you can try > downloading this patch. You will need to double click on the archive to > expand it and then follow the instructions in README.patch. I think you will > also need admin privileges though to make the changes described there. > > https://drive.google.com/file/d/1ezjiNIbGNrNAiYD5ciYxMO2SK-R5vz9A/view?usp=sharing > > - R. > >> On Nov 13, 2019, at 03:39, hj23 <h...@nyu.edu> wrote: >> >> External Email - Use Caution >> >> >> Hello FreeSurfer Developers, >> >> I’m attempting to run FreeSurfer commands via Matlab [system(‘fscmd’)]. Some >> of the commands work but some don’t, though all the commands work well when >> run in Terminal. >> >> >> Commands work in both Terminal and Matlab: >> >> When I run “tksurfer” in Terminal or system(’tksurfer’) in Matlab, I will >> get the help information for ’tksurfer'. >> >> >> Commands do not work in Matlab, but work in Terminal: >> >> For example, when I run “mri_info" in terminal, I will get the help >> information for “mri_info”. However, when I run system(‘mri_info’) in >> Matlab, I got the following error (screeshot also attached): >> >> =================================================================== >> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address >> Referenced from: >> /Applications/freesurfer_6.0/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_6.0/bin/../lib/gcc/lib/libgomp.1.dylib >> Expected in: /usr/lib/libSystem.B.dylib >> >> mri_info: Aborted >> >> ans = >> >> 134 >> =================================================================== >> >> I randomly tried some FreeSurfer commands and the commands do not work in >> Matlab (but work in Terminal) are: >> ‘mri_info’ >> ‘mri_coreg’ >> >> Commands work in both terminal and Matlab are: >> ’tksurfer’ >> ‘mri_convert’ >> ‘mri_head’ >> >> >> I did search for the error in FreeSurfer Archive and found the >> recommendation of disable System Integrity Protection. Before doing that, I >> wonder if there is any other solution to this. >> >> Also, I tried to run these commands in both FreeSurfer 5.3-HCP and >> FreeSurfer 6.0 (on the same computer), and interestingly, the commands via >> Matlab work well in FS 5.3 (except that ‘mri_coreg’ cannot be found in FS >> 5.3) but the error will show in FS 6.0. >> >> Additional information: >> 1) FreeSurfer version: error show for >> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c, but not for >> freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0-HCP >> 2) Platform: macOS Mojave (version 10.14.5) iMac Pro (2017) >> 3) uname -a >> Darwin ADUAED07785WKMX.local 18.6.0 Darwin Kernel Version 18.6.0: Thu Apr 25 >> 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64 x86_64 >> >> Please let me know if there is any other information will help. >> >> Thanks in advance, >> Haiyang >> >> >> <Screen Shot 2019-11-13 at 12.15.09 PM.png> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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