After setting FREESURFER_HOME on the commandline, you must source the
freesurfer setup script like so:
source $FREESURFER_HOME/SetUpFreeSurfer.csh
This will set some other parameters, like DYLD_LIBRARY_PATH, on mac. You should
try doing that and then running matlab from the current shell. If that doesn't
work, you could try setting DYLD_LIBRARY_PATH directly from matlab, like so:
setenv('DYLD_LIBRARY_PATH', ['/Applications/freesurfer/lib/gcc/lib:'
getenv('DYLD_LIBRARY_PATH')]);
As a last resort, you could avoid all of the DYLD_LIBRARY_PATH stuff by
downloading the dev distribution from the wiki (which is built with clang
instead of gcc) or you could try a patched 6.0 version available at
https://drive.google.com/file/d/1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR/view?usp=sharing
(unzip the file and follow the instructions in the README.patch)
best
Andrew
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
Fernández <miguelrivasf...@gmail.com>
Sent: Wednesday, February 12, 2020 3:34 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer error in matlab
External Email - Use Caution
Hi Andrew,
Yes, we are using FS 6.0 and I think that is correctly sourced in MATLAB
environment. I used the same commands that we are using in other Mac
workstation where all works fine. The commands used to source freesurfer in
Matlab were these:
bash_path=getenv ('PATH');
setenv(
'PATH',[bash_path,':/Applications/freesurfer',':/Applications/freesurfer/bin']);
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
How can I set the DYLD_LIBRARY_PATH?
Thanks in advance.
Best,
El mié., 12 feb. 2020 a las 1:15, Hoopes, Andrew
(<ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>>) escribió:
If I understand correctly, you're having trouble running freesurfer binaries
from within matlab, right? Is freesurfer fully sourced in your MATLAB
environment? I’m guessing this is an issue with your DYLD_LIBRARY_PATH not
being set, but it's possible there are other issues going on. You should check
to see if the DYLD_LIBRARY_PATH environment variable in your MATLAB shell
matches what you see in the terminal after sourcing freesurfer. Also, are you
using 6.0?
Best,
Andrew
________________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Miguel Ángel Rivas Fernández
<miguelrivasf...@gmail.com<mailto:miguelrivasf...@gmail.com>>
Sent: Friday, February 7, 2020 6:17 AM
To: Freesurfer support list
Subject: [Freesurfer] freesurfer error in matlab
External Email - Use Caution
Dear Freesurfer devs,
I am trying to run FreeSurfer in Matlab and I received the following error
message
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
I tried to fix this error disabling the SIP but this did not work. Maybe could
be due to the gcc compiler?
Any help would be appreciated
Thanks in advance
Best regards,
--
Miguel Ángel Rivas Fernández
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Miguel Ángel Rivas Fernández
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
