Thanks for the quick reply.
Other AFNI scripts work. I run the following code to make sure AFNI and MATLAB are working together:
setenv('DYLD_FALLBACK_LIBRARY_PATH',[ '/Users/conradbn/abin:' getenv('DYLD_FALLBACK_LIBRARY_PATH') ])
% is the path to AFNI already set?
[afninotfound, unixoutput] = unix('3dcopy');
% if not, then we will look for it...
if afninotfound
% is AFNI in /abin?
[afninotfound, unixoutput] = unix('/abin/3dcopy');
if ~afninotfound % found it!
setenv('PATH', [getenv('PATH') ':/abin']);
disp(sprintf('Adding /abin to Matlab''s path (for AFNI).'));
end
end
if afninotfound
% is AFNI in ~/abin?
[afninotfound, unixoutput] = unix('~/abin/3dcopy');
if ~afninotfound % found it!
current_directory = pwd;
eval('cd ~');
afni_directory = [pwd '/abin'];
setenv('PATH', [getenv('PATH') ':' afni_directory]);
disp(sprintf(['Adding ' afni_directory ' to Matlab''s path (for AFNI).']));
eval(['cd ' current_directory]);
clear current_directory afni_directory;
end
end
if afninotfound
% is AFNI in ~/Documents/abin?
[afninotfound, unixoutput] = unix('~/Documents/abin/3dcopy');
if ~afninotfound % found it!
current_directory = pwd;
eval('cd ~');
afni_directory = [pwd '/Documents/abin'];
setenv('PATH', [getenv('PATH') ':' afni_directory]);
disp(sprintf(['Adding ' afni_directory ' to Matlab''s path (for AFNI).']));
eval(['cd ' current_directory]);
clear current_directory afni_directory;
end
end
if afninotfound
% if AFNI is not in /abin nor ~/abin, then the user will have to add
% the correct path to AFNI before this function will work.
disp(sprintf('*****'));
disp(sprintf('The required AFNI functions cannot be found.'));
disp(sprintf('AFNI needs to be added to Matlab''s path.'));
disp(sprintf('You can do this with the following command:'));
disp(sprintf(' '));
disp(sprintf(' setenv(''PATH'', [getenv(''PATH'') '':/abin'']);'));
disp(sprintf(' '));
disp(sprintf('where (as an example) ''/abin'' is the AFNI directory.'));
disp(sprintf('Exiting...'));
disp(sprintf('*****'));
return;
end
clear afninotfound unixoutput;
To answer your questions:
The unix env is in zsh.
>> unix(['echo $0'])
/bin/zsh
ans =
0
However, python is not recognized. This is interested because other versions of Matlab have worked.
>> unix(['which python'])
python not found
ans =
1
>> unix(['python -V'])
zsh:1: command not found: python
ans =
127
>> unix(['/usr/bin/env python -V'])
env: python: No such file or directory
ans =
127
I've run these on a different computer with MATLAB 2019a and I get the expected returns that are provided from terminal.
I suspect I need to add a few lines of code to my start up script above to map python to the unix/system env in MATLAB?
