History of AFNI updates  

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April 18, 2022 04:48PM
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?
Subject Author Posted

calling afni python scrips through MATLAB

aclynn11 April 18, 2022 03:31PM

Re: calling afni python scrips through MATLAB

ptaylor April 18, 2022 04:16PM

Re: calling afni python scrips through MATLAB

Daniel Glen April 18, 2022 04:24PM

Re: calling afni python scrips through MATLAB

aclynn11 April 18, 2022 04:48PM

Re: calling afni python scrips through MATLAB

ptaylor April 18, 2022 05:01PM

Re: calling afni python scrips through MATLAB

aclynn11 April 18, 2022 05:04PM

Re: calling afni python scrips through MATLAB

ptaylor April 18, 2022 05:16PM

Re: calling afni python scrips through MATLAB

aclynn11 April 18, 2022 05:08PM

Re: calling afni python scrips through MATLAB

ptaylor April 18, 2022 05:17PM



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