run a bash script from matlab

Hi

I have been trying to run a bash script from matlab with this code. The bash script use a program from Freesurfer. How can I pass arguments and enviroments argumnets from matlab to a bash script. I have set the enviroment both in bash and within matlab.

I use this code to start the bash script.

 subject='bert';
 system(sprintf('subj2ascii_v2 %s',subject));

[Geoff Hayes]

Carlo Iaboni's answer moved here

Hello I tried everything. Can you see what I'm doing wrong?

contents of GO.m ----------------

cd('/Volumes/SSD/MATLAB/NIH_toolbox/MVPA');
saveDir = eval('pwd');
Afni3dinfoLocation = '/Volumes/Macintosh HD/abin';
cd(Afni3dinfoLocation);
dir 3dinfo
fileName = '/Volumes/SSD/MATLAB/NIH_toolbox/MVPA/COP19/STATS/3COMB_RUNS/ANATICOR/s19.TASK_c01a.GLM_ANATICOR_REML+orig.BRIK';
cmd=sprintf('3dinfo %s',fileName);
eval(sprintf('!3dinfo %s',fileName));
err=system(sprintf('3dinfo %s',fileName));
system('ls 3dinfo');
system(cmd);
display(cmd);
cd(saveDir);

------------------ results in:

>> GO

3dinfo  

/bin/bash: 3dinfo: command not found
/bin/bash: 3dinfo: command not found
3dinfo
/bin/bash: 3dinfo: command not found

cmd =

3dinfo /Volumes/SSD/MATLAB/NIH_toolbox/MVPA/COP19/STATS/3COMB_RUNS/ANATICOR/s19.TASK_c01a.GLM_ANATICOR_REML+orig.BRIK

[Geoff Hayes]

Carlo - how would you call 3dinfo from a terminal window? Just as

 3dinfo ....

or as

 ./3dinfo ...

You may also want to specify the full path to your executable as

 myExe = pathfullfile(pwd, Afni3dinfoLocation, '3dinfo');

and then using that from within your command.

Answer 1

[Geoff Hayes]

Knut - suppose that you have a bash script written as follows

 #!/bin/bash  

 args=("$@")  

 echo Number of arguments passed: $#

 for var in "$@"
 do
    echo "$var"
 done

All the script does is accept a variable list of arguments and echoes each one to the console (or Command Window when run in MATLAB). Save the above to a file named myBashScript.sh and assign executable privileges to it (easiest way is to just run chmod 777 myBashScript.sh in a terminal or other window, in the directory that contains this file).

In MATLAB do the following

 pathToScript = fullfile(pwd,'myBashScript.sh');  % assumes script is in curent directory

 subject1     = 'bert';
 subject2     = 'ernie';

 cmdStr       = [pathToScript ' ' subject1 ' ' subject2];

 system(cmdStr);

The output from this script, as shown in the MATLAB Command Window, would be

 Number of arguments passed: 2
 bert
 ernie

[Walter Roberson]

Better would be

   cmdStr = sprintf('''%s'' ''%s'' ''%s''', pathToScript, subject, subject2);

This version quotes the path and the arguments in case they contain spaces or shell metacharacters.