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run a bash script from matlab

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Knut Jørgen
Knut Jørgen on 3 Oct 2014
Commented: Geoff Hayes on 31 Jan 2016
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));
  2 Comments
Geoff Hayes
Geoff Hayes on 31 Jan 2016
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.

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Answers (1)

Geoff Hayes
Geoff Hayes on 3 Oct 2014
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
  1 Comment
Walter Roberson
Walter Roberson on 31 Jan 2016
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.

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