Unix commands in Matlab

Hi,

I've installed a series of binaries which appear in usr/local/bin on my MACOSX (They're called DCMTK). The usr/local/bin folder appears on the path as expected:

/Users/jim/Library/Enthought/Canopy_64bit/User/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:niftyreg_install/bin

I can run these commands as expected from any folder in a Terminal window, however I can't seem to run any of them from within Matlab (2014b) using the command:

cmd=['dcmdump -h'];
system(cmd)
/bin/bash: dcmdump: command not found

Running 'env' in a Terminal shows that I am using the same SHELL as Matlab:

SHELL=/bin/bash

My question is why is it when Matlab invokes bin/bash it is not finding the binaries in usr/local/bin? Is there something I need to update?

Thanks,

Jim

Answer 1

[Jim O'Doherty]

I've managed to get some help elsewhere on this issue, thought I'd post here in case anyone else has the same problem.

Echo the PATH from MATLAB itself:

cmd=['echo $PATH']; system(cmd);

In my case this gave:

/usr/bin:/bin:/usr/sbin:/sbin

and does not include the usr/local/bin where my binaries are stored. Therefor this needs to be added via

setenv('PATH', [getenv('PATH'),':','/usr/local/bin']);

which now gives:

cmd=['echo $PATH']; system(cmd);
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin

If you start Matlab from a terminal the PATH is different, and contains usr/local/bin, but starting it the "usual" way through Applications causes a different PATH. No idea why!

Jim

[Derek]

Thanks Jim. I've run into exactly the same problem. It would be great if Matlab run from the icon would grab all of the environmental variables.