Fix bug. In linux, shell=True prevents the elastix/transformix binaries from running

[rcasero]

I'm running Ubuntu zesty 64 bit, and with shell=True, the external command doesn't get called.

[rcasero]

Furthermore, I'm not sure one should be using shell=True in Windows. The documentation says:

https://docs.python.org/3/library/subprocess.html

On Windows with shell=True, the COMSPEC environment variable specifies the default shell. The only time you need to specify shell=True on Windows is when the command you wish to execute is built into the shell (e.g. dir or copy). You do not need shell=True to run a batch file or console-based executable.

Note Read the Security Considerations section before using shell=True.

[soupault]

Included into #20 . Thanks for investigating!