In order to use the standalone MCR version of spm, you need to ensure that the following commands are executed at the beginning of your script:
from nipype import spm
matlab_cmd = '/path/to/run_spm8.sh /path/to/Compiler_Runtime/v713/ script'
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
you can test by calling:
spm.SPMCommand().version
If you want to enforce the standalone MCR version of spm for nipype globally, you can do so by setting the following environment variables:
Information about the MCR version of SPM8 can be found at: