Interfacing/integrating between Matlab and MRIQC

Hi there

I haven’t used docker or MRIQC, but will be trying it out soon. I’m working on a Matlab toolbox (should I be saying that out loud? :P) which processes neuroimaging data, and after completing the pipeline in this toolbox I would like to send the required information to MRIQC in order to calculate functional image quality metrics. Is this possible? If so, how? Will I have to run Matlab from within the container as well? Or is it better to do the bare metal installation of MRIQC? If so, how will integration work?