This seems very strange, as you are using the same code. In general the only difference between MacOS and Linux is that file names are case specific in Linux ("img.dcm" is different from "imG.nii"), but in this case we explicitly scan all files. My instinct is that this is something specific to your setup, so please do double check that everything is set up correctly. One other comment is that the Linux version is built with an old compiler - it seems like many Linux users still use CentOS 6, so the version of dcm2niix distributed with MRIcroGL is built to support it. You can rebuild the software from source or get a compiled version using a more recent compiler from github, but I do not think that will resolve your issue.