Dear Lin,
in general you have to make sure that your input data are already normalized to the template that your mask(s) come from. That means if you want to use an MNI space based atlas, your data need to be normalized to MNI space. Please not that there are differences in MNI templates between FSL and SPM. Our toolbox is based on FSL. As Jorge has pointed out, mICA will check the bounding box of your input data and only allow MNI-based atlases if it matches that of the template. In every other case, it will only allow custom masks.

Hope that helps,

Florian