EEGLab doesn't work well due to the data being from a Neuromag MEG. Any thoughts for alternatives?
Fieldtrip implements ICA from EEGLab and works well with Neuromag (so far).
FieldTrip is the Matlab software toolbox for MEG and EEG analysis that is being developed at the Centre for Cognitive Neuroimaging of the Donders Institute for Brain, Cognition and Behaviour together with collaborating institutes. The development of FieldTrip is currently supported by funding from the BrainGain and the Human Connectome projects. The FieldTrip software is released as open source under the GNU general public license.
The software includes algorithms for simple and advanced analysis of MEG, EEG, and invasive electrophysiological data, such as time-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers and non-parametric statistical testing. It supports the data formats of all major MEG systems (CTF, Neuromag, BTi) and of the most popular EEG systems, and new formats can be added easily. FieldTrip contains high-level functions that you can use to construct your own analysis protocols in Matlab. Furthermore, it easily allows developers to incorporate low-level algorithms for new EEG/MEG analysis methods.