I am working with cortical thickness data in matlab and I have a t-statistic map that I'd like to firstly write to .mgh/mgz format so that I can overlay it in freeview. And secondly, convert it to MNI space and write it out as a volume (preferably nifti).

I think that save_mgh might be what I need but I don't understand what M is and how I would get that info for a statistical map in fsaverage space. Any ideas would be much appreciated.