Hello Jakob,
unfortunately I don't have any idea about the mat files themselves.
But using Marsbar should be identical for any kind of second-level analysis, be it VBM data or some fMRI analysis based on the con (beta) images. In the first case you extract the mean values of your e.g. sm0wrp1 files, in the second case the mean values of your con images.
And then there are options that make sense only in the context of first-level analyses and need the swaf files, e.g. extracting percentage signal change values.
Best,
Gabor
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