Dear Clas,
I'm afraid there isn't an easy way to do this in the released SPM8 software.
There is a new SPM batch module for running PPIs, but if I remember
correctly, it is not yet available in the public updates. Another batch
module will allow to run an arbitrary MATLAB function, but again this is not
yet released with the latest updates. Using this module, you could run
subsref on the variable loaded from the .mat file and reference the part of
the variable you are interested in.
Volkmar
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