I don't have time to read this thread, so I apologize if this is repeat info
or unhelpful. You can at least ditcht he .mat files using these instructions
Ashburner posted to the SPM list a while back:

-------------------------------

> I thought I saw discussed recently a way to trim the
> proliferation of the XXX.mat files. Specifically,
> when using other software as part of the analysis
> process, it would be nice to just _apply_ the .mat
> info to the data, so that the .mat file can be ignored.
>
> Was this discussed? If so, can somebody send me a link
> to it, I couldn't find it in the archives.
>
> If it wasn't discussed, is there a way to apply the .mat
> info to the img data, so that the .mat file is superfluous?

You can use the coregister button in order to reslice your data
to an image without a .mat file.

Alternatively, you may want to try the reorient.m function that I
distributed to the list:
[www.jiscmail.ac.uk]

Best regards,
-John

--
Dr John Ashburner.

-------------------------
HTH

rich