I don't know which SPM mat file are you talking about.
If you are talking about the SPM mat file that comes with its ANALYZE7.5 file and has the same prefix, PLSgui software can recognize the affine matrix in the SPM mat file.
e.g:
T1. img & T1.hdr is only in ANALYZE7.5 format.
However, SPM added a an affine matrix M in the SPM mat file:
T1.mat
PLSgui can recognize the combination of T1.img/.hdr/.mat
PLSgui does not support any other SPM mat files.
Jimmy