SPM5 no longer uses mat files as a default. Instead all information about the file is saved in the .hdr files. I believe it can read the .mat files when reading images from spm2 for example.

From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Yune Lee
Sent: Monday, June 30, 2008 4:59 PM
To: [log in to unmask]
Subject: [SPM] Is there any change in the .hdr file after estimate only in the SPM5?

 Dear SPM5 experts,
 I'm novice about SPM5 and wondering about a new way of doing realignment.
 I noticed that .hdr file is re-saved as of today after running estimate only in the SPM5.
 Does it change any parameter in the header file even without reslicing?
 All the transformation parameters should be in the .txt as well as .mat file.
 Yet, I'm wondering if .hdr is also changed after the realignment.
 Any help would be greatly appreciated.