Hi,

I am completely unaware of how the second-level SPM.mat file could change as it is independent of the gPPI scripts. If you have the date of the original results, you could check if the SPM.mat file has been changed since then.

The gPPI script creates a separate SPM.mat in a new directory for the gPPI analysis, so the task-activity SPM.mat should not change. I'd have to check if the script overwrites existing SPM.mat files for the gPPI analysis.

I don't think any of the following will provide a solution, but they are worth checking:
(1) In the results that you are comparing, are the T values the same? This would indicate that the thresholds are different and not the underlying data.
(2) Check if the second-level SPM.mat files are different -->MATLAB has a function to compare mat-files. Once you identify the differences there, you can look at the source of those differences.
(3) If you have old and new 1st-level gPPI SPM.mat files, you could compare the SPM.mat files to see how they are different. The first place I would look is the design matrix.

Hope this helps,
Donald