Many thanks to those who answered, (1 ->Bosky) Starting (& quitting) spm5 before executing the jobman in batch mode recently works but no longer. (2 -> Marko Wilke) Loading the default settings via spm_defaults works fine! (3 -> Ahmed) I created the job structure with the GUI, I clicked on Estimate, specified my SPM.mat file for the first person and saved it as 'estimate.mat'. In batch mode I first load this file, copy this file to a second structure called "jobsmod" and than update the location of the SPM.mat for the i-th person: The structure storing the location of the SPM.mat-files I use is vp(1,i).evaluation.specify.files.spmmat=... [vp(1,i).evaluation.specify.path.glm,'\SPM.mat'] In this case it is quite long: [D:\markus\Work In Progress\2007-04-19-Vorstudienanalyse\Auswertung\SPM5\01bg\GLM\SPM.mat] I use this structure to update the job for the i-th person, typing: jobsmod{1,1}.stats{1,1}.fmri_est.spmmat{1,1}=vp(1,i).evaluation.specify.file s.spmmat; Finally I run the job with spm_jobman('run',jobsmod). Regards, Markus