You can go to that directory and use the following commands: load SPM.mat % Estimate parameters spm_unlink(fullfile('.', 'mask.img')); % avoid overwrite dialog SPM = spm_spm(SPM); ----------sent by webmail ---- Ze Wang, Ph.D Research Assistant Professor of Biomedical Engineering, Treatment Research Center, Dept of Psychiatry, Med School, University of Pennsylvania, 3900 Chestnut St. Philadelphia, PA 19104 Tel: 215-222-3200-123 Fax: 215-386-6770 Tel at CFN: 215-662-7341 ----- Original Message ----- From: "Andreas Hahn" <[log in to unmask]> To: [log in to unmask] Sent: Thursday, January 7, 2010 8:32:17 AM GMT -05:00 US/Canada Eastern Subject: [SPM] first-level estimation from command line Dear SPM-experts, I have a very basic question concerning the batch mode in SPM5: How can I run my first-level analysis from the command line? I set up the job with spm_jobman, however, I don't know the commands which would substitute the "estimate" button. I also know that the batch mode in SPM8 has been improved a lot, however, I would prefer to stay with SPM5. Thanks in advance for your help, Andreas.