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To run a batch from MATLAB command line, SPM always has to be initialised. At least,
spm_jobman('initcfg')
should be run before. If one needs to rely on defaults which can not be set in a batch (e.g. in first level fMRI analysis), one should run
spm('defaults','fmri') r 'pet' or 'eeg', depending on the modality
spm_jobman('initcfg')
Best,
Volkmar