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Hi Steve, thanks very much for the hint - I preprocessed all the data using the feat interface, ie I ran the pre-stats module. Now I am wondering what would be the melodic command equivalent to the GUI. I think I need to feed in the filtered_func_data.nii.gz (-i ) data and can switch of the mask and bet option as the data is already processed. Then to threshold the ICA maps I'd use the --mmthresh=0.5 switch. Does the command below sound correct? melodic -i melodic_input_subject_ADOs_new_line.txt -o melodic_ados -a con cat --nomask --nobet --mmthresh=0.5 --tr=3 --report -v --Oall --Sdes=ados.mat --Scon=ados.con Thanks very much in advance! Torsten