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Hello, I have an idea of why my flirt command is not properly registering the flitered_func data to the standard, but not sure what to do about it. Looking at the log report file of groupwise melodic output each subject was successfully registered when I used a 3 step registration process to get each subjects func_data registered to the standard in a subset test group. In the Melodic GUI registration, I used the settings: 1. Expanded structural image: mean_func.nii.gz (subject specific, Normal search, 6 dof) 2. Main structural image: T1W_brain (subject specific, normal search, BBR), 3. Standard space: MNI152_T1_2mm_brain (normal search, 12 dof, resampling 4 mm) This seamed to work, better than past variations. When I look at the report log output from this melodic run, though, I don't really see how the mean_func was used, although did see the registration images with tight red lines around it. But do see the two flirt commands, one for the highres (T1W_brain) and the other for the functional data. When do the highres2standard.mat and example_func2standard.mat images get created? If in my case melodic is calling these images from the individual's prior .ica run file, then "standard" would be referring to the T1W_brain subject image, because I did not register to an actual standard (MNI) during the subject specific Melodic runs. Thank you for clarifying, Varina