Hi Nick,
It looks like when you hand meica.py the datasets, you're giving it the same dataset three times:
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-d 002.pre_rest_axial_epi.echo_001_dataset+orig,002.pre_rest_axial_epi.echo_001_dataset+orig,002.pre_rest_axial_epi.echo_001_dataset+orig
It seems more likely that you want this:
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-d 002.pre_rest_axial_epi.echo_001_dataset+orig,002.pre_rest_axial_epi.echo_002_dataset+orig,002.pre_rest_axial_epi.echo_003_dataset+orig
Good luck!
-Dave