I have a stats file that's in MNI space. If I want the cluster report generated via 3dclust to give me coordinates in MNI space, do I need to give any space arguments, or does it default to giving coordinates in the space of the dataset? If the latter, can I also assume that the cluster report generated in the GUI is giving coordinates appropriate to the dataset?
This seems obvious, but when I give the -mni argument to 3dclust, the results reported on the command line differ from those reported in the GUI, which leads me to believe that the TLRC -> MNI xformation is being applied even though the dataset is already in MNI space despite the docs suggesting that that won't happen:
N.B.2: If the input dataset is not in +tlrc coordinates,
then the only effect is to flip the output coordinates
to the 'LPI' (neuroscience) orientation, as if you
gave the '-orient LPI' option.)
So I'm trying to figure out which is ground truth here. Clarifications are appreciated.
