I thought it was worth clarifying, the data set is a few non-sequential 2D images. So felt 2D registration was more appropriate than using 3dvolreg. I referenced the discussion below to guide my choice to start this problem but the registration hasn't come out well at all. I've tried a few iterations tampering with the default values in 3dAllineate, but to no avail. My hope/thought is figuring how to source a ROI/mask of voxels in base to register ought to give the best result. I also tried -emask option using an inverted mask but was also worse. Any guidance with this is very much appreciated.
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afni.nimh.nih.gov]
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