Re. @chauffeur_afni: you can paste what you are trying with teh error involved, but also note that some examples (with the most modern @chauffeur_afni) now exist here:
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afni.nimh.nih.gov]
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I was fiddling with @chauffeur_afni, and having trouble overlaying my statistics onto a (tlrc) template brain. The afni viewer has no problem doing so, as the stats BRIK is identified as +tlrc, however, running 3dinfo shows that the stays are in ORIG template space.
--> it surprises me that it would be any different. @chauffeur* just runs AFNI in a virtual environment. I don't see how that same problem wouldn't happen in the viewer.
Also, if your stats have been calculated in an aligned space to "tlrc", then I don't see why they wouldn't have the +tlrc space value... If you want, you can upload the dataset and I can take a look at that aspect.
--pt