Hi Alfonso,

Yes the original files do not have the flipping problem. I think I have figured it out though.

The retroicor *.1D files covered only 179 volumes worth of data (I needed to pad an extra TR length when cropping the physio data to match where the scanner triggers are in the physio data files). 

After running 3dretroicor, the files look fine when viewing in freeview or fsleyes, but as soon as they are loaded into CONN volumes 2-180 are flipped A-P. I assume there's some interaction between the way that afni alters the headers and how CONN/SPM reads them that causes the files to flip. 

Either way I remade the .1D files and it seems to be fixed. I'll let you know if I run into further problems on this issue. 

Best,
- Harris