Without knowing the details, I can only guess at why your "image has been shifted down quite a bit". My guess is that the original data+orig dataset was not centered in the I-S direction, and that fact was recorded in the AFNI data+orig.HEAD file. However, the ANALYZE format does not provide a place to record volume offsets. When you read the data back into to3d, you didn't specify the slice offset on the command line, so to3d assumed that the dataset was centered in all 3 axes. For the in-slice axes, that is usually correct or very close to correct, but for the through-slice axis (I-S for axial slices), this assumption is usually not correct. But without further information, that's all that to3d can do.

The simplest way to fix that problem would be to use to3d with the "-geomparent data+orig" flag. This would tell the program to read the geometrical information (including slice offset) from the "data+orig" dataset, and then the new dataset would have lie in the same spatial location as the old one.

bob cox