I just ran across an "undocumented feature" (I believe?) in to3d while playing with DICOM files: to3d appears to ignore -xFOV (and friends) when the output prefix is .nii.gz, but not when the output is a BRIK file.

I also noticed that the extents given by 3dinfo -VERB are slightly different when outputting .nii.gz versus BRIK files. It's a small difference, so probably rounding errors from different calculations, although I can't guess why the calculations should be different. Maybe something to do with the obliquity support?

Can someone comment on the inconsistencies? The first one is a minor inconvenience for me since I make extensive use of the -xFOV arguments to shoehorn data into AFNI (Daniel and probably Rick have seen my siemenstoafni script). I can work around it by outputting a BRIK file and then using 3dcopy to turn it into .nii.gz.

Thanks.