Hi, Clement-

I guess you are asking both if *you* are right and if your dataset's *right hemisphere* is on the right?

Can I ask, is this possibly a sphinx-position dataset that you are aiming to un-sphinxify?

I guess I might do this in steps, because it sounds like you want to:
1) remove obliquity from the dataset
2) change definition of planes (so, what is currently an axial slice might become coronal or sagittal, say)
3) flip what is left and right
Is that right? Note that #2 and #3 can be a bit related as part of this.

I would start by copying the dataset, because 3drefit changes the header directly, and then do #1 separately (and you can put the coordinate origin in the middle of the volume or center of mass at the end, say):

3dcopy DSET_00 DSET_01
3drefit -deoblique DSET_01

Now it becomes a bit more difficult/open to decide what to do. I might use 3dresample to send the data to RAI orientation *also* changing the data so things look the same:

3dresample -orient RAI -input DSET_01 -prefix DSET_02

Now, if you only had a L-R flip to make, you could do "3drefit -orient LAI ..." on DSET_02. But you have multiple changes to make, I think; so you run the full set of them here:

3dcopy DSET_02 DSET_03
3drefit -orient <your choice of orient> DSET_03

Note that here, I have often used "LSP", "LIP" or "RIP", depending on the scanner and original orientation.

At the end, you might want to run this to put the coord origin in the center of the grid:

@Align_Centers -base "RAI:0,0,0" -grid -dset DSET_03 -prefix DSET_04

... or to put it at the dset center of mass, run:

3dCM -set 0 0 0 -automask DSET_03

--pt