Hello,

I am trying to use the 3dresample command to put a t-map image in the same orientation as the original functional image. I switched the original functional image to an ANALYZE format using directions in a previous thread on how to do that without messing up the file (ie. changing some environment variables.) Now that I have switched it back to AFNI format using:
3dcopy spmT_0001.hdr spmT_0001
it appears to be in LAI format (from looking at 3dinfo) and when I look at it in AFNI it is flipped anterior to posterior.

ITo fix this I tried the command:
3dresample -orient LPI -prefix spmT_0001_LPI -inset spmT_0001+orig.
and while the image changes very slightly, it is still A-P flipped. (When I say this I mean in the AFNI window the sagittal slice looks backwards, though 3dinfo says it's in orientation that I flipped it to.) In frustration, I actually tried all 8 combinations of orientation and all of them were A-P flipped opposite to my functional image. Am I misunderstanding the documentation on the resample command? How is best to flip the slices back?

Thanks very much,
Brianna Schuyler