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Hi, I have a problem with the orientation of images for FSL. I'm obliged to use a pre-existing script (for field map correction) to convert raw dicom images to NIFTI images for my FSL analysis. The script calls both afni and fsl commands along the way. When using afni I can see that the resulting NIFTI structural and functional images are nicely lined up and correctly oriented. But fslview shows both of the images upside down and back to front, in different ways, and while I can run registration and analysis, the results are also inverted and flipped. Apparently the problem relates to the way that the script program is putting Cartesian co- ordinates in the header. I can flip the images around using avwswapdim, but I don't think this is the correct thing to be doing (for example, the script made sure that the axially acquired structural image was converted into an oblique plane to match the functional - and avwswapdim won't respect this). I'd be much obliged for any help, and could easily provide the images. Many thanks Adam UC San Diego