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Hi Andrew,

Why do you think it is shown the wrong way?  Does the label left 
correspond to the left hemisphere (though shown on the right in the 
image), or, asking in a different way, do you know whether you look from 
the front or from the back on the brain slice?

see here, maybe this clarifies it better:
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils#Orientation-related_Utilities
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained

Fslview displays the brain according to radiologic standards, thus the 
image of the brain is displayed in a way as you would see the brain when 
looking from the front.

I hope I did not misunderstand your question.

Have fun,
wolf

On 1/12/14, 7:35 PM, Andrew Martin wrote:
> Dear Experts
> Left and right appear to be the wrong way around in FSLview (see file 
> attached). Is this indicative of a problem in my analysis?
> Regards
> Andrew