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Hi, Yes, I meant to type x -y z in the last email. If this is the anterior-posterior axis then you need to also swap the left-right axis (I assume it is x) in order to avoid the big warning message. It is really important that you do not continue to use any data *after* that warning. It is there to clearly state that such a command *will* swap the left-right orientation and you do not want this, as if the subsequent registration "looks" OK then it will really have left and right the wrong way around (assuming they were initially correct). There is no point sending me data if there are no markers in it as I will not be able to tell by eye which is left and which is right. If you take you original data and do fslswapdim with -x -y z then it should produce an image that looks pretty much the same, but will not produce any warnings and not swap the left-right orientation. All the best, Mark On 1 Sep 2010, at 12:23, Ed wrote: > Mark, > > I used the command fslswapdim in x -y z out. > It swapped the anterior-posterior axis. > > It would be helpful if I can upload one of the > stacks so that you can have a look at it. > > Ed >