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Try saving the batch job as a MATLAB .m file to see where the differences are. Your own script seems to miss out a number of the fields that are needed. Best regards, -John On 25 March 2011 13:14, Gael Varoquaux <[log in to unmask]> wrote: > On Fri, Mar 25, 2011 at 11:41:52AM +0000, John Ashburner wrote: >> If you check the initial alignment of the images using Check Reg, are >> they almost aligned? > > They are indeed. > >> If the relative displacement or rotation is too large, then there could >> be instabilities. > > Absolutely, I understand that. Why leaves me puzzle is that fact that it > works from the GUI and fails from the script. Both behaviors are very > reproducible. I am trying to understand where the difference comes from. > > Thanks, > > Gael >