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Thanks Mark! jack >Hi Jack, > >Sorry I haven't answered this before, I've been out of the lab quite a >lot. > >As for motion correction: >1 - we've only written motion correction to deal with a minimum of 6 dof > properly for 3D data, but it should only use 3 dof for 2D data. >2 - one slice will be picked as a reference and all other slices aligned > with the slice in your case (which slice can be selected using >-refvol). > This isn't really what you want. I think you'd be better off >scripting up > flirt calls rather than trying to do this with mcflirt, but this >problem is > still very difficult and I don't know that you'll have a lot of >success. > >For modelling, the second option does make the most sense to me. > >All the best, > Mark > >