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Hi Helmut, thank you for your reply. There is indeed a parameter that I am not sure about: Mask brain. If I tick Mask brain, the template image for brain masking is T1. Meanwhile my data is not normalized yet, plus when I substitute T1 with coregistered structural, I got an error. But fmap correction is applied in the beginning of the pipeline, so the data are not normalized anyways. Why is there a T1 default template then? How crucial is it if I don't apply masking? I tried both: visually masked and unmasked images do not differ. Thank you. best, Lara 2016-03-30 15:50 GMT+02:00 MRI More <[log in to unmask]>: > Dear Lara, > > If geometric distortions are rather small then there will not be that much > of a difference after correction of course (see the first figure in > http://www.fil.ion.ucl.ac.uk/spm/download/toolbox/FieldMap2/FieldMap_Manual_280207.pdf > ). However, it could also be due to incorrect settings when calculating the > VDM file. > > Best > > Helmut > > > >