Hi MH
Many thanks for the reply. I have what looks like the latest version of Chris Rorden's dcm2nii :: 12 12 2012, so I do not think this is the issue.
My question is whether it is correct to use the 'fused' echo1 &2 magnitude images in the FSL_prepare_fieldmap gui ( ie: since our scanner is saving both Echo 1 and Echo2 with the same headers: 1,1,2,2,3,3 etc I only get a single file for the magnitude images as opposed to a separate one for Echo1 and another for Echo2)?
Again many thanks for the time and help
Marta
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