Hi Lena,
you definitely want to avoid analyze format, as it will remove the direction cosine information you need for example to tell left from right (it's probably why you have a flip).
We don't have much experience with dicom. Have you tried using -it dicom in mri_convert to be explicit about the format?
cheers, Bruce
On Thu, 30 Jul 2009, Lena Palaniyappan wrote: