No, you can't use a 'fused' NII because presumably it contains duplicate
slices (one at each echo time)?
If you are willing to engage with Chris Rorden, I suspect he would be
interested in getting this data, to see why it isn't getting split into
separate echo time volumes by dcm2nii.
Your alternative is to manually separate the two sets of DICOMS (e.g., by
using the TE field) and then run dcm2nii once separated.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: [log in to unmask]
On 7/8/13 4:23 AM, "Marta Seretny" <[log in to unmask]> wrote:
>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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