Hi Gwladys,
sorry, I only now read your posting.
> I'm beginner with SPM. I use SPM2 to create fieldmap and match it to epi
> (toolboxe) and run Realign&Unwarp with spm5, as it was been suggested that
> it is possible.
It should be, although you may want to be careful when mixing data from
different spm-versions. Personally, my biggest problem of late has been
coregistration which failed dramatically in so many cases under spm5
that I gave up trying.
> *question 1)
> In spm help and FieldMapToolboxes of SPM2 it is recommanded to select the
> phase map for the first session without selecting any map for the
> remaining sessions(same indications in the Example Data).
>
> but, in the SPM5 manual I found: "only add similar step session data to a
> realign+unwarp branch, i.e., choose Data or Data+phase map for all
> sessions, but don't use them interchangably"
> that I translate : load data AND vdm for all sessions.
That is true and one of the drawbacks of the spm5 implementation. As you
said, if you leave out the fieldmap in spm2 for sessions 2:n, the
algorithm will assume that the fieldmap from the first session is to be
used. Therefore, one only has to match it to the first epi of the first
session as all other sessions will be matched to this one.
In spm5, however, the hirarchy only starts at the session, not the
subject level, and therefore using one map only does not seem to work
anymore. The alterantive is to make copies of the fieldmap and match one
each to the first epi of each session.
> *question 2) If I choose WRAP option (both in realign estimation options
> and in unwrap reslicing option) I know that I must choose Wrap in Y.
> But I don't know if it's a good idea..?? (images have not been resliced
> after slice timing)
I have no really informed opinion other than that I never used wrapping :)
> ... but I am novice and would appreciate some help !!
We all are, and we all do :)
Best,
Marko
--
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Marko Wilke (Dr.med./M.D.)
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Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
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