On Thu, 20 Jan 2005 11:02:57 -0800, Martin Zalesak <[log in to unmask]> wrote:
>Dear all,
>
>I noticed a wide variation in the global intensity of my (partial brain)
>epi volumes. I understand that there is some adjustment for this in SPM,
>but I was wondering at which stage does it take place and how exactly does
>it work.
>
>Thank you,
>Martin
SPM uses "grand mean scaling" by default, unless you specify something
else. But grand mean scaling (search the mailing list for more info)
won't itself handle varations within a session.
For most people, high-pass filtering helps ameloriate fluctuations.
Awhile back, people also did global scaling, whereby each volume is scaled
so its (adjusted) mean is some fixed quantity. But at least among the SPM
crowd, this technique is out of favor.
That all being said, EPI mean volume intensity shouldn't vary by all that
much. Quite often, fluctuations in the mean intensity (apart from the
initial few volumes, where the mean changes due to magnetization
saturation (?) issues---these volumes are usually dicarded) indicate
something went wrong with the scan. Maybe your experiment's design and
scanning protocol is atypical and the variation doesn't indicate a problem.
>Martin Zalesak, M.Sc.
>PhD Candidate in Medical Engineering
>Harvard-MIT Division of Health Sciences and Technology
>Admissions Building, Rm. # 347
>McLean Hospital
>115 Mill St.
>Belmont, MA 02478
>
>Phone: (617) 855-2961
>Fax: (617) 855-2985
>
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