Dear Jon,
the first idea I've got, when I read your e-mail, was, that you did not
rejected the first (dummy-) scans out of your time series or, there was a
mix up of different time points including possibly this first scans.
The reason for this is, that within in the first 2-3 scans, the signal of
the csf-compartment is not stable, so the signal intensity of this
compartment is a function of scanning timing, depending on your TR, flip
angle etc.
Having this scans in the realignment process, it can happen, that this
introduces a lot of 'pseudo' movements.
In cases of unclear movement corrections, I always use the spm_movie
function to get an overview across the timeserie. If there are some large
fluctuations of the signal, than you can get problems with the realignment.
In that case, it will be not a useful realignment, and therefore, the
inclusion of the realignment wouldn't help much. Off course, it will reduce
the variance by accounting for that fluctuation, but I guess, the
basic-problem is somewhere in the data acquisition or a previous step of
your preprocessing.
Good luck,
Karsten
------------------------------------------------
Dipl. Phys. Karsten Specht
(Medizin Center Bonn, Spessartstrasse 9, 53119 Bonn, Germany)
currently at:
---------------------
Department of Biological and Medical Psychology
Section of Cognitive Neuroscience
Aarstadveien 21
5009 Bergen
Norway
http://www.uib.no/ibmp/bjorg/english/
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--------------------------------------------------
> -----Opprinnelig melding-----
> Fra: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]På
> vegne av Jon Simons
> Sendt: Wednesday, November 21, 2001 4:42 PM
> Til: [log in to unmask]
> Emne: Bizarre realignment params
>
>
> Dear list,
>
> Apologies if this has been dealt with before, but I couldn't find a
> specific reference in the archive.
>
> I have been using a fairly standard fMRI preprocessing procedure, in
> which inspection of the realignment parameter plots has typically
> indicated subject movement over sessions of anywhere between 0-5 mm.
> I have been including these parameters as confounds of no interest in
> the model in order to reduce the likelihood of type I errors.
>
> Recently, however, a colleague and I independently came upon the
> bizarre situation where a single subject appears to have practically
> zero movement across sessions apart from in one session, where he
> apparently moved 50mm in one direction at the start of the session,
> stayed there for 100 or so timepoints, and then moved 50mm back to
> zero again at the end of the session.
>
> Obviously, the subject is unlikely to have undertaken these
> gymnastics without our noticing it. My question, therefore, is what
> might have caused SPM to think there is this much movement, and
> whether there is any way of using the data from this session. Can
> the inclusion of the realignment params in the model correct for this
> degree of apparent "motion"? Is there any other way of convincing
> SPM that in fact this movement does not exist? I have tried
> realigning the session without the first and last few timepoints, and
> there is no difference. I could just leave out this session, but if
> there is an alternative, that would be preferable.
>
> Any suggestions gratefully received.
>
> Thanks,
> Jon.
>
> --
> Dr Jon Simons
> Department of Psychology
> Harvard University
> Rm 860, William James Hall
> 33 Kirkland Street
> Cambridge, MA 02138
> USA
>
> Tel: + 1-617-495-3856
> Fax: + 1-617-496-3122
>
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