Hi Cornelius - I'm pretty sure I have the answer to this. I can get quite
nice looking activation maps for all contrasts:
The problem is that you have high frequency global noise in your data. The
whole brain image is (ie globally) fluctuating at quite high frequency,
giving huge noise in the analysis. This might be due to a number of
things, including even the data conversion process (for example, Philips
scanners can insert a random scaling factor for each image depending on
how you do the conversion).
The reason that you didn't see this before was that SPM does intensity
normalisation by default, which largely removes this problem. In FEAT this
is an option which we have turned off by default (because it's generally
an oversimplistic solution to these general issues) but when I turn it
back on for your data the results are then nice. (Also, it may well be
that the temporal smoothing in SPM, if you've used that, also reduces this
"noise". Temporal smoothing also is a non-default option in FEAT, as again
it's generally a bad thing to do.)
Note that this noise in the data is quite easy to see if you view the time
series in FSLView in movie mode; it's also clear as strong global
components (including one all-white-matter "activation" component) in a
MELODIC ICA analysis.
So - hope that helps. Cheers, Steve.
On Fri, 29 Oct 2004, Cornelius Werner wrote:
> Hi there,
> thanks for your offer. I'll try and get our IT staff to putting the data
> somewhere accessible. But this will take until the start of the next week,
> most probably...I'll keep you informed.
> Thank you very much again, and have a nice weekend :-) !
> Bye,
> Cornelius
>
>
> On Fri, 29 Oct 2004 10:16:07 +0100, Stephen Smith <[log in to unmask]>
> wrote:
>
> > Hi - it sounds from your description like you did things right, so yes I
> > suspect that the problem is somewhere in the details of the 3-column EV
> > setups. The best thing to do is to make a tar file of the output FEAT
> > directory plus the input 3-column text files, and put it on a web/ftp
> > site and we'll take a look.
> >
> > Cheers.
> >
> >
> > On Fri, 29 Oct 2004, Cornelius Werner wrote:
> >
> >> Dear all,
> >>
> >> I conducted an event related fMRI study, where people had to press
> >> visually cued buttons and were to evaluate the (visual) result by
> >> another
> >> button press, which could be either the expected one (c for congruent)
> >> or
> >> an unexpected one (ic for incongruent). Sometimes, there were null
> >> events
> >> interspersed (fixation cross only). (Actually, there was one more
> >> factor,
> >> which is of no interest right now).
> >> During analysis, I was interested in the hemodynamic response to the
> >> visual presentation of both the expected result, the unexpected result
> >> and
> >> the difference between both. Therefore, I created a "three-columns"
> >> design
> >> matrix with the actual presentation times (in seconds) of the respective
> >> event, the actual duration (in s) and simply "1" for the weighting
> >> factor.
> >> My contrasts were specified as follows:
> >>
> >> c ic null
> >> 1 0 -1 Main Effect Congruent
> >> 0 1 -1 Main Effect Incongruent
> >> -1 1 0 Differential Activation (ic > c)
> >>
> >> All preprocessing options were left on default (except for slice timing,
> >> which was turned on).
> >>
> >> The problem now is that there is NOTHING coming up in the results on the
> >> single subjects level - no higher level visual cortices, simply nil.
> >> When
> >> leaving the data unthresholded, some brainstem lights up, which doesn't
> >> help too much...
> >> Now, this really makes me wonder, as the same analysis performed with
> >> SPM2
> >> yields the expected results with not too weak t-values even in the
> >> differential contrast. So I suppose I did something wrong with the
> >> design
> >> matrix!?! Or are there any other typical pitfalls a beginner might
> >> stumble
> >> into which I am not aware of??
> >>
> >> I'd greatly appreciate your help with this!
> >> Best regards,
> >> Cornelius Werner
> >>
> >> --
> >> Cornelius Werner
> >> Institut fuer Medizin (IME)
> >> AG Kognitive Neurologie
> >> Forschungszentrum Juelich
> >> 52425 Juelich
> >> Germany
> >>
> >> Tel. +49-(0)2461-61-8609
> >>
> >
> > --
> > Stephen M. Smith DPhil
> > Associate Director, FMRIB and Analysis Research Coordinator
> >
> > Oxford University Centre for Functional MRI of the Brain
> > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> > +44 (0) 1865 222726 (fax 222717)
> >
> > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> >
>
>
>
> --
> Cornelius Werner
> Institut fuer Medizin (IME)
> AG Kognitive Neurologie
> Forschungszentrum Juelich
> 52425 Juelich
> Germany
>
> Tel. +49-(0)2461-61-8609
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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