Excellent - thanks a million!
Unfortunately, FSLView doesn't work yet on our machines, because our
admins refuse to install the necessary libcups.so.2 (but I'll get them
Yes, I also noted that in MELODIC I got one "whole brain activation"
component, but I wasn't able to figure out what that meant. But now,
things start looking somewhat different....!!
I'm extremely thankful that you took the time (over the weekend?) to look
into things - can't say how much!
Cheers and best greetings to Oxford,
On Sat, 06 Nov 2004 12:39:39 +0000, Stephen Smith <[log in to unmask]>
> 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.
> 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
> 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
> "noise". Temporal smoothing also is a non-default option in FEAT, as
> it's generally a bad thing to do.)
> Note that this noise in the data is quite easy to see if you view the
> 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
>> most probably...I'll keep you informed.
>> Thank you very much again, and have a nice weekend :-) !
>> On Fri, 29 Oct 2004 10:16:07 +0100, Stephen Smith <[log in to unmask]>
>> > 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
>> > 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
>> >> 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
>> >> and
>> >> the difference between both. Therefore, I created a "three-columns"
>> >> design
>> >> matrix with the actual presentation times (in seconds) of the
>> >> 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
>> >> which was turned on).
>> >> The problem now is that there is NOTHING coming up in the results on
>> >> single subjects level - no higher level visual cortices, simply nil.
>> >> When
>> >> leaving the data unthresholded, some brainstem lights up, which
>> >> 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
>> 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
Institut fuer Medizin (IME)
AG Kognitive Neurologie