Hi - you could probably just put a local copy of libcups into your home
directory somewhere and add that directory to LD_LIBRARY_PATH environment
variable.
Cheers, Steve.
On Mon, 8 Nov 2004, Cornelius Werner wrote:
> 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
> there...)
> 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,
> Cornelius
>
>
> On Sat, 06 Nov 2004 12:39:39 +0000, Stephen Smith <[log in to unmask]>
> wrote:
>
> > 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
> >
>
>
>
> --
> 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
|