indeed - or preprocesing with MELODIC to clean up the data would be a good
idea as well.
Cheers.
On Wed, 14 Apr 2004, Christian F. Beckmann wrote:
> Stephen,
>
> that's a tricky problem with no good answer. IMHO the best way of
> dealing with all these types of 'structured noise' is to remove their
> effect during pre-processing (motion-correction etc.)
>
> If you actually want to remove certain TRs from your measurements then
> I'd recommend not doing it from the filtered functional data - if the
> data is so bad that you decide to throw it away it certainly shouldn't
> be used during filtering, e.g. if there is a large intensity dropout at
> some TR this will have a negative impact on temporal filtering etc. In
> such cases you might even be better off by replacing the data by the
> average of neighbouring TRs prior to pre-processing.
>
> cheers
> christian
>
>
> On 13 Apr 2004, at 17:23, Stephen Wilson wrote:
>
> > Thanks for your replies, Jen and Christian. But I want to exclude some
> > volumes from the middle of the middle of the run. This means they still
> > need to be there when FEAT calculates the convolution with the
> > hemodynamic
> > response, whereas if I manipulate the input prior to running FEAT, then
> > FEAT will have no way of knowing that volumes were removed, so no way
> > of
> > knowing how to predict the response.
> >
> > There are several reasons I can think of why one might want to do this:
> > (1) to exclude volumes in which face/mouth motor tasks are performed
> > (this
> > is my present goal); (2) to exclude volumes with scanner artifacts;
> > (3) to
> > exclude volumes where there are saccades, or swallowing, or such, if
> > you
> > can monitor these.
> >
> > It would be nice if there was an option to input a file of time points
> > to
> > be excluded...
> >
> > best,
> >
> > Stephen
> >
> --
> Christian F. Beckmann
> Oxford University Centre for Functional
> Magnetic Resonance Imaging of the Brain,
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
> Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
>
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
|