Hi Jack,
On Mon, 5 May 2003, Jack Grinband wrote:
> >..."intensity normalisation", which also
> >includes a simple thresholding step as well. you won't be getting this
> >step in 3a and 3b, so that probably explains things.
>
> Is this a thresholding for extreme values?
no, it zeros values below a lowish threshold to remove background voxels
from further calculation.
> I often get ICs that are clearly motion artifacts. Since melodic performs motion
> correction before doing ICA, I assume that these components are due to the non-
> linear effects of motion. Presumably, any linear effects would be removed by mcflirt.
> Is that right?
that's pretty much it, yes. by "linear" you mean here "rigid body".
residual effects could be also be slight inaccuracies in the motion
estimation / interpolation artefacts (similar thing), or physics effects
such as "spin-history".
> I am interested in removing some of these components from my FEAT analysis. If I
> create regressors of no interest, it seems to me that I am reducing the power of my
> regressors of interest. Christian had mentioned in a previous message that it's
> possible to make a 4D representation of the noise and subtract it out. How can I do
> that?
you can do that with the -f option - if it's not already in the email
archive, Christian can mayb expand slightly on that.
Thanks, Steve.
Stephen M. Smith MA DPhil CEng MIEE
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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