Hi Clare,
I'm not an FSL expert, but wanted to add my 2 cents anyway.
Motion artifact is most likely explanation, commonly affects edges of
brain more than other regions, and produces ICA components with low
frequencies.
The fsl motion summary parameters, MAD and MRD, are mean values. So,
even tho you see mean relative displacement of .08, that doesn't mean
there wasn't some volume-to-volume movement big enough to produce
artifacts (it only takes about .2mm abrupt motion, sometimes less, to
produce an artifact that cannot be removed by standard motion
correction algorithms). If you look in the motion correction
directory "mc" you will see a textfile
prefiltered_func_data_mcf_rel.rms...this has the n-1 values for
volume-to-volume displacement (the 6 motion parameters are combined
into a single measure). If you plot these numbers, or just look at
them, you'll see whether any are unusually high...look especially for
>.5mm jumps... plotting them will tell you roughly what timepoint they
happened at (this will probably match up with the scans showing big
changes in the ICA component timecourse), then you can make sure to
check these timepoints during the movie Steve proposed. (also, to
make the movie, you can do: avwmaths filtered_func_data -sub
mean_func filtered_func_demeaned. removing the mean makes it much
easier to see the artifacts.)
Dan
On 2/14/07, Clare Kelly <[log in to unmask]> wrote:
> Thanks Steve I will try that - sorry about the image, it was to get the
> email under the 50K limit!
>
> Best,
> Clare
>
>
> On 2/14/07, Steve Smith < [log in to unmask]> wrote:
> > It's hrad to tell as the image you sent is very low res, but this
> > looks like a motion artefact. View the data as a movie before and
> > after motion correction and see if this makes sense....
> > Cheers.
> >
> >
> > On 13 Feb 2007, at 14:42, Clare Kelly wrote:
> >
> > >
> > > Hello all,
> > >
> > > I've been running some connectivity analyses with resting data and
> > > see some fairly large rim artifact for several seeds in many of my
> > > subjects.
> > >
> > > I re-ran my preprocessing with melodic and I see a component such
> > > as the one in the attached figure in several subjects. For this
> > > subject (who probably showed the most severe artifact), this was
> > > the second component, explaining 8.16% of the explained variance
> > > (7.6% of the total variance).
> > >
> > > I'm planning to include the timeseries for this component as a
> > > nuisance covariate in my analysis, but I'm wondering if anyone has
> > > any idea what it is, and if it's something I can prevent in the
> > > future. I didn't think it could be movement as the total (absolute)
> > > movement in this subject was only 0.23mm, relative movement was
> > > 0.08mm.
> > >
> > > Thanks for your help!
> > >
> > > Clare Kelly
> > > <IC_2_thresh.jpg>
> > > <f2-t2.jpg>
> >
> >
> >
> ------------------------------------------------------------------------
> > ---
> > Stephen M. Smith, Professor of Biomedical Engineering
> > Associate Director, Oxford University FMRIB Centre
> >
> > FMRIB, JR 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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