On 14 Feb 2007, at 19:04, Clare Kelly wrote:
>
> Thanks Daniel and Steve,
>
> You're completely right, when I look at the graphs and a movie
> there is a large rightward rotation of the head.
>
> So how come this artifact appears, despite motion correction and
> the inclusion of motion parameters in the model?
Normally because the motion is so large that there will be residual
effects (due to spin history, interpolation, nonlinear distortion
etc) even after perfect motion correction and inclusion of linear
motion regressors.
Cheers, Steve.
>
> I've attached the prefiltered_func_data_mcf_rel.rms graph.
>
> Thanks so much for all your help!
> Clare
>
>
>
>
> On 2/14/07, Daniel Wolf <[log in to unmask]> wrote: 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.
> > > >
>
>
>
> <sub8019movement.jpg>
------------------------------------------------------------------------
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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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