Hi - yes, this is a reasonable approach.
Cheers, Steve.
On 15 Feb 2007, at 16:13, Clare Kelly wrote:
> Thanks Steve..
>
> I don't mean to question the FSL's ability to deal with motion -
> it's just that I've never seen such a strong artifact before,
> appearing consistently across several subjects (which was also why
> I thought it might not be motion, but some sort of flow or weird
> scanner artifact) - it's showing up on a random-effects group
> analysis with 16 subjects!!
>
> What I did with that particular subject was: correlated the
> timeseries for the rim ICA component with the
> prefiltered_func_data_mcf_abs
> .rms to ensure it was motion-related, then entered it as a nuisance
> covariance in my correlation analysis. This worked really well,
> almost completely removing the artifact from the stat maps.
>
> I intend to do this for each subject who shows such rim-type
> artifacts (i.e., as long as the component correlates significantly
> with motion). Does this seem like a reasonable approach??
>
> Thanks again,
> Clare
>
>
> On 2/15/07, Steve Smith < [log in to unmask]> wrote: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>
>
>
> ----------------------------------------------------------------------
> --
> ---
> 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
> ----------------------------------------------------------------------
> --
> ---
>
------------------------------------------------------------------------
---
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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