Hi Clare,
I can't give you a good answer, but I can give you some references:
Wu DH, Lewin JS, Duerk JL. J Magn Reson Imaging. 1997 Mar-Apr;7(2):365-70.
Inadequacy of motion correction algorithms in functional MRI: role of
susceptibility-induced artifacts.
Also,for a broader discussion of artifacts:
Wager TD et al, Neuroimage 26 (2005) 99-113
Dan
On 2/14/07, Clare Kelly <[log in to unmask]> 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?
>
> 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.
> > > > >
> >
> >
>
>
>
>
|