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Subject:

Re: BOLD-signal from eyes movements

From:

Alexander Lebedev <[log in to unmask]>

Reply-To:

Alexander Lebedev <[log in to unmask]>

Date:

Thu, 2 Apr 2009 16:06:56 +0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (188 lines)

Thanks so much. I will try...

Best Regards


* Tom Johnstone <[log in to unmask]> [Thu, 2 Apr 2009 12:45:39 
+0100]:
> On Thu, Apr 2, 2009 at 12:25 PM, Alexander Lebedev <[log in to unmask]>
> wrote:
> > Thank you very much for anwsers!
> >
> > Our scanner is Siemens Magnetom Symphony 1.5 T. In our study we use
> the
> > modification of "Stroop-Task" in order to cause a frustration in
> Healthy
> > and Depressive subjects. I think that the optimal solution is by 
using
> > the "brainmask", isn't it?
>
> Also worth considering in that case then is that waiting until after
> you've spatially smoothed your data before you apply a mask might be a
> mistake, because the smoothing could blur some eye movement signal
> into adjacent regions of cortex such as the orbitofrontal cortex that
> might be of interest in emotion-related paradigms. So stripping out
> the eyes before model fitting might be worthwhile.
>
> -Tom Johnstone
>
>
> >
> > Best Regards
> > Alexander Lebedev
> >
> > * Torben Ellegaard Lund <[log in to unmask]> [Thu, 2 Apr 2009
> 10:52:20
> > +0200]:
> >>
> >> I completely agree! But then again some scanners suffer from 
serious
> >
> > N/
> >>
> >> 2 ghosting and then you would actually like to get the aliased eye
> >> movements removed from the visual cortex.
> >>
> >> Best
> >> Torben
> >>
> >>
> >>
> >> Den 02/04/2009 kl. 10.41 skrev Michael T Rubens:
> >>
> >> > Perhaps knowing a bit about the type of task would help determine
> >> > the best method. For many visual tasks it is likely that the 
signal
> >> > you would extract from the eyes would highly correlate with the
> >> > task, thereby regressing out signal of interest and killing your
> >> > power.
> >> >
> >> > -Michael
> >> >
> >> > On Thu, Apr 2, 2009 at 1:23 AM, Torben Ellegaard Lund
> >> <[log in to unmask]
> >> > > wrote:
> >> > Hi Dorain
> >> >
> >> > There are several ways this could be done, and which one you 
choose
> >> > should depend on your programming skills. But in general you 
should
> >> > have a pretty good prior hypothesis that the particular area you
> >> > want to mask out by regression will be a noise only area. But 
this
> >> > would e.g. apply to ventricles, major blood vessels and eyes.
> >> >
> >> > One way to do this is to use the Eigenvariate button, when you 
view
> >> > your results. Move the cursor to the eyes, and use the 
Eigenvariate
> >> > button to extract the timeseries from the region, or single 
pixel.
> >> > Now reanalyse your data with the extracted timeseries entered a a
> >> > covariate, much like you would do with motion parameters. The
> >> > timeseries you want to remove will be found in the variable xY.u
> >> >
> >> > Alternatively you could find typical MNI space locations for eyes
> >> > and ventricles and automatically extract timeseries from those
> >> > regions using spm_sample_vol.m This would require a bit of matlab
> >> > coding.
> >> >
> >> > The benefit of regression as opposed to masking is that noise 
could
> >> > be removed from other areas than the ones where you timeseries 
was
> >> > extracted from. The drawback is that you risk removing real 
signal,
> >> > if the noise looks like the signal.
> >> >
> >> >
> >> >
> >> > Best
> >> > Torben
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > Den 02/04/2009 kl. 06.49 skrev Dorian P.:
> >> >
> >> > Dear Torben,
> >> >
> >> > How can a time series from a specific voxel be added as a
> regressor?
> >> >
> >> > And can this be done to covary out the activity similar to any
> voxel
> >> > of artifactual activity?
> >> >
> >> > Thank you.
> >> > Dorian.
> >> >
> >> > 2009/4/1 Torben Ellegaard Lund <[log in to unmask]>:
> >> >
> >> > Dear Alexander
> >> >
> >> > If the eye-artefact is only there in some of the con images it 
will
> >> > not make
> >> > it through the threshold in the final second level analysis. This
> >> > could have
> >> > been the case in a fixed effects analysis but not in a random
> >
> > effects
> >>
> >> > analysis. If you want to avoid those artefacts you could include 
a
> >> > time-series from an eye-voxel in your design matrix. This would
> most
> >> > likely
> >> > remove the eye-artefact, but you risk removing some of the 
activity
> >> > as well.
> >> >
> >> > Best
> >> > Torben
> >> >
> >> >
> >> >
> >> > Den 31/03/2009 kl. 16.56 skrev Alexander Lebedev:
> >> >
> >> > Dear SPM experts
> >> >
> >> > I decided to check my old results, and found one problem. When I
> >
> > have
> >>
> >> > opened con*-files in xjview tbx, strange thing appears... There 
are
> >> > activations of eye movements (notwithstanding of Normalization) 
in
> >> > some
> >> > con*-files. May I include such results in group study? Could you
> >> > advice me
> >> > any solutions to prevent this trouble?
> >> >
> >> > Thank you beforehand
> >> >
> >> > Best Regards
> >> > --
> >> > Alexander Lebedev.
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > Research Associate
> >> > Gazzaley Lab
> >> > Department of Neurology
> >> > University of California, San Francisco
> >



--
Alexander Lebedev.

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