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
>
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