I haven't observed that problem, but here is a guess. I'm wondering if
this is due to a poor, asymmetric slice profile of the RF excitation
pulse. Do you have gaps between your slices? When you add them, does
the problem go away? I think the default pulse in the epibold sequence
is a spectral spatial pulse with Gaussian shape. You can try switching
to another RF excitation pulse like a sinc. Sinc pulses usually have
very clean edges, and you don't really need spectral spatial pulses for
brain imaging.
I hope that helps.
-Luis H.
Kent Kiehl wrote:
>
> Dear SPMers,
> We have recently run into an interesting 'feature' of our MR scanner
> that produces a small, but significant artifact in fMRI time series. We
> are curious to know if anyone else has observed this artifact or has
> come up with other ways to deal with it other than that listed below.
> It is my understanding that, by default (at least on GE scanners), rf is
> applied in an alternating fashion in EPI single shot acquisitions. This
> is known as rf-chop on our machine and it is typically used to increase
> SNR when combining acquisitions as in typical MR applications. However,
> we have observed that this feature produces stronger signal when rf is
> applied in one direction than when it is applied in the other direction.
> Moreover, these effects seem to be vary in different slices within
> acquisitions. Thus, there is a large amount of image intensity variance
> between acquisitions. The tell tale sign of this artifact is the
> presence of a small 'saw tooth' like (about .2 mm) movement estimate in
> the realignment output.
> We have recently been able to compensate for this feature by simply
> adding a covariate of no interest or 1 -1 1 -1 1 -1......etc for each
> image in the time series during statistical analyses. Of course, we do
> not convolve this with covariate of no interest with the hrf. This
> effectively removes the variance associated with this artifact from our
> data. Indeed, z-scores typically jump from the 5 to 5.5 range to over
> 6-7.0 range when controlling for this artifact.
>
> I would very much appreciate any comments that any other users,
> physicists in particular, might have on this issue.
>
> I discussed this issue with members from several other fMRI labs that
> have observed this artifact in their realignment time series at the
> recent Cognitive Neuroscience meeting in Washington. They had not been
> sure what to make of it. I hope that this note helps others as well.
>
> Best regards,
> Kent Kiehl
>
> :::::::::::::::::::::::::::::::::::::::::::
> Kent A. Kiehl
> 2255 Wesbrook Mall
> Departments of Psychiatry and Psychology
> University of British Columbia
> Vancouver, B.C., Canada V6T 2A1
> work (604)822-7128
> home (604)221-7809
> fax (604)822-7756
> email [log in to unmask]
> http://www.psychiatry.ubc.ca/sz/nilab/kiehl
> ::::::::::::::::::::::::::::::::::::::::::::
--
Luis Hernandez, Ph.D.
Research Fellow
Neurosurgery Dept.
Wake Forest University School of Medicine
Medical Center Blvd
Winston Salem NC 27157
336 713 8068
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