Dear Gabriella,
the imcalc expression should be exactly this:
mean(X)
When "Options->Data Matrix" is set to "yes", imcalc uses a single
variable named "X" to store image plane data.
Best,
Volkmar
Am Montag, dem 31.01.2022 um 20:46 -0800 schrieb Gabriella Imbriano:
> Hi Volkmar,
>
> Thank you for your response. Those images are con images. Both have
> been preprocessed in the same sequence except, the brighter one also
> underwent art global. The preprocessing pipeline includes
> slicetiming, realignment, coregistration, normalization and
> smoothing.
>
> I tried to implement the imcalc strategy because that seems like it
> could be really helpful in trying to figure out the source of the
> problem however I ran into an error. For the expression, should the
> entry be exactly "mean(x)" ? Are there any other steps to the process
> aside from the ones listed? Thank you for your help!
>
> Best,
> Gabby
>
> On Tue, Jan 18, 2022 at 12:32 AM Volkmar Glauche
> <[log in to unmask]> wrote:
> > Dear Gabriella,
> > what are we looking at here? Are these con or beta images, residual
> > images or something else? Are the images spatially normalised,
> > smoothed etc? If the images are normalised, what method and
> > parameters did you use? What are the actual voxel values? First you
> > should trace back the sources of striping to your raw, unprocessed
> > data and the acquisition process. A simple, but very effective
> > measure would be to compute mean and standard deviation images for
> > your raw time series using imcalc. In the imcalc batch module,
> > select
> > the original timeseries and set the following items:
> > - Expression: mean(X) for mean image, std(X) for standard deviation
> > - Options->Data Matrix: Yes
> > - Options->Interpolation: Nearest neighbour
> > Then, look at the resulting images and assess the size and extent
> > of
> > the effect. You may want to repeat this for intermediate time
> > series
> > data (realigned, slice timing corrected, normalised).
> >
> > If striping is already present in your original data and you have a
> > chance to modify your image acquisition protocol, you should do so.
> > If it appears after a certain processing step, you should review
> > the
> > parameters of this processing step (e.g. interpolation options,
> > smoothing).
> > Best regards,
> > Volkmar
>
>
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