Thanks for confirming Steve. For those who are interested, it looks
like AFNI has a function '3ddot' that supports computing correlations in
conjunction with input masks and thresholds to define the specific
voxels that contribute to the calculation.
cheers,
-MH
On Tue, 2011-11-01 at 14:42 +0000, Stephen Smith wrote:
> Hi
>
> On 1 Nov 2011, at 14:23, Michael Harms wrote:
>
> > Hi Matthew,
> > Maybe I'm not planning on using fslcc in the manner for which it was
> > intended, but doesn't that mean that the resulting correlations will
> > be
> > dependent on somewhat arbitrary things such as the number of 0
> > voxels?
> > i.e., the size of a brain mask that was previously applied?
> >
>
>
> That's right - it's just a simple dumb correlation tool - I guess you
> could script fslmaths and fslstats to do more complex stuff.
>
>
> Cheers.
>
>
>
>
>
>
>
>
>
> >
> > Also, to avoid anyone getting confused, I'm sure you meant to
> > include a
> > sqrt factor in your denominator, right? :)
> >
> > thanks,
> > -MH
> >
> > On Tue, 2011-11-01 at 13:53 +0000, Matthew Webster wrote:
> > > Hello Michael,
> > > No voxels are explicitly excluded from the
> > > calculation. The
> > > two input images are ( depending on command line options )
> > > demeaned and then all timepoints and voxels are looped
> > > across to generate
> > >
> > > (image1_timepoint1*image2_timepoint2)/(sumsquares
> > > (image1_timepoint1).sumsquares(image1_timepoint2))
> > >
> > > Hope this helps
> > >
> > > Matthew
> > > >
> > > > > Hello,
> > > > > I want to compute to the correlation (across voxels) of two
> > > > > images, and
> > > > > my understanding is that's what 'fslcc' is for. But, it isn't
> > > > > obvious
> > > > > to me what determines which specific voxels go into that
> > > > > calculation.
> > > > > If a voxel is zero in EITHER input volume, is that voxel then
> > > > > excluded
> > > > > from the calculation? (in which case I can control the voxels
> > > > > that
> > > > > contribute to the calculation by thresholding my input
> > > > > appropriately
> > > > > beforehand?)
> > > > >
> > > > > thanks,
> > > > > -MH
> > > > >
> > > > >
> > > >
> > > >
> >
> >
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>
>
>
>
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