Ok. For some reason I thought that the "vox_p" values were based on the
parametric t->p transformation. So, for the "vox_p" values, is the
empirical distribution calculated separately at each voxel, or is there
just a single empirical distribution formed by aggregating values from
all voxels within the mask that is then used to compute the empirical p-
value at each individual voxel?
thanks,
-MH
On Sat, 2010-03-13 at 09:45 +0000, Stephen Smith wrote:
> You are comparing the parametric t->p transformation (using the
> theoretical t distribution) with the nonparametric transformation
> (derived by permutation testing that estimates the _actual_ null
> distribution of the test statistic - here t). The whole point of
> randomise is that it estimates this transformation empirically (from
> the data) - so it won't be the same as the theoretical transformation
> unless your data+model _exactly_ follow the parametric distributional
> assumptions. For a large enough number of permutations the empirical
> approach is guaranteed to be more accurate.
> Cheers, Steve.
>
>
>
> On 12 Mar 2010, at 21:53, Michael Harms wrote:
>
> > Hello,
> > My understanding is that the "_vox_p_tstat1" output of randomise
> > (from
> > the -x flag) reflects the p-value calculated according to a t-
> > distribution, where the t-value itself is contained in the
> > "_tstat1.nii.gz" file.
> >
> > However, the two values do not always seem to match as I would
> > expect,
> > and to an extent that appears to be more than just "rounding error"
> > related to whatever library is used to compute statistical
> > distributions.
> >
> > For example, I'm looking at a voxel (using FSLView) for which the t-
> > value is 1.51444, and the p-value, according to "_vox_p" image is
> > 0.8818. This is from an analysis having 150 volumes, and 5 columns
> > in
> > the design matrix -- i.e., 145 dof.
> >
> > According to Matlab the p-value for that distribution is:
> > > > tcdf(1.51444,145)
> > ans =
> > 0.933954466613827
> >
> > which I consider a rather "large" discrepancy from the "_vox_p"
> > value of
> > 0.8818. Any idea as to the source of these difference?
> >
> > thanks,
> > -Mike H.
> >
> > --
> > Michael Harms, Ph.D.
> > --------------------------------------------------------------------
> > Conte Center for the Neuroscience of Mental Disorders
> > Washington University School of Medicine
> > Department of Psychiatry, Box 8134
> > Renard Hospital, Room 6604 Tel: 314-747-6173
> > 660 South Euclid Ave. Fax: 314-747-2182
> > St. Louis, MO 63110 Email: [log in to unmask]
> > --------------------------------------------------------------------
> >
> >
>
>
> ---------------------------------------------------------------------------
> 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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