Hi Matt,

Isaac answered the first part of your question, but as
Matthew_2 Wrote:
-------------------------------------------------------
> Dear AFNI gurus,
>
> I'm writing about using the AFNI matlab tool
> WriteBrik.m
>
> My intention is to run statistics in matlab and
> then write a brik that can be used in AFNI's
> viewer GUI with cluster thresholds defined from
> 3dClustSim.
>
>
> Moreover, it looks like the Clusterize tool is
> used with values OVER a certain threshold, so I
> imagine I could set the threshold at 0.95 and
> invert the p-values (i.e., 1 - p, for each voxel)
> in order to set a threshold that would correspond
> to a p-value of 0.05 in the original dataset. I
> imagine there may be a better way?

You could convert your p values to Z-scores. That would make more sense for the thresholding.

> Like can
> WriteBrik be used to create the sort of
> statistical maps that AFNI is use to? If so, what
> do you recommend?

Yes, but you will have to handle setting all header parameters yourself from matlab and that can get complicated though you could start by looking for the kinds of fields populated by AFNI programs that produce the kind of output you will. For information on AFNI's dataset header fields check out README.attributes. You can have afni open it for you with: apsearch -view_readme attri

cheers
Ziad

>
> Many thanks,
>
> Matthew