Nick,
I confess, I am not exactly sure what you mean by "turn off annotation display".  I tried a few things. 

These were the only ones that I could think of.  Is that what you meant or was it something else that I missed?

Thanks,
Devdutta

On Tue, Mar 3, 2009 at 7:12 PM, Nick Schmansky <nicks@nmr.mgh.harvard.edu> wrote:
What is displayed if you turn off the annotation display?

The threshold in the simulation is used to determine whether clusters
are found or not.  A threshold of 2 indicates a p-value of 0.01
(1/(10^2), 3 is 0.001, etc.  The threshold referred to in the tksurfer
display is just for color thresholding.

Nick

On Tue, 2009-03-03 at 17:17 -0600, Devdutta W wrote:
> Forgot the attachments earlier.  Here they are now
>
> On Tue, Mar 3, 2009 at 5:11 PM, Devdutta W <devdutta.w@gmail.com>
> wrote:
>         Hi Freesurfers,
>         More questions about this analysis.
>         1) Referring to the documentation, we used the following
>         command:
>          tksurfer fsaverage lh inflated -annot mc-
>         z.abs.2.sig.ocn.annot -fthresh 2 -curv -gray
>
>         The documentation says we should see an image as shown in
>         Figure 1 (attached).  But what we see is Figure 2 (also
>         attached).  Can somebody explain this?
>
>         2) When running the simulation does it matter what threshold
>         we use?  For example, can we use a threshold of 2 or 3
>         (instead of 4 as shown in documentation) when running
>         mri_glmfit-sim?  And do we have to use the same threshold
>         while displaying the clusters after?
>
>         Thanks for any help.
>
>         Devdutta
>
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