On Mon, Mar 9, 2009 at 11:20 AM, Devdutta W <devdutta.w@gmail.com> wrote:

Hi Nick,
Can you shed some light on why this might be happening? I will attach the two picture again in case you weren't able to view them last time. I tried what I thought you meant by "turn off annotation display" and I have stated what happened in my previous email (please see below)

If I don't include the -annot option in tksurfer it only displays the fsaverage, naturally.
If I toggle off the button that says "show labels", it looks like it is just the fsaverage as well.

If I toggle on the "Draw outlined labels" button it shows the same regions as before except they are merely outlined, not filled.
Any help you can give me will be appreciated.

Thanks,
Devdutta

On Wed, Mar 4, 2009 at 10:36 AM, Devdutta W <devdutta.w@gmail.com> wrote:

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

If I don't include the -annot option in tksurfer it only displays the fsaverage, naturally.

If I toggle off the button that says "show labels", it looks like it is just the fsaverage as well.
If I toggle on the "Draw outlined labels" button it shows the same regions as before except they are merely outlined, not filled.

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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