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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