Thanks Doug.
I have two follow-up questions: 1) How do you explicitly change the CW P threshold in the qdec gui? I'm attaching a pic of my qdec gui and the corresponding terminal output. According to your previous answer the vertex-wide threshold is .01 while the CW Pvalue threshold is .05 (see terminal output) and the visualization threshold is 2 (p < .01; please let me know if I'm wrong with any of this info). How do I go about changing the CW Pvalue threshold in the GUI?
2) why does the gui only display one cluster when I hit "find clusters and go to max" when the simulation outputs 2 clusters? According to previous posts I believe I should be setting my vertex-wide threshold to the same thing used in the simulation, which is 2 (p< .01), yet I'm getting different results. Can you please explain the discrepancy?
Thank you for your assistance,
Ashley
On Sun, Mar 30, 2014 at 11:47 AM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
On 3/29/14 3:09 PM, Ashley Shurick wrote:
Hi,
I have some questions about using monte carlo sim in qdec:
First of all, I just want to verify it's ok to use the simulation with a whole-brain analysis and not just an ROI analysis.
yes
Second, I'm a bit confused about how to calculate the p-threshold for my max clusters. Looking here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSumm...
tells me how to calculate the p-value of my clusters, but according to the page, max = -log(base10) (pvalue). The example given is the 13th cluster where max = -5.981, and the stated p value is p < .006. I can't figure out how you came up with this p-value, can you please clarify your calculations?
This is not the cluster-wise p-value, this the most significant vertex inside the cluster. This p-value is computed from the GLM and contrast that you supply. The cluster p-value is in a different column in the table.
Finally, in qdec when I change my "threshold" from say 1.3 (.05) to 2.0 (.01) I notice the CW Pvalue threshold doesn't change in the terminal output, and remains at .05. Can you please explain this? What exactly am I changing when I change the "threshold" in qdec?
That is the vertex-wise threshold. You need to explicitly change the CWP threshold in the qdec GUI doug
Thank you in advance for your assistance,
Ashley
-- Ashley A. Shurick Ph.D. Candidate Department of Psychology Stanford University
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