Hello Doug,
Thank you very much for the response. Any reason why I have a list of clusters when none of them were significant (based on the CWP). I thought clusters that appeared on the summary text file should always be significant because they survived correction.
Best, Paul
On Mon, Sep 25, 2017 at 6:01 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
On 09/24/2017 02:17 PM, miracle ozzoude wrote:
Sent from my BlackBerry 10 smartphone. *From: *miracle ozzoude miracooloz@gmail.com *Sent: *Friday, September 22, 2017 9:37 PM *To: *Douglas N Greve *Subject: *sim-sign abs/ cluster summary results confirmation
Hello,
I ran cortical thickness analyses using the following contrast and fsgd. After that, I corrected for multiple comparison using monte carlo 5000 with cluster forming threshold of 2 and unsigned/2-tailed t-test (abs). I wanted to confirm my interpretation of the results.
- Since my contrast is (-1 1 0 0 representing control>stroke), it
should be red/yellow and if blue, it should be control<stroke. However, I see clusters with colors different from the aformentioned (see attached screenshot). How should I interpret them?
That is a parcellation/segmentation of the clusters, and the colors don't have inherent value. Eg, when you look at the aparc, you see precentral and postcentral are red and blue, but those colors don't mean anything, they are just a way to distinguish between areas. You have chosen abs, so it is not possible to interpret the sign.
- I want to view the uncorrected p-values, which of the columns in
the summary text file should I concentrate, and should the p < or > 0.05?
The uncorrected p-values are the voxel-wise values. The stats file will have the maximum uncorrected p-value (actually, -log10(p)).
- Looking at the CWP column in the summary text file, can I conclude
that the obtained regions/clusters are significant? This is because non of the cluster-wise p-values are below 0.05 (--cwp 0.05).
Not sure which column you are talking about. All the CWP values are close to 1, so nothing is significant
- Which of the columns represent the sign of my contrast i.e. where
Control>Stroke and Control<Stroke because i used abs? Max?
if you used abs, then you can't interpret sign. Having said that, the "Max" column will indicate the sign of the vertex with the maximum -log10(p), and that will probably be the sign of the entire cluster
FSGD file GroupDescriptorFile Title StrokevsControl Class1 Stroke Class2 Control Variable bmi Input 6001 Stroke 20 Input 8001 Control 30
Contrast: -1 1 0 0 (Control>Stroke removing the effects of bmi)
Thank you, Paul
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