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.
>
> 1) 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.
>
> 2) 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)).
>
> 3) 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
>
> 4) 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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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