Hi, Donna,

My purpose is counting activated area size on each subject.

I did do significance test using Freesurfer on individual level. The results 
contained many files,for example, "sig.nii.gz" and "Fsig.nii.gz" corresponding 
to result of t and f test respectively. Is that right?
But I do not know how to determine tha suprathreshold on subject level as you 

For display and counting area size, I converted the results file(sig.nii.gz) to 
Caret. Then I count area size on Caret. When I counted area size, I selected a 
uniform threshold 1.3, i.e.-log10(0.05) for each subject. So I set the scale to 
1.3 ~ maxminum on Caret. Is this right?

So I could draw a border around the  suprathreshold region and generated a 
paint file. I got the area size of the region using the paint file.

Is there any step wrong?


At 2014-10-30 00:27:14, "Donna Dierker" <do...@brainvis.wustl.edu> wrote:
>Hi wangzhiwei,
>I'm a little confused by the question.  There mention of area size and scales 
>hints that there might be a confusion between tools used for quantification / 
>significance testing and those used for display purposes.
>Freesurfer has its own tools for significance testing, so you could use those. 
> We often use threshold-free cluster enhancement for that purpose, which finds 
>the significance threshold.  Suprathreshold area can be computed once this 
>threshold has been determined.
>But usually when I make a figure, I generate border around the suprathreshold 
>regions and display these bordersover the "real" t- or f-map, using a scale 
>that corresponds to my alpha (e.g., .05) divided by two (since I usually do 
>both right and left hem tests).  I compute this t or f-stat using my n / 
>degrees of freedom.
>So the significance testing and display steps are separate, the way I do it.
>Now you might not be going as far as significance testing.  Sometimes you just 
>want to look at some preliminary data -- particularly for a single subject.  A 
>good start might be to understand if this is a single subject, group results, 
>what kind of statistic.
>And certainly not everyone does this the way I do, so it would be helpful for 
>others to weigh in with their viewpoints/conventions.
>On Oct 28, 2014, at 9:53 PM, wangzhiwei3233 <wangzhiwei3...@126.com> wrote:
>> Hi, experts,
>> I converted fMRI results derived from freesurfer to caret, and not I want to 
>> count activation areas on caret. So there is a problem of threshold and 
>> scale.
>> Auto scale range is 0~60. I found that the area size was different when 
>> using scale 1.3~4 from when using scale 1.3~60. And the latter one was 
>> smaller. However , in the latter case(1.3~60),  the value of a point that 
>> was next to the border of activation area but in non-activation area was a 
>> little bit lager than the threshold 1.3. 
>> How to set the scale to guarantee the activation accurate?
>> Best!
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