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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