I'm sorry I don't know the answer to the Freesurfer question, but someone else 
might know.  And I confess I don't understand the rationale for thresholding at 
that value, possibly because I am unfamiliiar with the contents of those files.

So I'm keeping the responsibility for ensuring a reasonable threshold on you. 
;-)  But If it's each subject, then it's probably worth scripting it using 
these caret_command tools:

      caret_command -surface-region-of-interest-selection  
         [-metric  metric-file-name  column  min  max SEL-TYPE]

      caret_command -surface-roi-statistical-report  

And you can use each subject's surface/topo for that surface area calculation.  
Your min is your threshold and max something like 9999999.  Your report will 
include the area of the suprathreshold regions, and you can grep that line from 
the resulting report file.

On Oct 29, 2014, at 11:30 PM, wangzhiwei3233 <wangzhiwei3...@126.com> wrote:

> 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 
> mentioned. 
> 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?
> Thanks!
> Zhiwei
> 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.
> >
> >Donna
> >
> >
> >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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> >> caret-users@brainvis.wustl.edu
> >> http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >
> >
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