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! >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > >_______________________________________________ >caret-users mailing list >caret-users@brainvis.wustl.edu >http://brainvis.wustl.edu/mailman/listinfo/caret-users
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