OK. Thanks, Donna. Zhiwei
At 2014-10-30 22:29:32, "Donna Dierker" <do...@brainvis.wustl.edu> wrote: >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! >> >> >> >> >> >> _______________________________________________ >> >> 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 >> >> >> >> _______________________________________________ >> 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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