Dear Mathias,
You should be using the thresholded version of your statistics for
the file "your_funcdata" in the call that Wolf suggested. For example,
"thresh_zstat1". Then it will only count voxels that survived the threshold.
All the best,
Mark
On 31 Aug 2011, at 15:57, Mathias Warnke wrote:
> Thanks Wolf
>
> I tried this option but i think there must be some extra way to threshold the func data first because it seems that the -V option also considers the gray scale voxels.
>
> your help will be greatly appreciated.
>
> Best regards.
>
> 2011/8/30 wolf zinke <[log in to unmask]>
> On 30/08/11 22:19, Mathias Warnke wrote:
> Hi FSL forum.
>
> Can anyone help me determining the amount of activated voxels contained within a userdefined ROI?
> I have used some commands like --volume and fslmaths but I'm afraid it returns the whole voxels inside
> a ROI and not only the activated voxels I want to assess (see the attached image). I.e. these commands
> output the anatomical scan plus the activated voxels.
>
> Thanks in advanced.
>
> Best regards.
> Hi
>
> Try: fslstats your_funcdata -k your_roi -V
>
> I think that's doing what you want.
>
> good luck,
> wolf
>
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