Dear Mathias,
That is right - the rendered images are a nasty mixture of
structural and functional data. They are only useful to look
at. Never use them as a source of numerical data. Always
use the thresholded or unthresholded statistical images
directly.
All the best,
Mark
On 31 Aug 2011, at 16:59, Mathias Warnke wrote:
> Thanks Wolf and Mark
>
> It seems you are right. I tried this two following options:
>
> fslstats thresh_zstat1.nii.gz -k cingulate.nii.gz -V
> 212 212.000000
>
> fslstats rendered_thresh_zstat1.nii.gz -k cingulate.nii.gz -V
> 1630 1630.000000
>
> Which confirms that the structural image is also considered when using the second option.
>
> Best regards.
>
>
> 2011/8/31 wolf zinke <[log in to unmask]>
> Hi,
>
> what do you mean by grey voxels? Do you use the functional data as thresholded z-map, or do you try to run the call on a rendered image that overlaid the statistics on the structural brain. For the latter I won't be surprised, if it also uses the grey voxels of your structural image. Use this call on the thresholdes z-stat image, and it should work.
>
> fslstats your_roi -V # should give the number of voxels / volume of your roi
> fslstats your_funcdata -k your_roi -V # gives the number of voxels within this roi, that are superthreshold (as long you use the stats image only)
>
> good luck,
> wolf
>
>
>
> On 31/08/11 16:57, 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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