Hello Birgit,
You can use fslmaths to threshold out all but the values of the areas you are interested in ( 453 and 454 ) and then binarise to create your mask. Alternatively the latest versions of FSL have a specific subthalamic nucleus atlas, kindly provided by Birte Forstmann of the University of Amsterdam.
Kind Regards
Matthew
> Dear all,
>
>
> I would like to use an atlas to create a mask of the subthalamic nucleus.
> As far as I can see, this structure is only provided by the 'Talairach Daemon Labels'.
>
> However if I select (in the Atlas Inspector) the structure 'Right Brainstem.*.Gray Matter.Subthalamic Nucleus' and press the '+' button, a brain structure that covers almost the entire brain with values ranging from 0 to approximately 1100 is displayed in fslview.
> Is it also possible to display (and save as mask image) only the subthalamic nucleus?
>
>
> With kind regards,
> Birgit
>
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