I do not really get what this black region that I see in brain’s atlases such as Yeo and others?
That is the distinction between cortical and subcortical. The Yeo 2011 atlas that I believe you depicted there is a cortical atlas. Those dark regions are sub-cortical and not included in that atlas.
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Usually, the subcortical are given label ‘0’, correct?
As a side note this is Schaefer’s Atlas