Yes, this would be the default setting for fMRI. The second-level analysis is based on those voxels which are included in all of the individual first-level fMRI models. So if you didn't cover one region in a single subject, this region would be lost from second-level analysis.
However, in case of VBM analyses (where there is no first-level analysis but rather the GM or WM volumes), you would want to use an explicit intensity threshold.
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