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First of all, sorry for the late response, we are currently focused on the development of the new version of Braph 2.0, which is expected to be released in May, and we forgot to review the questions in braph 1 forum.
We can provide you with the coordinates of these subcortical regions (hippocampus, amygdala, and thalamus) to then you can incorporate them in an excel file with braph 1.0 format shown here.
Hippocampus left: -26.09 (x), -24.43 (y), -15.15 (z)
Hippocampus right: 27.74 (x), -23.38 (y), -14.99 (z)
Amygdala left: -23.91 (x), -7.34 (y), -20.64 (z)
Amygdala right: 24.94 (x), -6.01 (y), -20.74 (z)
Thalamus left: -11.75 (x), -19.88 (y), 5.17 (z)
Thalamus right: 12.49 (x), -19.23 (y), 5.66 (z)
Let us now if you need other subcortical regions, in that case we can email you an excel file with all of them.