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I have the gradient later applied on the black mask, but it just turned the black mask white.
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After importing your model to Substance Painter did you bake a position map ? That is needed as an input to the 3D Linear Gradient generator.
Just off the bottom of your screenshot should be an image input showing that map - which it should use automatically provided you baked it.
If you did not, go to Texture Settings >Bake Mesh Maps and bake the map
Dave