[Abridged] We present the first direct comparison of the distribution of the gas, as traced by the [OI] 6300 AA emission, and the dust, as traced by the 10 micron emission, in the protoplanetary disk around three intermediate-mass stars: HD 101412, HD 135344 B and HD 179218. N-band visibilities were obtained with VLTI/MIDI. Simple geometrical models are used to compare the dust emission to high-resolution optical spectra in the 6300 AA [OI] line of the same targets. The disks around HD 101412 and HD 135344 B appear strongly flared in the gas, but self-shadowed in the dust beyond ~ 2 AU. In both systems, the 10 micron emission is rather compact (< 2 AU) while the [OI] brightness profile shows a double peaked structure. The inner peak is strongest and is consistent with the location of the dust, the outer peak is fainter and is located at 5-10 AU. Spatially extended PAH emission is found in both disks. The disk around HD 179218 is flared in the dust. The 10 micron emission emerges from a double ring-like structure with the first ring peaking at ~ 1 AU and the second at ~ 20 AU. No dust emission is detected between ~ 3 -- 15 AU. The oxygen emission seems also to come from a flared structure, however, the bulk of this emission is produced between ~ 1 -- 10 AU. This could indicate a lack of gas in the outer disk or could be due to chemical effects which reduce the abundance of OH -- the parent molecule of the observed [OI] emission -- further away from the star. The three systems, HD 179218, HD 135344 B and HD 101412, may form an evolutionary sequence: the disk initially flared becomes flat under the combined action of gas-dust decoupling, grain growth and dust settling.
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