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What do you mean remove the carbon? May be a stupid question but I don't understand.It's white poop, right? If it is, your gourami has parasites. And you can treat it now, I don't see a reason to wait. And make sure you remove the carbon
I have flake food, do I still add medicine to it or do I need pellets?There is a good video put out by The Inquisitive Fish Guy on treating with General Cure.
They have charcoal in them. Open the clip at the top and dump the charcoal out. (Although you are treating internally with food which is the best way for internal parasites, but if you were treating the water column you would need to dump that charcoal.