The brain is logical in thinking whereas heart is not logical (this is what I have understood). When we think from brain we are being very logical but when we do it from our heart we are doing it out of emotion no matter how illogical it might seem. So, even if the brain produces emotion I guess, we are more prone to take the emotional decision from the heart. The dominance of emotional decision from the heart is very high than the brain. So if you appreciate someone from the bottom of the brain instead of from the bottom of the heart it might not go too well for the recipient no matter how well and with good intentions you have wished that person.
'Idhuvum Kadandhu Pogum "
Even this challenging situation would ease
The heart is always a symbol of warmth, love,affection and sincerity. To me when we say something with real meaning to some one, the prefix - heartfelt implies that it's true with warmth and profoundness.
Like Neethu has mentioned, imagine telling someone 'my brainfelt congratulations'. doesn't come out well and doesn't sound well.
Let's stick to the heart that's a sign of love and kindness.
Do what inspires you !!