Preheat the oven to 375 degrees F. Lightly coat the muffin tin with cooking spray.
In a medium bowl, whisk together flour, baking soda, cinnamon, nutmeg, ginger and salt.
In a large bowl, combine the applesauce, Greek yogurt, brown sugar, canola oil and egg. Stir together until the mixture is smooth.
Stir the dry ingredients into the applesauce mixture until combined. Stir in the carrot, raisins and chopped pecans.
Spoon the muffin batter into the prepared muffin cups.
Bake for 7 minutes. Place one pecan half on top of each muffin. Bake until a toothpick inserted in the center of the muffins comes out clean, an additional 7 to 9 minutes.
Remove muffins from the pan and allow to cool. Serve.