If you change the input size, the size of the last convolutional layer that is reshaped to connect to the first fully connected layer changes. in that case the input size of the first fully connected layer should change. For e.g. for alexnet taking in 224x224 you get 6x6 in the last conv layer, for 48x48 you might expect this to be 2x2 (guessing, the best way would be to pass the image through the features part and see the size of the output)