Computer Vision: Handling dataset(3D data or scan) with different timesteps
I would use an LSTM-RNN to encode sequences of arbitrary length (length meaning the number of slices) into fixed-size output. It should be very easy to implement it in Keras :)

Then feed the sequences in your CNN.

Check sequence-to-sequence encoder-decoder scheme, like this one.

The same concept is applied with state-of-the-art algorithms that require fixed size inputs, like this one.