I might need clarification regarding the structure of your images as usually images are represented as a mxn or mxnx3 matrix...depending on the nature of the image
your description outlines a 3D output matrix; however, it only has two layers and is 129x1 dimensions?
For changing the size of output (image size), I would recommend using the imresize() function. This function can be used to either scale an image by a factor or resize images to a desired height (rows) and width (columns). As far as image convolution methods, MATLAB allows for you to specificy which method/kernel to use in the resizing of the image. Again, I may be misinterpreting your question and need more clarificaton about what you mean by "structure windows of the convolution layers".
