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Main VoxelMorph tutorial is out of date #634

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@20millot

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@20millot

Hi.

It seem the mainVoxelMorph tutorial is out of date and do not works on Colab anymore.
Problems are:

  • Voxelmorph install not working
  • unet.input is now a list of a keras tensor instead of just the keras tensor
  • vxm_data_generator yield a tuple of 2 lists instead of tuples
  • Uses of model.fit_generator instead of model.fit
  • The output of model.predict is a list instead of tuple
  • In tf.keras.optimizers.Adam uses lr instead of learning_rate

I made an updatedColab notebook that works in the meantime but it's more of a patched up version than a real replacement because some changes feel unsatisfactory:

  • extracting the keras tensor from the unet.input list to keep the rest as is
  • converting the output of the network into tuples for visualization to keep the rest as is

As a side note, the Voxelmorph install not working using:

!pip install voxelmorph

Is a recurring issue for multiple people. I do not know if it is because they are trying to use the tutorial or it also occurs on their local installation. (e.g.#633 )

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