How can I get access to intermediate activation ma

Question

I could download and successfully test brain parcellation demo of NiftyNet package. However, this only gives me the ultimate parcellation result of a pre-trained network, whereas I need to get access to the output of the intermediate layers too.

According to this demo, the following line downloads a pre-trained model and a test MR volume:

wget -c https://www.dropbox.com/s/rxhluo9sub7ewlp/parcellation_demo.tar.gz -P ${demopath}

where ${demopath} is the path to the demo folder. Extracting the downloaded file will create a .ckpt file which seems to contain a pre-trained tensorflow model, however I could not manage to load it into a tensorflow session.

Is there a way that I can load the pre-trained model and have access to the all its intermediate activation maps? In other words, how can I load the pre-trained models from NiftyNet library into a tensorflow session such that I can explore through the model or probe certain intermediate layer for a any given input image?

Finally, in NiftyNet's website it is mentioned that "a number of models from the literature have been (re)implemented in the NiftyNet framework". Are pre-trained weights of these models also available? The demo is using a pre-trained model called HighRes3DNet. If the pre-trained weights of other models are also available, what is the link to download those weights or saved tensorflow models?

Answer 1

To answer your 'Finally' question first, NiftyNet has some network architectures implemented (e.g., VNet, UNet, DeepMedic, HighRes3DNet) that you can train on your own data. For a few of these, there are pre-trained weights for certain applications (e.g. brain parcellation with HighRes3DNet and abdominal CT segmentation with DenseVNet).

Some of these pre-trained weights are linked from the demos, like the parcellation one you linked to. We are starting to collect the pre-trained models into a model zoo, but this is still a work in progress.

Eli Gibson [NiftyNet developer]