How can I get access to intermediate activation ma

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?

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]