First U-Net Layers Contain More Domain Specific Information Than The Last Ones

This is the repository with the code of experiments for the paper "First U-Net Layers Contain More Domain Specific Information Than The Last Ones"

https://arxiv.org/abs/2008.07357

Libraries:

1. Add damri to the local python:

ln -sfn ~/workspace/domain_adaptation_mri/damri ~/miniconda3/lib/python3.*/site-packages/

where * is the version of your python.

2. Install deep_pipe:

git clone https://github.com/neuro-ml/deep_pipe.git
cd deep_pipe
git checkout 5c08d5759d51c0731cc636c2866bb3a538ffab7a
pip install -e .

3. Install surface-distance:

git clone https://github.com/deepmind/surface-distance.git
pip install surface-distance/

Original repository: https://github.com/deepmind/surface-distance

There is a minor error in surface_distance/metrics.py: the line 102 should be commented, please do it (might be already fixed by the time you are reading this_

4. Python & Torch versions we used:

1. Python: 3.7.6
2. Torch: 1.5.0

Experiment Reproduction

1. The path to your local copy of CC359 should be specified here: config/assets/dataset/cc359.config. You should place notebook/meta.csv in the same folder with the data. From the available in CC359 ground truths we used the "Silver standard" binary mask (https://sites.google.com/view/calgary-campinas-dataset/download)

2. You should specify the 'device' on which you are going to run an experiment by setting the corresponding variable 'device', e.g., in ~/config/experiments/unet2d/unfreeze_first.config

3. To run a single experiment, please follow the steps below:

First, the experiment structure should be created:

dpipe-build /path/to/the/config /path/to/the/experiment
# e.g.
dpipe-build ~/config/experiments/unet2d/unfreeze_first.config ~/dart_results/unfreeze_first

where the first argument is the path to the .config file and the second argument is the path to the folder where the experiment structure will be organized.

Then, to run an experiment please go to the experiment folder inside the created structure (i corresponds to the particular experiment, i.e. to the particular source-target pair):

cd ~/dart_results/unfreeze_first/experiment_{i} 

and call the following command to start the experiment:

dpipe-run ../resources.config

where resources.config is the general .config file of the experiment.

4. Note that switching on/off the augmentation is controlled by augm_fn variable in the .config files. The number of scans to fine-tune on is controlled by n_add_ids, while the share of available slices from a certain scan by slice_sampling_interval