This is the code that was used for our participation in 2017's Automatic Cardiac Diagnosis Challenge. We were happy to achieve the first place in the segmentation part of the contest with the highest Dice scores achieved for all classes and time steps (ED/ES). An extended version of our paper will be published in the MICCAI STACOM proceedings. A preliminary version of our paper can be found here: https://arxiv.org/abs/1707.00587
The challenge leaderboard is available here: http://acdc.creatis.insa-lyon.fr/#phase/5966175c6a3c770dff4cc4fb (login required, unfortunately)
Batchgenerators (which we use in training) do not work with Windows yet, so you won't be able to run the training if you are on Windows. Sorry for the inconvenience
This code was cleaned up and made usable for external users, but is still what the authors would like to call 'messy'. As you can imagine, a challenge deadline will lead to very rapid code development in the very end which ultimately produces less user friendly code. We did our best to improve the usability so that you should be able to reproduce our results easily.
We use two different architectures for this challenge, a 2D and a 3D UNet. The way the code looks for these networks is very different because they were initially taken from different projects. UNet2D has simple training and architecture files whereas UNet3D is object oriented. You don't need to deal with this if you just wish to train the networks and use our results.
Our code is only compatible with python 2.7. Running it with python 3 will need modifications.
We depend on some python packages which need to be installed by the user (may be incomplete):
- theano
- lasagne
- SimpleITK
- sklearn
- numpy
- batchgenerators (get it here: https://github.com/MIC-DKFZ/batchgenerators)
You need to have downloaded at least the training set of the ACDC challenge.
python dataset_utils.py -i INPUT_FOLDER -out2d OUTPUT_FOLDER_FOR_2D_DATA -out3d OUTPUT_FOLDER_FOR_3D_DATA
INPUT_FOLDER: Folder to which you downloaded and extracted the training data
OUTPUT_FOLDER_FOR_2D_DATA: Where to save training data for 2d network
OUTPUT_FOLDER_FOR_3D_DATA: Where to save training data for 3d network
First go into the UNet2D_config.py and UNet2D_config.py and adapt all the paths to match your file system and the
download locations of training and test sets.
Training the networks requires a GPU with at least 12 GB of VRAM. On a Pascal Titan X, a 2D UNet trains in < 1d and a 3D UNet takes approx. 2 days.
python run_training_2D.py -f FOLD -c CONFIG_FILE_2D
python run_training_3D.py -f FOLD -c CONFIG_FILE_3D
FOLD is the fold id of the cross-validation (0, 1, 2, 3, 4) and CONFIG_FILE_2D/CONFIG_FILE_3D is the path to UNet2D_config.py/UNet3D_config.py. You need to train all 5 folds for 2D and 3D UNet to be able to predict the test set (test results are obtained by using the 10 resulting networks as ensemble).
You can run the validation of the cross-validation like this:
python run_validation_2D.py -f FOLD -c CONFIG_FILE_2D
python run_validation_3D.py -f FOLD -c CONFIG_FILE_3D
Change into the test_set direcory, then run
python predict_test_2D_net.py -f FOLD -c CONFIG_FILE_2D
python predict_test_3D_net.py -f FOLD -c CONFIG_FILE_3D
for all five folds and both networks.
Finally, consolidate the predictions of the networks with
python create_final_submission_files.py -c2d CONFIG_FILE_2D -c3d CONFIG_FILE_3D -o OUTPUT_FOLDER
The predicted test set will be saved in OUTPUT_FOLDER
If you wish to contact us regarding problems, questions or suggestions, please write an email to either Fabian (f.isensee@dkfz.de) or Paul (p.jaeger@dkfz.de)