<commit_before># Automatic Cranial Implant Design: AutoImplant 2020 1st Place Solution
1. Open terminal and setup 3DUNetCNN repository:
```
git clone https://github.com/ellisdg/3DUnetCNN.git
cd 3DUnetCNN
export PYTHONPATH=${PWD}:${PYTHONPATH}
``` 
2. ```cd``` into the ```autoimplant2020``` example directory:

```cd examples/autoimplant2020``` 

3. Download the augmented dataset and un-archive it into the current directory ("examples/autoimplant2020"):

[https://zenodo.org/record/4270278](https://zenodo.org/record/4270278)

4. Train the model:

```python -W ignore::UserWarning:nilearn.image.resampling:273 ../../unet3d/scripts/train.py --config_filename ./crossvalidation/autoimplant_config_fold0.json --model_filename ./autoimplant_unet3d_fold0.h5 --training_log_filename ./autoimplant_unet3d_fold0_training_log.csv --nthreads <nthreads> --ngpus <ngpus> --fit_gpu_mem <gpu_mem>```

```<nthreads>```,<commit_msg>FIX: sets the config files so that they work<commit_after># Automatic Cranial Implant Design: AutoImplant 2020 1st Place Solution
1. Open terminal and setup 3DUNetCNN repository:
```
git clone https://github.com/ellisdg/3DUnetCNN.git
cd 3DUnetCNN
export PYTHONPATH=${PWD}:${PYTHONPATH}
``` 
2. ```cd``` into the ```autoimplant2020``` example directory:

```cd examples/autoimplant2020``` 

3. Download the augmented dataset and un-archive it into the current directory ("examples/autoimplant2020"):

[https://zenodo.org/record/4270278](https://zenodo.org/record/4270278)

4. Train the model:

```python -W ignore::UserWarning:nilearn.image.resampling:273 ../../unet3d/scripts/train.py --config_filename ./autoimplant_config.json --model_filename ./autoimplant_unet3d_fold0.h5 --training_log_filename ./autoimplant_unet3d_fold0_training_log.csv --nthreads <nthreads> --ngpus <ngpus> --fit_gpu_mem <gpu_mem>```

```<nthreads>```,
{'fraction_non_alphanumeric': 0.14525745257452574, 'fraction_numerical': 0.051490514905149054, 'mean_word_length': 5.688405797101449, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 11, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4313163', 'n_tokens_mistral': 702, 'n_tokens_neox': 625, 'n_words': 143}