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Dec 13, 2022
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update detection readme and add pip install packages #1103

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78ec3a8
update readme and add pip install packages
Can-Zhao Dec 13, 2022
09758d0
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 13, 2022
98bf483
update readme and add pip install packages
Can-Zhao Dec 13, 2022
a1173f4
Merge branch 'detection_readme' of github.com:Can-Zhao/tutorials into…
Can-Zhao Dec 13, 2022
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typo
Can-Zhao Dec 13, 2022
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7 changes: 6 additions & 1 deletion detection/README.md
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Expand Up @@ -32,6 +32,11 @@ In these files, the values of "box" are the ground truth boxes in world coordina
- For bugs relating to the running of a tutorial, please create an issue in [this repository](https://github.com/Project-MONAI/Tutorials/issues).

### 3. Run the example
#### 3.0 Setup environment
```bash
pip install -r requirements.txt
```

#### [3.1 Prepare Your Data](./luna16_prepare_images.py)
We provide [resampled Nifti images](https://drive.google.com/drive/folders/1JozrufA1VIZWJIc5A1EMV3J4CNCYovKK?usp=share_link) for users to download (recommended).
If you do this, please open [luna16_prepare_env_files.py](luna16_prepare_env_files.py), change the value of "raw_data_base_dir" and "resampled_data_base_dir" to the directory where you store the downloaded images, and the value of "downloaded_datasplit_dir" to where you downloaded the data split json files.
Expand Down Expand Up @@ -60,7 +65,7 @@ python3 luna16_prepare_images_dicom.py -c ./config/config_train_luna16_16g.json
```
Note that for DICOM data, the data split json files are based on data downloaded with [NBIA Data Retriever](https://wiki.cancerimagingarchive.net/display/NBIA/Downloading+TCIA+Images).

The resampled images will be with Nifti format.
The resampled images will be with Nifti format. The number of resampled images will be less than the original images, this is because LUNA16 annotation includes only nodules >= 3 mm accepted by at least 3 out of 4 radiologists, and excluded the images without such nodules.


#### [3.2 3D Detection Training](./luna16_training.py)
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4 changes: 4 additions & 0 deletions detection/requirements.txt
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monai-weekly[nibabel]
itk>=5.2; python_version < "3.10"
tensorboard
torchvision