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update detection readme #1066

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9 changes: 7 additions & 2 deletions detection/README.md
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Expand Up @@ -34,9 +34,14 @@ In these files, the values of "box" are the ground truth boxes in world coordina
### 3. Run the example
#### [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 skip Sec. 3.1 and go directly to Sec. 3.2.
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.

Alternatively, users can download the original data and resample them with the following steps. Users can either download 1) mhd/raw data from [LUNA16](https://luna16.grand-challenge.org/Home/) or its [copy](https://drive.google.com/drive/folders/1-enN4eNEnKmjltevKg3W2V-Aj0nriQWE?usp=share_link), or 2) DICOM data from [LIDC-IDRI](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=1966254) with [NBIA Data Retriever](https://wiki.cancerimagingarchive.net/display/NBIA/Downloading+TCIA+Images).
Then run the following command and go directly to Sec. 3.2.
```bash
python3 luna16_prepare_env_files.py
```

Alternatively, you can download the original data and resample them by yourself with the following steps. Users can either download 1) mhd/raw data from [LUNA16](https://luna16.grand-challenge.org/Home/) or its [copy](https://drive.google.com/drive/folders/1-enN4eNEnKmjltevKg3W2V-Aj0nriQWE?usp=share_link), or 2) DICOM data from [LIDC-IDRI](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=1966254) with [NBIA Data Retriever](https://wiki.cancerimagingarchive.net/display/NBIA/Downloading+TCIA+Images).

The raw CT images in LUNA16 have various of voxel sizes. The first step is to resample them to the same voxel size, which is defined in the value of "spacing" in [./config/config_train_luna16_16g.json](./config/config_train_luna16_16g.json).

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