From d04418902985c4f0c77ddf766a848f51b9ea4801 Mon Sep 17 00:00:00 2001 From: melanibe Date: Thu, 22 Feb 2024 11:30:23 +0000 Subject: [PATCH] readme --- README.md | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9bda714..b16810e 100644 --- a/README.md +++ b/README.md @@ -16,11 +16,17 @@ The repository is divided in three main parts: ### Code dependencies The code is written in PyTorch, with PyTorch Lightning. -You can install all our dependencies using our conda enviromnent requirements file `environment_gpu.yml'. +You can install all our dependencies using our conda enviromnent requirements file `environment_gpu.yml`. ### Datasets You will need to download the relevant datasets to run our code. -You can find the datasets at XXX, XXXX, XXX. +All datasets are publicly available and be downloaded at: +* PadChest [https://bimcv.cipf.es/bimcv-projects/padchest/](https://bimcv.cipf.es/bimcv-projects/padchest/), [https://www.sciencedirect.com/science/article/pii/S1361841520301614](https://www.sciencedirect.com/science/article/pii/S1361841520301614) +* RSNA Pneumonia Detection Dataset: [https://www.kaggle.com/c/rsna-pneumonia-detection-challenge](https://www.kaggle.com/c/rsna-pneumonia-detection-challenge) +* CheXpert [https://stanfordaimi.azurewebsites.net/datasets/8cbd9ed4-2eb9-4565-affc-111cf4f7ebe2](https://stanfordaimi.azurewebsites.net/datasets/8cbd9ed4-2eb9-4565-affc-111cf4f7ebe2) +* EMBED [https://pubs.rsna.org/doi/full/10.1148/ryai.220047](https://pubs.rsna.org/doi/full/10.1148/ryai.220047), [https://github.com/Emory-HITI/EMBED_Open_Data/tree/main](https://github.com/Emory-HITI/EMBED_Open_Data/tree/main) +* VinDR Mammo [https://vindr.ai/datasets/mammo](https://vindr.ai/datasets/mammo) + Once you have downloaded the datasets, please update the corresponding paths at the top of the `mammo.py` and `xray.py` files. Additionally, for EMBED you will need to preprocess the original dataframes with our script `data_handling/csv_generation_code/generate_embed_csv.ipynb`. Similarly for RSNA please run first `data_handling/csv_generation_code/rsna_generate_full_csv.py`.