license: apache-2.0
Dataset Summary
Healthy CT data for abdominal organs (liver, pancreas and kidney) are filtered out from public dataset.
Downloading Instructions
1- Install the Hugging Face library:
pip install -U "huggingface_hub[cli]"
2- Download the dataset:
mkdir HealthyCT
cd HealthyCT
huggingface-cli download qicq1c/HealthyCT --repo-type dataset --local-dir . --cache-dir ./cache
[Optional] Resume downloading
In case you had a previous interrupted download, resume it by adding “--resume-download” to the download command:
huggingface-cli download qicq1c/HealthyCT --repo-type dataset --local-dir . --cache-dir ./cache --resume-download
3- Extract files: the dataset is formatted as a multi-part zip file. Use the first part (AbdomenAtlasMini.zip.001) to extract the dataset. With the GUI,
just right-click on the file and select "Extract Here". With the command-line, we suggest using 7zip (faster, see below). If it is not available, you can concatenate the files and unzip (slower):
cat healthy_ct.zip* > HealthyCT.zip
unzip -o -q HealthyCT.zip
[Optional] 7zip
7z x healthy_ct.zip.001
Installing 7zip (optional):
For Debian/Ubuntu:
sudo apt update
sudo apt install p7zip-full
For Fedora:
sudo dnf install p7zip
For CentOS/RHEL:
sudo yum install p7zip
Uploading Instructions
0- Install 7zip
For Debian/Ubuntu:
sudo apt update
sudo apt install p7zip-full
[Optional] Other operating systems
For Fedora:
sudo dnf install p7zip
For CentOS/RHEL:
sudo yum install p7zip
For MacOS:
brew update
brew install p7zip
If you do not have brew installed, another possible solution is:
sudo port install p7zip
1- Compress the folder for uploading
To compress the folder you want to upload into multi-part zip file with parts of 5GB (-v5g), take "AbdomenAtlas1.0" as an example:
Note: if AbdomenAtlas1.0ZipFolder and AbdomenAtlas1.0 share the same parent directory, please use the relative path for AbdomenAtlas1.0ZipFolder. Otherwise, please use the absolute path for AbdomenAtlas1.0ZipFolder.
mkdir /path/to/the/HealthyCT_ZipFolder
cd /path/to/the/HealthyCT
cd ..
7z -v5g a /path/to/the/HealthyCT_ZipFolder/healthy_ct.zip HealthyCT/
After zipping, the structure of the compressed folder (e.g., AbdomenAtlas1.0ZipFolder) will be:
HealthyCT_ZipFolder
├── healthy_ct.zip.001
├── healthy_ct.zip.002
├── healthy_ct.zip.003
├── ...
2- Upload to Hugging Face
Create a repository at Hugging Face (e.g., a repository named AbdomenAtlas1.0)
Install huggingface_hub from the PyPi registry
pip install --upgrade huggingface_hub
Upload the compressed folder (e.g., AbdomenAtlas1.0ZipFolder) to this repository
python uploading_files_to_hugging_face.py --folder_directory /path/to/the/HealthyCT_ZipFolder --repository qicq1c/HealthyCT --repository_type dataset