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

With 7zip, just run:

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