Datasets:

---

AbdomenAtlas

/

_AbdomenAtlas1.1Mini

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AbdomenAtlas 22

A working Python script:

Note that some images are missing (echo to https://huggingface.co/datasets/AbdomenAtlas/_AbdomenAtlas1.1Mini/discussions/1#66daaa6a2e82d53d3bf160d8)

  # Download dataset
    snapshot_download(
        repo_id="AbdomenAtlas/_AbdomenAtlas1.1Mini",
        repo_type="dataset",
        local_dir=".",
    )

    # Create directory for merged contents
    img_raw_dir = "Images-raw"
    os.makedirs(img_raw_dir, exist_ok=True)

    # Extract all tar.gz files
    for tar_file in glob.glob("*.tar.gz"):
        print(f"Extracting {tar_file}")
        # Extract the tar file directly to dest_dir
        try:
            # Check archive integrity first
            check_result = subprocess.run(["gzip", "-t", tar_file], capture_output=True)
            if check_result.returncode == 0:
                subprocess.run(["tar", "-xzf", tar_file, "-C", img_raw_dir], check=True)
            else:
                print(f"Warning: {tar_file} appears to be corrupted, skipping...")
        except subprocess.CalledProcessError as e:
            print(f"Error extracting {tar_file}: {e}")

    # Move contents from subfolders to Images-raw
    subfolders = [
        f"{img_raw_dir}/AbdomenAtlas1.1Mini_BDMAP_00005001_00005195",
        f"{img_raw_dir}/AbdomenAtlas1.1Mini_BDMAP_00005196_00009262"
    ]
    for subfolder in subfolders:
        if os.path.exists(subfolder):
            for item in os.listdir(subfolder):
                src = os.path.join(subfolder, item)
                dst = os.path.join(img_raw_dir, item)
                shutil.move(src, dst)
            os.rmdir(subfolder)

    # Create Images and Masks directories
    os.makedirs("Images", exist_ok=True)
    os.makedirs("Masks", exist_ok=True)

    # Process each case folder
    for case_dir in glob.glob(os.path.join(img_raw_dir, "BDMAP*")):
        if os.path.isdir(case_dir):
            case_name = os.path.basename(case_dir)

            # Move CT images
            ct_src = os.path.join(case_dir, "ct.nii.gz")
            if os.path.exists(ct_src):
                shutil.move(ct_src, os.path.join("Images", f"{case_name}.nii.gz"))

            # Move mask files
            mask_src = os.path.join(case_dir, "combined_labels.nii.gz")
            if os.path.exists(mask_src):
                shutil.move(mask_src, os.path.join("Masks", f"{case_name}.nii.gz"))

> ls Images | wc -l
5195
> ls Masks/  |wc -l
9262

Update:

• [7 Mar 2025] These are the same 5195 cases in AbdomenAtlas1.0Mini