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| import SimpleITK as sitk | |
| import os | |
| import argparse | |
| import glob | |
| from tqdm import tqdm | |
| def convert_dicom_series_to_nifti(dicom_dir, output_file): | |
| """ | |
| Convert a single DICOM series to NIFTI format | |
| Args: | |
| dicom_dir: Directory containing DICOM files for one scan | |
| output_file: Output NIFTI file path | |
| Returns: | |
| bool: True if conversion successful, False otherwise | |
| """ | |
| try: | |
| reader = sitk.ImageSeriesReader() | |
| # get all the scans in the dir | |
| dicom_files = sorted(glob.glob(os.path.join(dicom_dir, "*.dcm"))) | |
| if not dicom_files: | |
| print(f"No DICOM files found in: {dicom_dir}") | |
| return False | |
| reader.SetFileNames(dicom_files) | |
| # load dicom images | |
| image = reader.Execute() | |
| sitk.WriteImage(image, output_file) | |
| return True | |
| except Exception as e: | |
| print(f"Error converting {dicom_dir}: {str(e)}") | |
| return False | |
| def convert_dicom_to_nifti(input_dir, output_dir): | |
| """ | |
| Convert multiple DICOM series to NIFTI format | |
| Args: | |
| input_dir: Root directory containing subdirectories of DICOM series | |
| output_dir: Output directory for NIFTI files | |
| """ | |
| # Create output directory if it doesn't exist | |
| os.makedirs(output_dir, exist_ok=True) | |
| input_dir = os.path.abspath(input_dir) | |
| output_dir = os.path.abspath(output_dir) | |
| print(f"Looking for DICOM series in: {input_dir}") | |
| # Check if directory exists | |
| if not os.path.isdir(input_dir): | |
| print(f"Error: {input_dir} is not a directory") | |
| return | |
| scan_dirs = [d for d in os.listdir(input_dir) | |
| if os.path.isdir(os.path.join(input_dir, d))] | |
| if not scan_dirs: | |
| print("No subdirectories found in the input directory") | |
| return | |
| print(f"Found {len(scan_dirs)} potential scan directories") | |
| # Process each scan directory | |
| successful = 0 | |
| failed = 0 | |
| for scan_dir in tqdm(scan_dirs, desc="Converting scans"): | |
| input_path = os.path.join(input_dir, scan_dir) | |
| output_file = os.path.join(output_dir, f"{scan_dir}.nii.gz") | |
| if convert_dicom_series_to_nifti(input_path, output_file): | |
| successful += 1 | |
| else: | |
| failed += 1 | |
| print("\nConversion Summary:") | |
| print(f"Successfully converted: {successful} scans") | |
| print(f"Failed conversions: {failed} scans") | |
| print(f"Output directory: {output_dir}") | |
| if __name__ == "__main__": | |
| parser = argparse.ArgumentParser(description="Convert DICOM series to NIFTI format") | |
| parser.add_argument("--input", "-i", required=True, | |
| help="Input directory containing subdirectories of DICOM series") | |
| parser.add_argument("--output", "-o", required=True, | |
| help="Output directory for NIFTI files") | |
| args = parser.parse_args() | |
| convert_dicom_to_nifti(args.input, args.output) |