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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) |