dicom_to_nifti

Convert a directory of DICOM slices (one series) into a single NIfTI volume.

dicom_to_nifti(
    dicom_dir: str,
    output_path: str,
    debug: bool = False
) -> str

Overview

Reads a DICOM series with SimpleITK’s GDCM reader and writes it as a single .nii.gz volume, preserving spacing, origin, and orientation. The output is named after the DICOM directory.

Parameters

Name	Type	Default	Description
dicom_dir	str	required	Directory holding the .dcm slices of one series.
output_path	str	required	Directory where the NIfTI volume is saved.
debug	bool	False	If True, logs the output path and slice count.

Returns

str – Path to the saved NIfTI file.

Output File

<DIRNAME>.nii.gz

Example: Input directory dicom/case_01/ → Output case_01.nii.gz

Exceptions

Exception	Condition
FileNotFoundError	dicom_dir is not a directory
FileNotFoundError	No DICOM series is found in dicom_dir

Usage Notes

• One series per folder: the reader uses the series found in dicom_dir; keep each series in its own directory.
• Geometry preserved: spacing, origin, and orientation are carried over from the DICOM headers.

Examples

from nidataset.transforms import dicom_to_nifti

dicom_to_nifti("dicom/case_01/", "out/")
# Output: out/case_01.nii.gz

Typical Workflow

import os
from nidataset.transforms import dicom_to_nifti

# Convert a folder of per-case DICOM series to NIfTI
root = "dicom_cases/"
for case in os.listdir(root):
    case_dir = os.path.join(root, case)
    if os.path.isdir(case_dir):
        dicom_to_nifti(case_dir, "nifti_cases/")