dcmstack

0.9.0 verified Sat May 09 auth: no python maintenance

dcmstack is a Python library (currently v0.9.0, last released stable) that stacks DICOM images into 3D volumes and converts them to NIfTI format. It has a very slow release cadence (last release in 2015) and supports Python >=2.7. The project is effectively in maintenance mode.

pip install dcmstack

Common errors

error ModuleNotFoundError: No module named 'dcmstack' ↓

cause dcmstack is not installed or installed in the wrong Python environment.

fix

Run: pip install dcmstack

error AttributeError: 'DicomStack' object has no attribute 'add_file' ↓

cause Using an outdated version (<0.8.0) where the API was different.

fix

Upgrade to version 0.9.0: pip install dcmstack==0.9.0

Warnings

deprecated dcmstack is no longer actively maintained. The last release was in 2015, and it only supports Python 2.7 officially. Consider using dcm2niix or Dicom2Nifti for modern projects. ↓

fix Migrate to dcm2niix (command-line) or the Python library dicom2nifti.

gotcha The library does not handle gzipped NIfTI output directly; you must use nibabel to save as .nii.gz. ↓

fix After calling stack.to_nifti(), save the resulting nibabel image using nib.save(img, 'output.nii.gz').

Imports

dcmstack
```
import dcmstack
```
The library is imported directly; there are no submodules.

Quickstart

Basic usage: add DICOM files to a DicomStack and convert to NIfTI.

import dcmstack
from glob import glob

# Stack a series of DICOM files into a NIfTI file
file_list = sorted(glob('path/to/dicom/*.dcm'))
stack = dcmstack.DicomStack()
for f in file_list:
    stack.add_file(f)
nifti_img = stack.to_nifti()
nib.save(nifti_img, 'output.nii.gz')