Lossless DICOM ⇄ NIfTI round trips for MRI series, as a basis for derivatives (segmentations, ADC/QSM maps) that are written back as properly referenced DICOM (SEG, Parametric Map, or derived MR images for any PACS).
Research use only — not for clinical or diagnostic use. A converted dataset identifies patients (file names are built from PatientName and StudyDate): never share it as is.
uv sync
uv run dcmtether run /path/to/dicom -o /path/to/dataset # scan + convert (rerunnable; default output: the DICOM folder)
uv run dcmtether to-dcm DATASET/sub-…/….nii.gz rebuilt/ # back to identical DICOM
uv run dcmtether to-seg NIFTI labels.nii.gz seg-template.json seg.dcm
The same from Python (API):
import dcmtether as dt
result = dt.run("/path/to/dicom", "/path/to/dataset")
print(result.converted, result.failed) # manifest ids
dt.to_dcm("dataset/sub-…/….nii.gz", "rebuilt/")- Usage: workflow and every command.
- Python API: the commands as functions.
- Formats: dataset layout, file names,
*.tether.json, sidecar, manifest, log. - Supported inputs: what converts, what does not, and why.
- Example metadata templates:
docs/examples/; writing your own: segmentation templates. - Roadmap: ideas for later versions.
- Changelog.
uv run ruff format --check . && uv run ruff check . && uv run pytest
The first test run downloads public test data and the DICOM standard into .cache/. Test data
coverage: docs/dev/test-data.md.
dcmtether: lossless DICOM ⇄ NIfTI round trips for MRI series. Copyright (C) 2026 Thomas Thiel
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details: LICENSE.