Metadata-Version: 2.4
Name: cs_dmri
Version: 0.1.0
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: License :: OSI Approved :: MIT License
Classifier: License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Rust
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Dist: numpy>=1.24
Requires-Dist: nibabel>=5
Requires-Dist: dipy>=1.10 ; extra == 'dipy'
Requires-Dist: pytest ; extra == 'test'
Provides-Extra: dipy
Provides-Extra: test
Summary: Diffusion MRI quality control, SHORE compressed-sensing fits, RESTORE tensors and SS3T-CSD, in Rust
Keywords: diffusion-mri,quality-control,shore,csd,neuroimaging
Home-Page: https://github.com/PennLINC/cs_dmri
Author-email: Matt Cieslak <mattcieslak@gmail.com>
License: (MIT OR Apache-2.0) AND MPL-2.0 AND BSD-3-Clause
Requires-Python: >=3.9
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
Project-URL: Documentation, https://cs-dmri.readthedocs.io
Project-URL: Homepage, https://github.com/PennLINC/cs_dmri
Project-URL: Issues, https://github.com/PennLINC/cs_dmri/issues
Project-URL: Source, https://github.com/PennLINC/cs_dmri

# cs_dmri

Python interface to cs_dmri, a Rust library for the analysis of diffusion MRI
data: image quality control, 3D-SHORE reconstruction, robust diffusion tensor
estimation (RESTORE) and single-shell three-tissue constrained spherical
deconvolution.

```bash
pip install cs_dmri
```

```python
import cs_dmri as cs

dwi = cs.DWI.from_files("dwi.nii.gz", "dwi.bval", "dwi.bvec", mask="mask.nii.gz")

qc = dwi.qc()                                   # image-quality metrics
qc.to_dict()                                    # one row of a QC table
cs.QCReport.column_descriptions()               # its data dictionary

tensor = cs.RestoreModel(dwi.gtab).fit(dwi)     # FA, MD, S0, principal direction
shore = cs.ShoreModel(dwi.gtab).fit(dwi)        # 3D-SHORE coefficients and diagnostics
ss3t = cs.ss3t_pipeline(dwi)                    # single-shell three-tissue CSD

ss3t.export("ss3t.odx")                         # ODX; also .fz, .fib.gz, .pam5, .mif
```

Documentation: <https://cs-dmri.readthedocs.io>

License: `(MIT OR Apache-2.0) AND MPL-2.0 AND BSD-3-Clause`; see the
documentation for details.

