omnimira 0.2.0__tar.gz

omnimira-0.2.0/LICENSE

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+   APPENDIX: How to apply the Apache License to your work.
+
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omnimira-0.2.0/MODEL_LICENSE.md

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+# OmniMIRA model-weight license
+
+The pretrained OmniMIRA checkpoint files distributed with this project are
+licensed under the Creative Commons Attribution-NonCommercial 4.0
+International License (CC BY-NC 4.0):
+
+https://creativecommons.org/licenses/by-nc/4.0/
+
+You may share and adapt the model weights provided that you give appropriate
+credit, provide a link to the license, indicate whether changes were made, and
+do not use the weights or derivatives for commercial purposes. No warranties
+are provided. This weight license does not change the Apache License 2.0 that
+applies to the source code, and it does not grant rights to third-party data,
+atlases, templates, trademarks, or clinical use.
+
+Copyright 2026 OmniMIRA authors.

omnimira-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: omnimira
+Version: 0.2.0
+Summary: OmniMIRA: per-ROI universal brain feature space
+License-Expression: Apache-2.0
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: MODEL_LICENSE.md
+License-File: THIRD_PARTY_NOTICES.md
+Requires-Dist: torch>=2.0
+Requires-Dist: numpy>=1.23
+Requires-Dist: nibabel>=5.0
+Requires-Dist: scipy>=1.10
+Requires-Dist: pyyaml>=6.0
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.5; extra == "viz"
+Provides-Extra: demo
+Requires-Dist: matplotlib>=3.5; extra == "demo"
+Requires-Dist: gradio>=4.0; extra == "demo"
+Requires-Dist: nilearn>=0.10; extra == "demo"
+Dynamic: license-file
+
+# OmniMIRA
+
+### An anatomically indexed foundation model across structural, molecular and metabolic neuroimaging
+
+OmniMIRA learns brain-region representations from T1-weighted MRI, amyloid PET, FDG PET and CT. It combines local image features within atlas-defined regions, allowing the same embeddings to be used for downstream prediction and regional analysis.
+
+## Release status
+
+Version 0.2 provides the OmniMIRA v9 inference architecture, its multi-atlas resources and an epoch-1000 checkpoint. It produces anatomically indexed features and is intended for research use, not clinical diagnosis.
+
+## Installation
+
+Requires Python 3.9 or later and PyTorch 2.0 or later.
+
+```bash
+pip install omnimira
+```
+
+## Usage
+
+The wheel contains the checkpoint, model-space templates and atlas definitions. Input NIfTI images must already be spatially normalized to MNI space. The package resamples them to the committed model grid and applies modality-specific intensity normalization.
+
+```python
+from omnimira import from_pretrained
+
+model = from_pretrained(device="cpu")
+features = model.extract("scan_mni.nii.gz", modality="t1")
+print(features["aal3"].shape)  # (166, 128)
+```
+
+The command-line interface writes an NPZ with ROI identifiers, names and features:
+
+```bash
+omnimira scan_mni.nii.gz features.npz --modality t1
+```
+
+The output contains 128-dimensional embeddings for each region: 166 AAL3 regions, 69 Harvard–Oxford regions and 7 Yeo networks.
+
+The modality options are `t1` (T1-weighted MRI), `av45` (amyloid PET), `fdg` (FDG PET) and `ct` (CT).
+
+## Documentation
+
+- [Input preparation](docs/input_preparation.md)
+- [Atlas setup](docs/atlas_setup.md)
+- [Output format](docs/output_format.md)
+- [Model architecture](docs/model_architecture.md)
+- [Pretraining](docs/training.md)
+
+## Tests
+
+Model and loss tests use synthetic inputs:
+
+```bash
+pip install pytest
+python -m pytest -q tests/test_model_forward.py tests/test_losses.py
+```
+
+The full test suite also requires the atlas and template files.
+
+## Questions
+
+For questions about the code, please [open an issue](https://github.com/YixinChen-AI/MIRA-Brain-FM/issues).
+
+## License
+
+Source code is available under the [Apache 2.0 license](LICENSE). The bundled pretrained model weights are licensed separately under [CC BY-NC 4.0](MODEL_LICENSE.md), which does not permit commercial use. Third-party resources have [separate terms](THIRD_PARTY_NOTICES.md).
+
+For research use only; not for clinical diagnosis.

omnimira-0.2.0/README.md

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+# OmniMIRA
+
+### An anatomically indexed foundation model across structural, molecular and metabolic neuroimaging
+
+OmniMIRA learns brain-region representations from T1-weighted MRI, amyloid PET, FDG PET and CT. It combines local image features within atlas-defined regions, allowing the same embeddings to be used for downstream prediction and regional analysis.
+
+## Release status
+
+Version 0.2 provides the OmniMIRA v9 inference architecture, its multi-atlas resources and an epoch-1000 checkpoint. It produces anatomically indexed features and is intended for research use, not clinical diagnosis.
+
+## Installation
+
+Requires Python 3.9 or later and PyTorch 2.0 or later.
+
+```bash
+pip install omnimira
+```
+
+## Usage
+
+The wheel contains the checkpoint, model-space templates and atlas definitions. Input NIfTI images must already be spatially normalized to MNI space. The package resamples them to the committed model grid and applies modality-specific intensity normalization.
+
+```python
+from omnimira import from_pretrained
+
+model = from_pretrained(device="cpu")
+features = model.extract("scan_mni.nii.gz", modality="t1")
+print(features["aal3"].shape)  # (166, 128)
+```
+
+The command-line interface writes an NPZ with ROI identifiers, names and features:
+
+```bash
+omnimira scan_mni.nii.gz features.npz --modality t1
+```
+
+The output contains 128-dimensional embeddings for each region: 166 AAL3 regions, 69 Harvard–Oxford regions and 7 Yeo networks.
+
+The modality options are `t1` (T1-weighted MRI), `av45` (amyloid PET), `fdg` (FDG PET) and `ct` (CT).
+
+## Documentation
+
+- [Input preparation](docs/input_preparation.md)
+- [Atlas setup](docs/atlas_setup.md)
+- [Output format](docs/output_format.md)
+- [Model architecture](docs/model_architecture.md)
+- [Pretraining](docs/training.md)
+
+## Tests
+
+Model and loss tests use synthetic inputs:
+
+```bash
+pip install pytest
+python -m pytest -q tests/test_model_forward.py tests/test_losses.py
+```
+
+The full test suite also requires the atlas and template files.
+
+## Questions
+
+For questions about the code, please [open an issue](https://github.com/YixinChen-AI/MIRA-Brain-FM/issues).
+
+## License
+
+Source code is available under the [Apache 2.0 license](LICENSE). The bundled pretrained model weights are licensed separately under [CC BY-NC 4.0](MODEL_LICENSE.md), which does not permit commercial use. Third-party resources have [separate terms](THIRD_PARTY_NOTICES.md).
+
+For research use only; not for clinical diagnosis.

omnimira-0.2.0/THIRD_PARTY_NOTICES.md

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+# Third-party resources
+
+The repository code is offered under Apache License 2.0 as stated in
+`LICENSE`. The OmniMIRA pretrained checkpoint is offered separately under
+CC BY-NC 4.0 as stated in `MODEL_LICENSE.md`. Neither license automatically
+grants rights to atlas data, upstream datasets, or other third-party assets.
+
+| Asset | Source/version | SHA256 | Redistribution status |
+|---|---|---|---|
+| AAL3v1 label volume | AAL3v1, Rolls et al. 2020, NITRC AAL project | `aa44bb1767594f560e811cd917fee5833c2f843b81a8febd614db20284b11a34` | Unverified |
+| AAL3v1 labels | internal label export corresponding to AAL3v1 | `5c643d5bef449948af5d92f116cc2eeb670777a500882ce6e523a033837ffd08` | Unverified |
+| Harvard-Oxford-69 | derived from FSL Harvard-Oxford cortical and subcortical max-probability atlases through nilearn | `9ad6acc55d44c988bf30e997737d20aa6b94453624f4669bdad39f3a7a104e2e` | FSL documents Harvard--Oxford under CC BY-SA 4.0; attribution and derivative distribution review remains open |
+| Yeo-7-Network | Yeo et al. 2011 7-network parcellation obtained through nilearn | `5b13f9eebcfdb103455a4a424f762f936a2df1c4c185ae3726f4eff68e3cf1a7` | Upstream redistribution terms unverified |
+
+Raw third-party atlas images are not distributed in the Python package. The
+package contains a compact model-space ROI membership contract and reference
+grids needed to reproduce model inference; these do not include source cohort
+images or upstream training data.
+
+The file versions required by the implementation are listed in
+[Atlas setup](docs/atlas_setup.md). The hashes identify those versions;
+they do not grant permission to redistribute the files.

omnimira-0.2.0/omnimira/__init__.py

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+"""OmniMIRA — per-ROI universal brain feature space."""
+from omnimira.models.omnimira import OmniMIRA, HeadSpec, HEAD_FAMILIES
+from omnimira.inference import (
+    extract_roi_features,
+    load_omnimira,
+    save_roi_features,
+    source_metadata,
+    validate_source_metadata,
+)
+from omnimira.atlas import AtlasMeta, build_patch_to_roi_lookup
+from omnimira.io import load_volume
+from omnimira.pretrained import OmniMIRAExtractor, from_pretrained
+from omnimira.losses import OmniMIRALoss, LOSS_REGISTRY
+
+__all__ = [
+    "OmniMIRA", "HeadSpec", "HEAD_FAMILIES",
+    "load_omnimira", "extract_roi_features", "save_roi_features",
+    "source_metadata", "validate_source_metadata",
+    "AtlasMeta", "build_patch_to_roi_lookup",
+    "load_volume",
+    "OmniMIRAExtractor", "from_pretrained",
+    "OmniMIRALoss", "LOSS_REGISTRY",
+]
+__version__ = "0.2.0"