Ebrains Sibra Atlas Tool & DICOM Prepocessor #3
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agents/sibra_tool.py- SiibraAtlasTool wrappingsiibra-python(Julich-Brain v2.9). Takes the SAM3 binary mask centroid, converts pixel coordinates to MNI152 mm (via NIfTI affine → DICOM header → pixel fallback), and queries the EBRAINS probabilistic atlas to assign the lesion to a named cytoarchitectonic region (e.g. "Frontal-I (GapMap) left") with probability scores.agents/dicom_tool.py- DICOMPreprocessor that accepts a single .dcm slice or a full series directory, normalises pixel arrays to PNG (ready for CNN/MedGemma), selects the representative mid-slice from multi-slice series, and extracts DICOM header metadata (ImagePositionPatient, PixelSpacing, etc.) injected into NeuroimagingState.serialised in FHIR output. NeuroimagingState extended with atlas_enrichment,
dicom_metadata, anddicom_pathfields.utils/convert_h5.py- BraTS2020 h5-to-PNG+NIfTI converter. Stacks per-slice h5 files into a 3D volume with the known BraTS MNI152 affine, auto-selects the slice with most tumour content.tests/test_atlas_enrichment.py- Standalone test for the atlas node; supports PNG-only, PNG+NIfTI, PNG+DICOM inputs and--outputflag to save result JSON.