Three-dimensional multi-echo MRI provides rich anatomical and quantitative information, but repeated volumetric encoding prolongs acquisition and motivates k-space undersampling. Reconstructing undersampled multi-echo data requires exploiting shared anatomy while preserving echo-dependent signal variation; full-volume modeling also introduces substantial computational and memory demands. We propose MIGA, a scan-specific framework comprising shared anisotropic Gaussian geometry, a coordinate-conditioned multi-output amplitude network, and explicit echo-specific phase variables. The Gaussian geometry provides common spatial support across echoes, the implicit network models spatially structured amplitude variations, and the phase variables retain echo-specific complex signal information. All components are jointly optimized using only the acquired multi-coil k-space, requiring no fully sampled training data. Experiments showed that MIGA consistently outperformed the comparison methods across imaging tasks and acceleration factors, with larger improvements under stronger undersampling. MIGA also achieved a favorable quality-cost balance among the evaluated full-volume multi-echo methods. These results support the effectiveness of combining shared Gaussian geometry with implicit echo-dependent amplitude modeling for accelerated 3D multi-echo MRI reconstruction.

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