M-Gaussian: An Magnetic Gaussian Framework for Efficient Multi-Stack MRI Reconstruction
Authors: Kangyuan Zheng, Xuan Cai, Jiangqi Wang, Guixing Fu, Zhuoshuo Li, Yazhou Chen, Xinting Ge, Liangqiong Qu, +1 more
Organizations: School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China. · the School of Information Science and Engineering, Shandong Normal University, Shandong, China. · School of Computing and Data Science, The University of Hong Kong, Hong Kong, China.
Magnetic Resonance Imaging (MRI) is a crucial non-invasive imaging modality. In routine clinical practice, multi-stack thick-slice acquisitions are widely used to reduce scan time and motion sensitivity, particularly in challenging scenarios such as fetal brain imaging. However, the resulting severe through-plane anisotropy compromises volumetric analysis and downstream quantitative assessment, necessitating robust reconstruction of isotropic high-resolution volumes. Implicit neural representation methods, while achieving high quality, suffer from computational inefficiency due to complex network structures. We present M-Gaussian, adapting 3D Gaussian Splatting to MRI reconstruction. Our contributions include: (1) Magnetic Gaussian primitives with physics-consistent volumetric rendering, (2) neural residual field for high-frequency detail refinement, and (3) multi-resolution progressive training. Our method achieves an optimal balance between quality and speed. On the FeTA dataset, M-Gaussian achieves 40.31 dB PSNR while being 14 times faster, representing the first successful adaptation of 3D Gaussian Splatting to multi-stack MRI reconstruction.
Figures & tables
Figure 1: Overview of the M-Gaussian framework. (a) The training pipeline integrates Gaussian rendering with a Neural Residual Field (NRF) refinement module. (b) Point cloud construction is performed via multi-stack registration and devoxelization to initialize the Gaussians. (c) The inference stage generates the final volume through Gaussian sampling and aggregation at the target resolution.
Figure 2: Comparison between original 3D Gaussian Splatting primitives and the proposed Magnetic Gaussian primitives. The original 3DGS utilizes view-dependent spherical harmonic coefficients for color representation, whereas M-Gaussian employs a single intensity value to model tissue-specific MRI signal properties, which significantly reduces memory overhead.
Methods
PSNR (dB) ↑
SSIM ↑
NCC ↑
NRMSE ↓
Runtime (min) ↓
FeTA Dataset
NiftyMIC [ 6 ]
36.08
0.9857
0.9932
0.0157
79.12
SVRTK [ 11 ]
34.64
0.9861
0.9916
0.0185
14.75
NeSVoR [ 17 ]
31.35
0.9588
0.9546
0.0414
31.75
M-Gaussian (Ours)
40.31
0.9936
0.9975
0.0096
5.63
FaBiAN Dataset
Table 1: Quantitative comparison with baseline slice-to-volume MRI reconstruction methods across three datasets. Metrics include PSNR, SSIM, NCC, and NRMSE for reconstruction quality, and runtime for computational efficiency. Best results are in bold , second-best are underlined .
Figure 3: Qualitative comparison of slice-to-volume MRI reconstruction methods. Each row shows results from a different dataset (FeTA, FaBiAN, HCP). The Input column displays one representative stack from the multi-stack acquisition. Our M-Gaussian method produces reconstructions with sharper anatomical boundaries and fewer artifacts compared to baseline methods.
Figure 4: Qualitative ablation results on Progressive resolution (P.R.) training and SSIM loss. Progressive resolution training stabilizes convergence, while the inclusion of SSIM loss significantly enhances the preservation of structural integrity and contrast. The effect is particularly significant on FeTA dataset.
Figure 5: Qualitative ablation results on Neural Residual Field (NRF). The NRF suppresses noise and refines high-frequency details, which is prominent on the HCP dataset.
Figure 6: Qualitative ablation results on Anisotropic Regularization (A.R.). The absence of A.R. leads to needle-like artifacts due to degenerate Gaussian geometries. These artifacts are effectively mitigated in the full model, which is most pronounced on the FaBiAN dataset.
Configuration
FeTA
FaBiAN
HCP
PSNR
SSIM
PSNR
SSIM
PSNR
SSIM
Full model
40.31
0.9936
32.26
0.9521
33.10
0.9776
w/o SSIM
32.24
0.9611
31.01
0.9388
32.56
0.9582
w/o SSIM & P.R.
31.07
0.9573
28.43
0.9272
31.36
0.9512
w/o NRF
39.11
0.9893
30.93
0.9387
31.96
0.9538
w/o A.R.
39.49
0.9902
30.02
0.9486
32.82
0.9606
Table 2: Ablation study quantifying the contribution of structural similarity loss (SSIM), progressive resolution training (P.R.), Neural Residual Field (NRF), and anisotropic regularization (A.R.).
Resolution
PSNR ↑
SSIM ↑
Time (min) ↓
503
30.27
0.9352
10.82
1503
31.31
0.9505
16.43
2503
31.50
0.9527
24.70
3503
31.76
0.9547
27.07
4003
31.63
0.9546
30.30
Table 3: Impact of Gaussian grid resolution on reconstruction fidelity and training time using the HCP dataset. The models were trained with fixed resolutions, excluding the effect of progressive training strategy.
Figure 10
Block Radius
PSNR ↑
SSIM ↑
Time (min) ↓
3
32.40
0.9733
7.62
4
32.67
0.9768
11.13
5
33.10
0.9776
17.28
6
32.77
0.9778
26.32
7
32.89
0.9780
34.24
Table 4: Quantitative assessment of reconstruction performance under different block radius settings. The results illustrate the trade-off between reconstruction quality and runtime.
Structure
Dice ↑
HD95 (mm) ↓
ASSD (mm) ↓
NiftyMIC
SVRTK
NeSVoR
M-Gaussian
NiftyMIC
SVRTK
NeSVoR
M-Gaussian
NiftyMIC
SVRTK
NeSVoR
M-Gaussian
External CSF
0.859
0.883
0.888
0.905
1.43
1.42
1.10
0.97
0.55
0.53
0.46
0.41
Grey Matter
0.832
0.816
0.843
0.846
0.82
0.85
0.68
0.66
0.37
0.38
0.34
0.32
White Matter
0.945
0.937
0.951
0.953
0.95
1.11
0.80
0.69
0.39
0.46
0.36
0.34
Ventricles
0.914
0.818
0.906
0.917
0.64
1.23
0.65
0.63
0.28
0.52
0.30
0.28
Cerebellum
0.924
0.934
0.941
0.931
1.12
0.94
0.87
1.05
0.46
0.40
0.36
0.42
Table 5: Quantitative evaluation of segmentation performance on the FeTA dataset. Metrics include Dice, HD95, and ASSD. Best results are bold , second-best are underlined .
Figure 9: Qualitative comparison of downstream segmentation results on the FeTA dataset. M-Gaussian reconstructions yield segmentation masks with the closest correspondence to ground truth, particularly for large-scale structures such as the cortical ribbon and ventricular boundaries.
High-resolution Magnetic Resonance Imaging (MRI) is vital for clinical diagnosis but limited by long acquisition times and motion artifacts. Super-resolution (SR) reconstructs low-resolution scans into high-resolution images, yet existing methods are mutually constrained: paired-data methods achieve efficiency only by relying on costly aligned datasets, while implicit neural representation approaches avoid such data needs at the expense of heavy computation. We propose a zero-shot MRI SR framework using explicit Gaussian representation to balance data requirements and efficiency. MRI-tailored Gaussian parameters embed tissue physical properties, reducing learnable parameters while preserving MR signal fidelity. A physics-grounded volume rendering strategy models MRI signal formation via normalized Gaussian aggregation. Additionally, a brick-based order-independent rasterization scheme enables highly parallel 3D computation, lowering training and inference costs. Experiments on two public MRI datasets show superior reconstruction quality and efficiency, demonstrating the method's potential for clinical MRI SR.
Shuting Liu, Lei Zhang, Wei Huang +2
School of Artificial Intelligence, Sichuan University, Chengdu 610065, China · Institute of High Performance Computing, A*STAR, Singapore 138632
Three-dimensional (3D) multi-contrast magnetic resonance imaging (MCMRI) provides rich anatomical and quantitative information but requires long acquisition times, motivating k-space undersampling. However, reconstruction of large volumetric datasets imposes substantial computational and memory demands. To address this challenge, we propose SGAM, a memory-efficient, scan-specific framework for joint full-volume 3D MCMRI reconstruction. SGAM is based on a shared-geometry Gaussian representation in which amplitudes are modeled by a multi-output implicit neural representation (INR) and contrast-specific phases by explicit variables. This design exploits common anatomical structure across contrasts while preserving contrast-specific signal variations. The representation is jointly optimized using only the acquired multi-coil k-space without external training data. Experiments showed that SGAM consistently outperformed the comparison methods across imaging tasks and acceleration factors, with greater improvements under stronger undersampling. SGAM also achieved a favorable balance between reconstruction quality and computational cost, demonstrating its effectiveness for 3D multi-contrast MRI reconstruction.
Jingran Xu, Dong Liang, Hairong Zheng +2
Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
Slice-based volumetric imaging is widely applied and it demands representations that compress aggressively while preserving internal structure for analysis. We introduce GaussianPile, unifying 3D Gaussian splatting with an imaging system-aware focus model to address this challenge. Our proposed method introduces three key innovations: (i) a slice-aware piling strategy that positions anisotropic 3D Gaussians to model through-slice contributions, (ii) a differentiable projection operator that encodes the finite-thickness point spread function of the imaging acquisition system, and (iii) a compact encoding and joint optimization pipeline that simultaneously reconstructs and compresses the Gaussian sets. Our CUDA-based design retains the compression and real-time rendering efficiency of Gaussian primitives while preserving high-frequency internal volumetric detail. Experiments on microscopy and ultrasound datasets demonstrate that our method reduces storage and reconstruction cost, sustains diagnostic fidelity, and enables fast 2D visualization, along with 3D voxelization. In practice, it delivers high-quality results in as few as 3 minutes, up to 11x faster than NeRF-based approaches, and achieves consistent 16x compression over voxel grids, offering a practical path to deployable compression and exploration of slice-based volumetric datasets.
Di Kong, Yikai Wang, Wenjie Guo +8
Tsinghua University · Zhongguancun Academy · Beijing Normal University +3