Eleftherios Garyfallidis

Shreyas Fadnavis, Jens Sjölund, Anders Eklund et al.

Diffusion MRI (dMRI) is the only non-invasive technique sensitive to tissue micro-architecture, which can, in turn, be used to reconstruct tissue microstructure and white matter pathways. The accuracy of such tasks is hampered by the low signal-to-noise ratio in dMRI. Today, the noise is characterized mainly by visual inspection of residual maps and estimated standard deviation. However, it is hard to estimate the impact of noise on downstream tasks based only on such qualitative assessments. To address this issue, we introduce a novel metric, Noise Uncertainty Quantification (NUQ), for quantitative image quality analysis in the absence of a ground truth reference image. NUQ uses a recent Bayesian formulation of dMRI models to estimate the uncertainty of microstructural measures. Specifically, NUQ uses the maximum mean discrepancy metric to compute a pooled quality score by comparing samples drawn from the posterior distribution of the microstructure measures. We show that NUQ allows a fine-grained analysis of noise, capturing details that are visually imperceptible. We perform qualitative and quantitative comparisons on real datasets, showing that NUQ generates consistent scores across different denoisers and acquisitions. Lastly, by using NUQ on a cohort of schizophrenics and controls, we quantify the substantial impact of denoising on group differences.

Sreekar Chigurupati, Eleftherios Garyfallidis

We present SuCor, a method for correcting susceptibility induced geometric distortions in echo planar imaging (EPI) using optimal transport (OT) along the phase encoding direction. Given a pair of reversed phase encoding EPI volumes, we model each column of the distortion field as a Wasserstein-2 barycentric displacement between the opposing-polarity intensity profiles. Regularization is performed in the spectral domain using a bending-energy penalty whose strength is selected automatically via the Morozov discrepancy principle, requiring no manual tuning. On a human connectome project (HCP) dataset with left-right/right-left b0 EPI pairs and a co-registered T1 structural reference, SuCor achieves a mean volumetric mutual information of 0.341 with the T1 image, compared to 0.317 for FSL TOPUP, while running in approximately 12 seconds on a single CPU core.

Jong Sung Park, Shreyas Fadnavis, Eleftherios Garyfallidis

Brain extraction is one of the first steps of pre-processing 3D brain MRI data and a prerequisite for any forthcoming brain imaging analyses. However, it is not a simple segmentation problem due to the complex structure of the brain and human head. Although multiple solutions have been proposed in the literature, we are still far from having truly robust methods. While previous methods have used machine learning with structural/geometric priors, with the development of Deep Learning (DL), there has been an increase in proposed Neural Network architectures. Most models focus on improving the training data and loss functions with little change in the architecture. However, the amount of accessible training data with expert-labelled ground truth vary between groups. Moreover, the labels are created not from scratch but from outputs of non-DL methods. Thus, most DL method's performance depend on the amount and quality of data one has. In this paper, we propose a novel architecture we call EVAC+ to work around this issue. We show that EVAC+ has 3 major advantages compared to other networks: (1) Multi-scale input with limited random augmentation for efficient learning, (2) a unique way of using Conditional Random Fields Recurrent Layer and (3) a loss function specifically created to enhance this architecture. We compare our model to state-of-the-art non-DL and DL methods. Results show that even with little change in the traditional architecture and limited training resources, EVAC+ achieves a high and stable Dice Coefficient and Jaccard Index along with a desirable lower surface distance. Ultimately, our model provides a robust way of accurately reducing segmentation errors in complex multi-tissue interfacing areas of brain.

Mohamed Abouagour, Eleftherios Garyfallidis

Automated floor plan generation lies at the intersection of combinatorial search, geometric constraint satisfaction, and functional design requirements -- a confluence that has historically resisted a unified computational treatment. While recent deep learning approaches have improved the state of the art, they often struggle to capture architectural reasoning: the precedence of topological relationships over geometric instantiation, the propagation of functional constraints through adjacency networks, and the emergence of circulation patterns from local connectivity decisions. To address these fundamental challenges, this paper introduces GFLAN, a generative framework that restructures floor plan synthesis through explicit factorization into topological planning and geometric realization. Given a single exterior boundary and a front-door location, our approach departs from direct pixel-to-pixel or wall-tracing generation in favor of a principled two-stage decomposition. Stage A employs a specialized convolutional architecture with dual encoders -- separating invariant spatial context from evolving layout state -- to sequentially allocate room centroids within the building envelope via discrete probability maps over feasible placements. Stage B constructs a heterogeneous graph linking room nodes to boundary vertices, then applies a Transformer-augmented graph neural network (GNN) that jointly regresses room boundaries.

Juhyung Ha, Jong Sung Park, David Crandall et al.

Medical image translation is the process of converting from one imaging modality to another, in order to reduce the need for multiple image acquisitions from the same patient. This can enhance the efficiency of treatment by reducing the time, equipment, and labor needed. In this paper, we introduce a multi-resolution guided Generative Adversarial Network (GAN)-based framework for 3D medical image translation. Our framework uses a 3D multi-resolution Dense-Attention UNet (3D-mDAUNet) as the generator and a 3D multi-resolution UNet as the discriminator, optimized with a unique combination of loss functions including voxel-wise GAN loss and 2.5D perception loss. Our approach yields promising results in volumetric image quality assessment (IQA) across a variety of imaging modalities, body regions, and age groups, demonstrating its robustness. Furthermore, we propose a synthetic-to-real applicability assessment as an additional evaluation to assess the effectiveness of synthetic data in downstream applications such as segmentation. This comprehensive evaluation shows that our method produces synthetic medical images not only of high-quality but also potentially useful in clinical applications. Our code is available at github.com/juhha/3D-mADUNet.

Mohamed Abouagour, Eleftherios Garyfallidis

We introduce ResPlan, a large-scale dataset of 17,000 detailed, structurally rich, and realistic residential floor plans, created to advance spatial AI research. Each plan includes precise annotations of architectural elements (walls, doors, windows, balconies) and functional spaces (such as kitchens, bedrooms, and bathrooms). ResPlan addresses key limitations of existing datasets such as RPLAN (Wu et al., 2019) and MSD (van Engelenburg et al., 2024) by offering enhanced visual fidelity and greater structural diversity, reflecting realistic and non-idealized residential layouts. Designed as a versatile, general-purpose resource, ResPlan supports a wide range of applications including robotics, reinforcement learning, generative AI, virtual and augmented reality, simulations, and game development. Plans are provided in both geometric and graph-based formats, enabling direct integration into simulation engines and fast 3D conversion. A key contribution is an open-source pipeline for geometry cleaning, alignment, and annotation refinement. Additionally, ResPlan includes structured representations of room connectivity, supporting graph-based spatial reasoning tasks. Finally, we present comparative analyses with existing benchmarks and outline several open benchmark tasks enabled by ResPlan. Ultimately, ResPlan offers a significant advance in scale, realism, and usability, providing a robust foundation for developing and benchmarking next-generation spatial intelligence systems.

Shreyas Fadnavis, Hamza Farooq, Maryam Afzali et al.

Fitting multi-exponential models to Diffusion MRI (dMRI) data has always been challenging due to various underlying complexities. In this work, we introduce a novel and robust fitting framework for the standard two-compartment IVIM microstructural model. This framework provides a significant improvement over the existing methods and helps estimate the associated diffusion and perfusion parameters of IVIM in an automatic manner. As a part of this work we provide capabilities to switch between more advanced global optimization methods such as simplicial homology (SH) and differential evolution (DE). Our experiments show that the results obtained from this simultaneous fitting procedure disentangle the model parameters in a reduced subspace. The proposed framework extends the seminal work originated in the MIX framework, with improved procedures for multi-stage fitting. This framework has been made available as an open-source Python implementation and disseminated to the community through the DIPY project.

Mohamed Abouagour, Atharva Shah, Eleftherios Garyfallidis

Diffusion MRI microstructure fitting is nonconvex and often performed voxelwise, which limits fiber peak recovery in narrow crossings. This work introduces PRISM, a differentiable analysis-by-synthesis framework that fits an explicit multi-compartment forward model end-to-end over spatial patches. The model combines cerebrospinal fluid (CSF), gray matter, up to K white-matter fiber compartments (stick-and-zeppelin), and a restricted compartment, with explicit fiber directions and soft model selection via repulsion and sparsity priors. PRISM supports a fast MSE objective and a Rician negative log-likelihood (NLL) that jointly learns sigma without oracle information. A lightweight nuisance calibration module (smooth bias field and per-measurement scale/offset) is included for robustness and regularized to identity in clean-data tests. On synthetic crossing-fiber data (SNR=30; five methods, 16 crossing angles), PRISM achieves 3.5 degrees best-match angular error with 95% recall, which is 1.9x lower than the best baseline (MSMT-CSD, 6.8 degrees, 83% recall); in NLL mode with learned sigma, error drops to 2.3 degrees with 99% recall, resolving crossings down to 20 degrees. On the DiSCo1 phantom (NLL mode), PRISM improves connectivity correlation over CSD baselines at all four tracking angles (best r=.934 at 25 degrees vs. .920 for MSMT-CSD). Whole-brain HCP fitting (~741k voxels, MSE mode) completes in ~12 min on a single GPU with near-identical results across random seeds.

Nancy R. Newlin, Kurt Schilling, Serge Koudoro et al.

White matter alterations are increasingly implicated in neurological diseases and their progression. International-scale studies use diffusion-weighted magnetic resonance imaging (DW-MRI) to qualitatively identify changes in white matter microstructure and connectivity. Yet, quantitative analysis of DW-MRI data is hindered by inconsistencies stemming from varying acquisition protocols. There is a pressing need to harmonize the preprocessing of DW-MRI datasets to ensure the derivation of robust quantitative diffusion metrics across acquisitions. In the MICCAI-CDMRI 2023 QuantConn challenge, participants were provided raw data from the same individuals collected on the same scanner but with two different acquisitions and tasked with preprocessing the DW-MRI to minimize acquisition differences while retaining biological variation. Submissions are evaluated on the reproducibility and comparability of cross-acquisition bundle-wise microstructure measures, bundle shape features, and connectomics. The key innovations of the QuantConn challenge are that (1) we assess bundles and tractography in the context of harmonization for the first time, (2) we assess connectomics in the context of harmonization for the first time, and (3) we have 10x additional subjects over prior harmonization challenge, MUSHAC and 100x over SuperMUDI. We find that bundle surface area, fractional anisotropy, connectome assortativity, betweenness centrality, edge count, modularity, nodal strength, and participation coefficient measures are most biased by acquisition and that machine learning voxel-wise correction, RISH mapping, and NeSH methods effectively reduce these biases. In addition, microstructure measures AD, MD, RD, bundle length, connectome density, efficiency, and path length are least biased by these acquisition differences.

Jong Sung Park, Juhyung Ha, Siddhesh Thakur et al.

While many skull stripping algorithms have been developed for multi-modal and multi-species cases, there is still a lack of a fundamentally generalizable approach. We present PUMBA(PUrely synthetic Multimodal/species invariant Brain extrAction), a strategy to train a model for brain extraction with no real brain images or labels. Our results show that even without any real images or anatomical priors, the model achieves comparable accuracy in multi-modal, multi-species and pathological cases. This work presents a new direction of research for any generalizable medical image segmentation task.

Eleftherios Garyfallidis, Shreyas Fadnavis, Jong Sung Park et al.

Clustering is a fundamental problem in machine learning where distance-based approaches have dominated the field for many decades. This set of problems is often tackled by partitioning the data into K clusters where the number of clusters is chosen apriori. While significant progress has been made on these lines over the years, it is well established that as the number of clusters or dimensions increase, current approaches dwell in local minima resulting in suboptimal solutions. In this work, we propose a new set of distance threshold methods called Theta-based Algorithms (ThetA). Via experimental comparisons and complexity analyses we show that our proposed approach outperforms existing approaches in: a) clustering accuracy and b) time complexity. Additionally, we show that for a large class of problems, learning the optimal threshold is straightforward in comparison to learning K. Moreover, we show how ThetA can infer the sparsity of datasets in higher dimensions.

Shreyas Fadnavis, Joshua Batson, Eleftherios Garyfallidis

Diffusion-weighted magnetic resonance imaging (DWI) is the only noninvasive method for quantifying microstructure and reconstructing white-matter pathways in the living human brain. Fluctuations from multiple sources create significant additive noise in DWI data which must be suppressed before subsequent microstructure analysis. We introduce a self-supervised learning method for denoising DWI data, Patch2Self, which uses the entire volume to learn a full-rank locally linear denoiser for that volume. By taking advantage of the oversampled q-space of DWI data, Patch2Self can separate structure from noise without requiring an explicit model for either. We demonstrate the effectiveness of Patch2Self via quantitative and qualitative improvements in microstructure modeling, tracking (via fiber bundle coherency) and model estimation relative to other unsupervised methods on real and simulated data.