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Vivek Gopalakrishnan

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NeurIPS Conference 2025 Conference Paper

PolyPose: Deformable 2D/3D Registration via Polyrigid Transformations

  • Vivek Gopalakrishnan
  • Neel Dey
  • Polina Golland

Determining the 3D pose of a patient from a limited set of 2D X-ray images is a critical task in interventional settings. While preoperative volumetric imaging (e. g. , CT and MRI) provides precise 3D localization and visualization of anatomical targets, these modalities cannot be acquired during procedures, where fast 2D imaging (X-ray) is used instead. To integrate volumetric guidance into intraoperative procedures, we present PolyPose, a simple and robust method for deformable 2D/3D registration. PolyPose parameterizes complex 3D deformation fields as a composition of rigid transforms, leveraging the biological constraint that individual bones do not bend in typical motion. Unlike existing methods that either assume no inter-joint movement or fail outright in this under-determined setting, our polyrigid formulation enforces anatomically plausible priors that respect the piecewise-rigid nature of human movement. This approach eliminates the need for expensive deformation regularizers that require patient- and procedure-specific hyperparameter optimization. Across extensive experiments on diverse datasets from orthopedic surgery and radiotherapy, we show that this strong inductive bias enables PolyPose to successfully align the patient's preoperative volume to as few as two X-rays, thereby providing crucial 3D guidance in challenging sparse-view and limited-angle settings where current registration methods fail. Additional visualizations, tutorials, and code are available at https: //polypose. csail. mit. edu.

YNIMG Journal 2020 Journal Article

Variability and heritability of mouse brain structure: Microscopic MRI atlases and connectomes for diverse strains

  • Nian Wang
  • Robert J. Anderson
  • David G. Ashbrook
  • Vivek Gopalakrishnan
  • Youngser Park
  • Carey E. Priebe
  • Yi Qi
  • Rick Laoprasert

Genome-wide association studies have demonstrated significant links between human brain structure and common DNA variants. Similar studies with rodents have been challenging because of smaller brain volumes. Using high field MRI (9. 4 T) and compressed sensing, we have achieved microscopic resolution and sufficiently high throughput for rodent population studies. We generated whole brain structural MRI and diffusion connectomes for four diverse isogenic lines of mice (C57BL/6J, DBA/2J, CAST/EiJ, and BTBR) at spatial resolution 20, 000 times higher than human connectomes. We measured narrow sense heritability (h2 ) I. e. the fraction of variance explained by strains in a simple ANOVA model for volumes and scalar diffusion metrics, and estimates of residual technical error for 166 regions in each hemisphere and connectivity between the regions. Volumes of discrete brain regions had the highest mean heritability (0. 71 ± 0. 23 SD, n = 332), followed by fractional anisotropy (0. 54 ± 0. 26), radial diffusivity (0. 34 ± 0. 022), and axial diffusivity (0. 28 ± 0. 19). Connection profiles were statistically different in 280 of 322 nodes across all four strains. Nearly 150 of the connection profiles were statistically different between the C57BL/6J, DBA/2J, and CAST/EiJ lines. Microscopic whole brain MRI/DTI has allowed us to identify significant heritable phenotypes in brain volume, scalar DTI metrics, and quantitative connectomes.

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