Shounak Nandi
Neuroimaging Researcher · MRI · Diffusion Imaging · Reproducible Pipelines
New York City, USA
I work on multi-modal MRI analysis with a focus on diffusion microstructure modeling, low-field and accessible MRI, and scalable neuroimaging pipelines on HPC systems.
Projects
NODDI-Bingham GPU pipeline
End-to-end diffusion MRI microstructure modeling pipeline with GPU acceleration and HPC scheduling for large-scale datasets (e.g., HCP-style acquisitions).
Low-field MRI texture biomarkers
Texture-based and volumetric analysis of subcortical structures to evaluate sensitivity of low-field MRI biomarkers in substance use disorder cohorts.
Multimodal MRI preprocessing & QC pipelines
Reproducible preprocessing and quality-control workflows for diffusion MRI, fMRI, ASL, and structural MRI using standardized neuroimaging toolchains.
Research Interests
- Diffusion MRI microstructure modeling (e.g., NODDI-Bingham)
- Low-field and accessible MRI
- Robust and reproducible neuroimaging pipelines (HPC, Slurm)
- Multimodal MRI preprocessing and quantitative biomarkers
- Statistical analysis and machine learning for neuroimaging
Education
M.Sc., Biomedical Engineering & Medical Physics
Technical University of Munich, Germany (2024)
B.Tech., Biomedical Engineering
Maulana Abul Kalam Azad University of Technology, India (2017)
Research & Professional Experience
Study Coordinator, Radiology
Albert Einstein College of Medicine, New York, USA (2024 – Present)
- Pre- and post-processing of diffusion MRI, fMRI, ASL, and structural MRI
- Development of scalable preprocessing pipelines using FSL, FreeSurfer, AFNI, ANTs, SPM, and DIPY
- Data curation, quality control, and HPC-based workflow automation
- Support for study protocols, regulatory documentation, and student mentoring
Visiting Scholar, Accessible MR Laboratory
Johns Hopkins University School of Medicine, USA (2024)
- Low-field MRI optimization and quantitative image analysis
- Volumetric and texture-based biomarker development
Associate Researcher I, Accessible MR Laboratory
Icahn School of Medicine at Mount Sinai, USA (2023)
- MRI preprocessing and segmentation using FSL, FreeSurfer, and ANTs
- Support for spectroscopy localization and analysis
Student Research Assistant, Interdisciplinary Research Lab
Technical University of Munich, Germany (2022)
- PET–MR DICOM sorting automation and image registration
- Optical tracking calibration using Python and C++
Publications
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Nandi S, Poojar P, Taufique S, et al.
Magnetic Resonance Imaging textural changes are more sensitive than volumetric changes in the amygdala of cocaine use disorder patients.
NMR in Biomedicine, 2026.
https://doi.org/10.1002/nbm.70193 -
McKenna FF, Nandi S, et al.
Microvascular and microstructural brain abnormalities in pediatric hematologic cancer survivors.
British Journal of Haematology, 2025.
(Co-first author)
https://doi.org/10.1111/bjh.70300
Conference Presentations (Selected)
- ISMRM 2024, Singapore — Texture-based biomarkers in cocaine use disorder (Poster)
- ISMRM 2024 — MRI4ALL Hackathon: open-source ultra-low-field MRI (Oral)
- ISMRM Workshop on Accessible MRI 2024 — Low-field translation of texture biomarkers (Poster)
Technical Skills
- Programming: Python, C++, MATLAB, R, SQL, Bash, LaTeX
- Neuroimaging: FSL, FreeSurfer, AFNI, ANTs, SPM, DIPY
- Tools: Git, Conda, VS Code, PyCharm, HPC, Slurm
- Systems: Linux, macOS, Windows
Awards
- ISMRM Trainee Stipend, 2024
- TUM Conference Travel Award (1000 Euros)
- JIS College Blue 2017 (Best Student Award), JIS College of Engineering
- JIS Samman (Departmental Topper), 2015–2016