Cape Town - 2026 ISMRM-ISMRT Annual Meeting and Exhibition
9 May 2026 – 14 May 2026 · Cape Town, South Africa
507-04-006 ISMRM Abstract

HypSeg: A Deep Learning Pipeline for Hypothalamic Subregion Segmentation Trained on High-Resolution 7 Tesla MRI

Primary: Analysis Methods - Segmentation and Detection
Secondary: Physics & Engineering - High-Field MRI
507-04-006 · Advanced Segmentation in MRI Across Scales and Domains · Wednesday, 13 May, 4:00 PM–5:50 PM · Meeting Room 1.40
Keywords: Segmentation Deep learning Hypothalamus 7T MRI NnU-Net
Accepted
Haihan Zhao1, William Salmon2, Jinghang Li2, Martina Bocchetta3, Rebecca Thurston4, Sossena Wood1, Tales Santini2, Tamer Ibrahim2
1Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, United States of America
2Bioengineering, University of Pittsburgh, Pittsburgh, United States of America
3The Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, United Kingdom
4Department of Psychiatry, University of Pittsburgh, Pittsburgh, United States of America
Presenting Author: Madison Lewis

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References

1. L. T. Tran, S. Park, S. K. Kim, J. S. Lee, K. W. Kim, and O. Kwon, “Hypothalamic control of energy expenditure and thermogenesis.,” Exp. Mol. Med., vol. 54, no. 4, pp. 358–369, Apr. 2022, doi: 10.1038/s12276-022-00741-z. [doi]
2. F. Isensee, P. F. Jaeger, S. A. A. Kohl, J. Petersen, and K. H. Maier-Hein, “nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation.,” Nat. Methods, vol. 18, no. 2, pp. 203–211, Feb. 2021, doi: 10.1038/s41592-020-01008-z. [doi]
3. B. Billot, M. Bocchetta, E. Todd, A. V. Dalca, J. D. Rohrer, and J. E. Iglesias, “Automated segmentation of the hypothalamus and associated subunits in brain MRI.,” NeuroImage, vol. 223, p. 117287, Dec. 2020, doi: 10.1016/j.neuroimage.2020.117287. [doi]
4. T. Santini, S. Wood, N. Krishnamurthy, T. Martins, H. J. Aizenstein, and T. S. Ibrahim, “Improved 7 Tesla transmit field homogeneity with reduced electromagnetic power deposition using coupled Tic Tac Toe antennas,” Sci. Rep., vol. 11, no. 1, Art. no. 1, Feb. 2021, doi: 10.1038/s41598-020-79807-9. [doi]
5. A. N. Sajewski et al., “RF shimming strategy for an open 60-channel RF transmit 7T MRI head coil for routine use on the single transmit mode.,” Magn. Reson. Med., vol. 94, no. 4, pp. 1804–1816, Oct. 2025, doi: 10.1002/mrm.30563. [doi]
6. A. Hoopes, J. S. Mora, A. V. Dalca, B. Fischl, and M. Hoffmann, “SynthStrip: skull-stripping for any brain image.,” NeuroImage, vol. 260, p. 119474, Oct. 2022, doi: 10.1016/j.neuroimage.2022.119474. [doi]
7. Y. Li et al., “Automatic Segmentation of Medial Temporal Lobe Subregions in Multi-Scanner, Multi-Modality Magnetic Resonance Imaging of Variable Quality.,” Hippocampus, vol. 35, no. 6, p. e70036, Nov. 2025, doi: 10.1002/hipo.70036. [doi]
8. M. Bocchetta et al., “Detailed volumetric analysis of the hypothalamus in behavioral variant frontotemporal dementia.,” J. Neurol., vol. 262, no. 12, pp. 2635–2642, Dec. 2015, doi: 10.1007/s00415-015-7885-2. [doi]

Cite this abstract

http://echo.ismrm.org/p/ISMRM2026/507-04-006