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<!DOCTYPE html>
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<head>
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<meta name="description" content="Andrew Hoopes Publications">
<meta name="authors" content="Andrew Hoopes">
<meta name="keywords" content="FreeSurfer, Brain, MRI, Neuroimaging, Biomedical Imaging, Cortical, Cortex, Segmentation, Registration, Skullstrip, Andrew Hoopes, HyperMorph, Deep Learning, Machine Learning, Surface Reconstruction, Mesh, Graph Convolution, Geometric Deep Learning">
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<title>Andrew Hoopes</title>
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<h1 class="mt-5" style="line-height: 1.5em; padding-top: 0; margin-bottom: 0;">Andrew Hoopes</h1>
<p style="line-height: 1.2em; margin-bottom: 0; padding-top: 0; color: gray;">PhD Student, Computer Science & Artificial Intelligence Lab, EECS, MIT</p>
<p style="line-height: 1.5em; margin-bottom: 0; padding-top: 0; color: gray;">Martinos Center for Biomedical Imaging, Massachusetts General Hospital</p>
<div style="line-height: 1.5em; margin-bottom: 0; padding-top: 0; color: lightgray;">
<a href="https://github.com/ahoopes" class="header-link-button" style="padding-right: 4px;">GitHub</a>|
<a href="https://scholar.google.com/citations?user=_OVlcIUAAAAJ" class="header-link-button">Google Scholar</a>
</div>
<!-------------------------------- PUBLICATIONS -------------------------------->
<h4 style="margin-top: 35px;">Publications</h4>
<div class="paper">
<p style="margin-bottom: 0; line-height: 1.5;"><b>SynthStrip: Skull-Stripping for Any Brain Image</b></p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">Andrew Hoopes, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl*, Malte Hoffmann*</p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;"><em>NeuroImage 260, 119474. 2022.</em></p>
<div style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">
<a href="https://www.sciencedirect.com/science/article/pii/S1053811922005900" class="link-button">Paper</a>
<a href="https://surfer.nmr.mgh.harvard.edu/docs/synthstrip" class="link-button">Website</a>
</div>
</div>
<div class="paper">
<p style="margin-bottom: 0; line-height: 1.5;"><b>Learning the Effect of Registration Hyperparameters with HyperMorph</b></p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">Andrew Hoopes, Malte Hoffmann, Douglas Greve, John Guttag, Bruce Fischl, Adrian Dalca</p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;"><em>MELBA: Journal of Machine Learning for Biomedical Imaging. 2022.</em></p>
<div style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">
<a href="https://arxiv.org/pdf/2203.16680.pdf" class="link-button">Paper</a>
<a href="https://ahoopes.github.io/hypermorph" class="link-button">Website</a>
<a href="https://github.com/voxelmorph/voxelmorph/blob/dev/scripts/tf/train_hypermorph.py" class="link-button">Code</a>
</div>
</div>
<div class="paper">
<p style="margin-bottom: 0; line-height: 1.5;"><b>TopoFit: Rapid Reconstruction of Topologically-Correct Cortical Surfaces</b></p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">Andrew Hoopes, Juan Eugenio Iglesias, Bruce Fischl, Douglas Greve*, Adrian Dalca*</p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;"><em>In proceedings of MIDL: Medical Imaging with Deep Learning. 2022.</em></p>
<div style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">
<a href="https://openreview.net/pdf?id=-JiHeZNDY3a" class="link-button">Paper</a>
<a href="https://github.com/ahoopes/topofit" class="link-button">Code</a>
</div>
</div>
<div class="paper">
<p style="margin-bottom: 0; line-height: 1.5;"><b>Hypermorph: Amortized Hyperparameter Learning for Image Registration</b></p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">Andrew Hoopes, Malte Hoffmann, Bruce Fischl, John Guttag, and Adrian Dalca</p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;"><em>In proceedings of IPMI: International Conference on Information Processing and Medical Imaging, 12729, pp. 3-17. 2021.</em></p>
<div style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">
<a href="https://arxiv.org/pdf/2101.01035.pdf" class="link-button">Paper</a>
<a href="https://ahoopes.github.io/hypermorph" class="link-button">Website</a>
<a href="https://github.com/voxelmorph/voxelmorph/blob/dev/scripts/tf/train_hypermorph.py" class="link-button">Code</a>
</div>
</div>
<div class="paper">
<p style="margin-bottom: 0; line-height: 1.5;"><b>A Deep Learning Toolbox for Automatic Segmentation of Subcortical Limbic Structures from MRI Images</b></p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">Douglas Greve, Benjamin Billot, Devani Cordero, Andrew Hoopes, Malte Hoffmann, Adrian Dalca, Bruce Fischl, Juan Eugenio Iglesias, Jean Augustinack</p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;"><em>NeuroImage 244, 118610. 2021.</em></p>
<div style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">
<a href="https://www.sciencedirect.com/science/article/pii/S1053811921008831" class="link-button">Paper</a>
<a href="https://github.com/freesurfer/freesurfer/tree/dev/mri_sclimbic_seg" class="link-button">Code</a>
</div>
</div>
<div class="paper">
<p style="margin-bottom: 0; line-height: 1.5;"><b>A Longitudinal Method for Simultaneous Whole-Brain and Lesion Segmentation in Multiple Sclerosis</b></p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">Stefano Cerri, Andrew Hoopes, Douglas Greve, Mark Mühlau, Koen Van Leemput</p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;"><em>Machine Learning in Clinical Neuroimaging and Radiogenomics in Neuro-oncology, pp. 119-128. 2020.</em></p>
<div style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">
<a href="https://arxiv.org/abs/2008.05117.pdf" class="link-button">Paper</a>
</div>
</div>
<div class="paper">
<p style="margin-bottom: 0; line-height: 1.5;"><b>PSACNN: Pulse Sequence Adaptive Fast Whole Brain Segmentation</b></p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">Amod Jog, Andrew Hoopes, Douglas Greve, Koen Van Leemput, Bruce Fischl</p>
<p style="margin-bottom: 0; padding-top: 0; line-height: 1.5;"><em>NeuroImage 199, 553-569. 2019.</em></p>
<div style="margin-bottom: 0; padding-top: 0; line-height: 1.5;">
<a href="https://arxiv.org/abs/1901.05992.pdf" class="link-button">Paper</a>
<a href="https://github.com/freesurfer/freesurfer/tree/dev/psacnn_brain_segmentation" class="link-button">Code</a>
</div>
</div>
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