Publications

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On this page: peer reviewed papers · peer reviewed workshops · theses · books and proceedings

Peer Reviewed Publications

2026
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conference

Unified Brain Surface and Volume Registration.
M. Abulnaga, A. Hoopes, M. Hoffmann, R. Magnet, M. Ovsjanikov, L. Zollei, J. Guttag, B. Fisch^‡, A. V. Dalca^‡
ICLR: International Conference on Learning Representations. 2026.
[ published paper | arXiv preprint | Graphics x Science workshop, ACM SIGGRAPH Best Paper Award ]
conference

Deep infant brain segmentation from multi-contrast MRI.
M. Hoffmann, L. Zollei^‡, A. V. Dalca^‡
IEEE: Proc of Asilomar Conference on Signals, Systems, and Computers. pp. 974-981. 2026.
[ published paper | arXiv preprint ]
journal

The Brain Imaging and Neurophysiology Dataset of large-scale multimodal neural data.
C. Maschke, P. N. Hadar, Y. Zhang, J. Li, G. Ganjoo, A. Hoopes, A. Guazzo, A. Gupta, M. Ghanta, B. Nearing, C. T. Silvers, B. Gunapati, R. Thomas, J. A. Kim, S. S. Mukerji, A. V. Dalca, S. Zafar, A. D. Lam, E. Mignot & M. B. Westover
Nature Scientific Data. 13. Article 1176. 2026.
[ medRxiv preprint | Nature link ]
conference

GEMCONT: Genetics-based Multimodal Contrastive Learning Enhances Phenotypic embeddings and Boosts Genetic Discovery.
D. Sens, L. Shilova, A. V. Dalca, J. Schnabel, F. P. Casale
MIDL: Medical Imaging with Deep Learning. PMLR 315. pp. 3443-3463. 2026.
[ published paper | OpenReview ]
journal

Structural Connectome Analysis using a Graph-based Deep Model for Prediction of Non-Imaging Variables.
Kazi A, Mora J, Fischl B, A. V. Dalca, Aganj I
Frontiers in Neuroscience. 20. Article 1786355. 2026.
[ published paper ]
journal

AtlasMorph: Learning conditional deformable templates for brain MRI
M. Rakic, A. Hoopes, M. Abulnaga, M. Sabuncu, J. Guttag, A.V. Dalca.
MedIA: Medical Image Analysis. 110. 103893. 2026.
[ published paper | arXiv preprint ]
journal

Seamless neuroimaging visualization: The NiiVue wrapper ecosystem.
K. Eckstein, A. Androulakis, T. T. Dao, C. Drake, T. Hanayik, C. O’Reilly, C. Prahm, Z. Wang, P. Wighton, A. V. Dalca, S. Bollmann, C. Rorden
Aperture Neuro. 6. 2026.
[ published paper ]
journal

The Brain Tumor Sequence Registration (BraTS-Reg) Challenge for Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients.
B. Baheti, S. Chakrabarty, H. Akbari, M. Bilello, B. Wiestler, J. Schwarting, E. Calabrese, J. Rudie, S. Abidi, M. Mousa, J. Villanueva-Meyer, B. K. K. Fields, F. Kofler, R. T. Shinohara, J. E. Iglesias, T. C. W. Mok, A. C. S. Chung, M. Wodzinski, A. Jurgas, N. Marini, M. Atzori, H. Muller, C. Grobroehmer, H. Siebert, L. Hansen, M. P. Heinrich, L. Canalini, J. Klein, A. Gerken, S. Heldmann, A. Hering, H. K. Hahn, M. Meng, L. Bi, D. Feng, J. Kim, R. A. Zeineldin, M. E. Karar, F. Mathis-Ullrich, O. Burgert, J. Abderezaei, A. Pionteck, A. Chopra, M. Kurt, K. Yan, Y. Yan, Z. Tang, J. Ma, S. Almahfouz Nasser, N. C. Kurian, M. Meena, S. Shamsi, A. Sethi, N. J. Tustison, B. B. Avants, P. Cook, J. C. Gee, L. Tian, H. Greer, M. Niethammer, A. Hoopes, M. Hoffmann, A. V. Dalca, S. Christodoulidis, T. Estiene, M. Vakalopoulou, N. Paragios, D. S. Marcus, C. Davatzikos, A. Sotiras, B. Menze, S. Bakas, D. Waldmannstetter
Scientific Reports. 2026. In press.
[ arXiv preprint ]
2025
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conference

Pancakes: Consistent Multi-Protocol Image Segmentation Across Biomedical Domains.
M. Rakic, S. Gai, E. Chollet, J. Guttag, A. V. Dalca
NeurIPS: Advances in Neural Information Processing Systems. 38. pp. 47673-47708. 2025.
[ published paper | arXiv preprint ]
conference

MultiverSeg: Scalable Interactive Segmentation of Biomedical Imaging Datasets with In-Context Guidance.
H. Wong, J.J.G. Ortiz, J. Guttag, A. V. Dalca
ICCV: International Conference on Computer Vision. pp. 20966-20980. 2025.
[ published paper | arXiv preprint ]
journal

Supervision by Denoising.
S. I. Young, A. V. Dalca, E. Ferrante, P. Golland, C. A. Metzler, B. Fischl, J. E. Iglesias
IEEE TPAMI: Transactions on Pattern Analysis and Machine Intelligence -- ICCP Special Issue. 47(9). pp. 7279-7291. 2025.
[ published paper | arxiv ]
conference

MultiMorph: On-demand Atlas Construction.
M. Abulnaga, A. Hoopes, N. Dey, M. Hoffmann, B. Fischl, J. Guttag, A.V. Dalca
CVPR: Computer Vision and Pattern Recognition. pp. 30906-30917. 2025.
[ published paper | arxiv ]
journal

BrainMorph: A Foundational Keypoint Model for Robust and Flexible Brain MRI Registration .
A.Q. Wang, R. Saluja, H. Kim, X. He, A. V. Dalca, M. R. Sabuncu
MELBA: Machine Learning for Biomedical Imaging. 2025:010. pp. 181-203.
[ arXiv preprint | MELBA open access ]
conference

Learning General-purpose Biomedical Volume Representations using Randomized Synthesis.
N. Dey, B. Billot, H.E. Wong, C.J. Wang, M Ren, P. E. Grant, A.V. Dalca, P. Golland
ICLR: International Conference on Learning Representations. pp. 1-32. 2025.
[ published paper | arxiv ]
conference

Learning Accurate Rigid Registration for Longitudinal Brain MRI From Synthetic Data.
J. Fu, A.V. Dalca, B. Fischl, R. Moreno, M. Hoffmann
IEEE ISBI: International Symposium on Biomedical Imaging. pp. 1-5. 2025.
[ published paper | arxiv ]
2024
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conference

ScribblePrompt: Fast and Flexible Interactive Segmentation for Any Biomedical Image .
H. Wong, M. Rakic, J. Guttag, A. V. Dalca
ECCV: European Conference on Computer Vision. LNCS 15098. pp. 207-229. 2024.
[ published paper | arXiv preprint | website | CVPR-DCAMI Oral | CVPR-DCAMI Bench to Bedside Award ]
conference

Tyche: Stochastic In-Context Learning for Medical Image Segmentation.
M. Rakic, H. E. Wong, J. J. G. Ortiz, B. Cimini, J. Guttag, A. V. Dalca
CVPR: Computer Vision and Pattern Recognition. pp. 11159-11173. 2024.
[ published paper | arxiv | CVPR Highlight (2.8% of submissions) ]
conference

Magnitude Invariant Parametrizations Improve Hypernetwork Learning.
J.J.G. Ortiz, J. Guttag, A. V. Dalca
ICLR: International Conference on Learning Representations. pp. 1-20. 2024.
[ published paper | arxiv ]
journal

Anatomy-aware and acquisition-agnostic joint registration with SynthMorph.
M. Hoffmann, A. Hoopes, D.N. Greve, B. Fischl^‡, A.V. Dalca^‡,
Imaging Neuroscience. 2. pp. 1-33. 2024.
[ published paper | website | arXiv preprint ]
journal

JOSA: Joint surface-based registration and atlas construction of brain geometry and function.
J. Li, G. Tuckute, E. Fedorenko, B. L. Edlow, A. V. Dalca^‡, B. Fischl^‡
MedIA: Medical Image Analysis. 98. 103292. 2024.
[ published paper | arXiv preprint ]
journal

Synthetic data in generalizable, learning-based neuroimaging.
K. Gopinath, A. Hoopes, D.C. Alexander, S.E. Arnold, Y. Balbastre, B. Billot, A. Casamitjana, Y. Cheng, R.Y.Z. Chua, B.L. Edlow, B. Fischl, H. Gazula, M. Hoffmann, C.D. Keene, S. Kim, W.T. Kimberly, S. Laguna, K.E. Larson, K. Van Leemput, O. Puonti, L.M. Rodrigues, M.S. Rosen, H.F.J. Tregidgo, D. Varadarajan, S.I. Young, A. V. Dalca^‡, J.E. Iglesias^‡
Imaging Neuroscience. 2. pp. 1-22. 2024.
[ published paper ]
conference

AnyStar: Domain randomized universal star-convex 3D instance segmentation.
N. Dey, S.M. Abulnaga, B. Billot, E.A. Turk, P.E. Grant, A.V. Dalca, P. Golland
WACV: Winter Conference on Applications of Computer Vision. pp. 7593-7603. 2024.
[ published paper | arXiv preprint ]
conference

Boosting skull-stripping performance for pediatric brain images.
W. Kelley, N. Ngo, A.V. Dalca, B. Fischl, L. Zollei, M. Hoffmann
IEEE ISBI: International Symposium on Biomedical Imaging. pp. 1-5. 2024.
[ published paper | arXiv preprint ]
journal

Learning Task-Specific Strategies for Accelerated MRI.
Z. Wu, T. Yin, Y. Sun, S. Frost, A. van der Kouwe, A. V. Dalca, K. Bouman
IEEE TCI: Transactions on Computational Imaging. 10. pp. 1040-1054. 2024.
[ published paper | arXiv preprint ]
journal

Scaling behaviors of deep learning and linear algorithms for the prediction of stroke severity.
A. Bourached, A. K Bonkhoff, M. D. Schirmer, R. W. Regenhardt, M. Bretzner, S. Hong, A.V. Dalca, A.-K. Giese, S. Winzeck, C. Jern, A. G. Lindgren, J. Maguire, O. Wu, J. Rhee, E. Y. Kimchi, N. S. Rost
Brain Communications. 6(1):fcae007. 2024.
[ published paper ]
journal

Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology.
H Gazula, H Tregidgo, B Billot, Y Balbastre, J Williams-Ramirez, R Herisse, L Deden-Binder, A Casamitjana, E Melief, C Latimer, M Kilgore, M Montine, E Robinson, E Blackburn, M Marshall, T Connors, D Oakley, M Frosch, S Young, K Leemput, A.V. Dalca, B Fischl, C MacDonald, C Keene, B Hyman, Juan E Iglesias
eLife. 12. RP91398. 2024.
[ published paper ]
2023
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conference

Scale-Space Hypernetworks for Efficient Biomedical Image Analysis.
J.J.G. Ortiz, J. Guttag, A. V. Dalca
NeurIPS: Advances in Neural Information Processing Systems. 36. Pp 12760-12773. 2023.
[ published paper | arxiv ]
conference

UniverSeg: Universal Medical Image Segmentation.
V.I. Butoi*, J.J.G. Ortiz*, T.Ma, M.R. Sabuncu, J. Guttag, A. V. Dalca
ICCV: International Conference on Computer Vision. pp. 21381-21394. 2023.
[ published paper | arxiv | website | tutorial | code ]
conference

Neuralizer: Neuroimage Analysis without Re-Training.
S. Czolbe, A. V. Dalca
CVPR: Computer Vision and Pattern Recognition. pp. 6217-6230. 2023.
[ published paper | arXiv preprint ]
conference

Joint cortical registration of geometry and function using semi-supervised learning.
J. Li, G. Tuckute, E. Fedorenko, B. L. Edlow, B. Fischl^‡, A. V. Dalca^‡
MIDL: Medical Imaging with Deep Learning. PMLR 227. pp. 862-876. 2023.
[ published paper | arXiv preprint ]
conference

Anatomy-specific acquisition-agnostic affine registration learned from fictitious images.
M. Hoffmann, A. Hoopes, B. Fischl^‡, A. V. Dalca^‡
Proc. SPIE: Medical Imaging 2023: Image Processing. 12464. Article 1246402. 2023.
[ SPIE paper ]
conference

AngioMoCo: Learning-based Motion Correction in Digital Subtraction Angiography.
R. Su, P. van der Sluijs, S. Cornelissen, W. van Zwam, A. van der Lugt, W. Niessen, D. Ruijters, T. van Walsum, A. V. Dalca
MICCAI: Medical Image Computing and Computer-Assisted Intervention. LNCS 14226. Pp 770-780. 2023.
[ published paper | arXiv preprint ]
journal

SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining.
B. Billot, D. Greve, O. Puonti, A. Thielscher, K. Van Leemput, B. Fischl, A. V. Dalca, J. E. Iglesias
MedIA: Medical Image Analysis, 86. 102789. 2023.
[ paper | arXiv preprint ]
journal

A robust and interpretable deep learning framework for multi-modal registration via keypoints .
A. Q. Wang, E. M. Yu, A. V. Dalca M. R. Sabuncu
MedIA: Medical Image Analysis. 90. 102962. 2023.
[ published paper | arXiv preprint ]
journal

Hyper-Convolutions via Implicit Kernels for Medical Image Analysis.
T. Ma, A.Q. Wang, A. V. Dalca, M.R. Sabuncu
MedIA: Medical Image Analysis, 86. 102796. 2023.
[ published paper | arXiv preprint ]
conference

Data Consistent Deep Rigid MRI Motion Correction.
N. M. Singh, N. Dey, M. Hoffmann, B. Fischl, E. Adalsteinsson, R. Frost, A. V. Dalca, P. Golland
MIDL: Medical Imaging with Deep Learning. 227. pp. 368-381. 2023.
[ published paper | arXiv preprint | Oral Presentation | Best Presentation Award ]
journal

A cellular resolution atlas of Broca's area.
I. Costantini, L. Morgan, J. Yang, Y. Balbastre, et al (39 authors)
AAAS Science Advances. 9 (41). pp eadg3844 1-14. 2023.

[ published paper ]
journal

Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning.
A. Hering, L. Hansen, T. Mok, A. Chung, H. Siebert, S. Häger, . . . . ., A.V. Dalca, M. P. Heinrich.
IEEE TMI: Transactions on Medical Imaging, 42, (3), pp. 697-712, 2023.
[ published paper | arXiv preprint ]
2022
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conference

TopoFit: Rapid Reconstruction of Topologically-Correct Cortical Surfaces.
A. Hoopes, J. E. Iglesias, B. Fischl, D. Greve^‡, A. V. Dalca^‡
MIDL: Medical Imaging with Deep Learning. PMLR 172. pp 508-520. 2022.
[ Open Review | Oral Presentation ]
journal

SynthMorph: learning contrast-invariant registration without acquired images.
M. Hoffmann, B. Billot, D.N. Greve, J.E. Iglesias, B. Fischl, A.V. Dalca
IEEE TMI: Transactions on Medical Imaging. 41(3). pp. 543-558. 2022.
[ published paper | website | arXiv preprint | video ]
journal

Learning the Effect of Registration Hyperparameters with HyperMorph.
A. Hoopes, M. Hoffmann, D.N. Greve, B. Fischl, J. Guttag, A.V. Dalca
MELBA: Machine Learning for Biomedical Imaging. 2022:003. pp. 1-30.
[ published paper | arXiv preprint ]
conference

KeyMorph: Robust Multi-modal Affine Registration via Unsupervised Keypoint Detection .
E. M. Yu, A. Q. Wang, A. V. Dalca^‡ M. R. Sabuncu^‡
MIDL: Medical Imaging with Deep Learning. PMLR 172. pp 1482-1503. 2022.
[ Open Review | Oral Presentation ]
journal

Joint Frequency and Image Space Learning for MRI Reconstruction and Analysis.
N.M. Singh, J.E. Iglesias, E. Adalsteinsson, A.V. Dalca, P. Golland
MELBA: Machine Learning for Biomedical Imaging. 2022:018. pp. 1-28.
[ arXiv preprint | paper ]
journal

Computing Multiple Image Reconstructions with a Single Hypernetwork.
A.Q. Wang, A.V. Dalca, M. R. Sabuncu
MELBA: Machine Learning for Biomedical Imaging. 2022:017. pp. 1-25.
[ published paper | arXiv preprint ]
journal

SynthStrip: Skull-Stripping for Any Brain Image.
Andrew Hoopes, Jocelyn S. Mora, A.V. Dalca, Bruce Fischl ^‡, Malte Hoffmann ^‡
Neuroimage. 260. 119474. pp 1-13. 2022.
[ published paper | arXiv preprint | website | ^‡ equal contribution ]
journal

Learned iterative segmentation of highly variable anatomy from limited data: Applications to whole heart segmentation for congenital heart disease.
D. Pace, A.V. Dalca, T. Brosch, T.Geva, A.J. Powell, J. Weese, M.H. Moghari, P. Golland.
MedIA: Medical Image Analysis, 80, pp. 102469, 2022.
[ paper ]
journal

How Machine Learning is Powering Neuroimaging to Improve Brain Health .
N.M. Singh, J.B. Harrod, S. Subramanian, M. Robinson, K. Chang, S. Cetin-Karayumak, A.V. Dalca, S. Eickhoff, M. Fox, L. Franke, P. Golland, D. Haehn, J.E. Iglesias, L.J. O'Donnell, Y. Ou, Y. Rathi, S.H. Siddiqi, H. Sun, M.B. Westover, S. Whitfield-Gabrieli, R.L. Gollub
Neuroinformatics. 20(4):943–964, 2022.
[ published paper ]
journal

Augmenting existing deterioration indices with chest radiographs to predict clinical deterioration.
E. Mu, S. Jabbour, A. V. Dalca, J. Guttag, J. Wiens, M.W. Sjoding
Plos one. 17 (2), e0263922. 2022.
[ Paper ]
journal

Mapping the subcortical connectivity of the human default mode network.
J. Li, W.H. Curley, B. Guerin, D.D. Dougherty, A.V. Dalca, B. Fischl, A. Horn, B.L. Edlow.
Neuroimage. 245, 118758. 2021.
[ Paper ]
journal

Sex-specific lesion pattern of functional outcomes after stroke.
A Bonkhoff, M Bretzner, S Hong, M Schirmer, A Cohen, R Regenhardt, K Donahue, M Nardin, A.V. Dalca, et al (58 authors)
Brain Communications. 4(2). Article fcac020. 2022.
[ Paper ]
2021
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conference

HyperMorph: Amortized Hyperparameter Learning for Image Registration.
A. Hoopes, M. Hoffmann, B. Fischl, J. Guttag, A.V. Dalca
IPMI: Information Processing and Medical Imaging. 12729. pp. 3-17. 2021.
[ published paper | website | arXiv preprint | Oral Presentation (video) | Runner up: Erbsmann prize. ]
conference

Learning MRI contrast-agnostic registration.
M. Hoffmann, B. Billot, J.E. Iglesias, B. Fischl, A.V. Dalca
ISBI: International Symposium on Biomedical Imaging. pp. 899-903. 2021.
[ published paper | arXiv preprint | Oral Presentation (video) ]
conference

Hyper-Convolution Networks for Biomedical Image Segmentation.
T. Ma, A.V. Dalca, M. Sabuncu
WACV: Winter Conference on Applications of Computer Vision. pp. 1933-1942. 2022.
[ published paper | arXiv preprint ]
conference

Generative Adversarial Registration for Improved Conditional Deformable Templates.
N. Dey, M. Ren, A.V. Dalca, G. Gerig
ICCV: International Conference on Computer Vision. pp 3929-3941. 2021.
[ published paper | arXiv preprint ]
conference

End-to-End Sequential Sampling and Reconstruction for MR Imaging.
T. Yin, Z. Wu, H. Sun, A.V. Dalca, Y. Yue, K.L. Bouman
ML4H: Machine Learning for Health. PMLR 158:261-281. 2021.
[ published paper | arXiv preprint | Oral Presentation. | Best Paper Award. | website ]
conference

Learning to Predict with Supporting Evidence: Applications to Clinical Risk Prediction.
A. Raghu, J. Guttag, K. Young, E. Pomerantsev, A.V. Dalca, C. Stultz
ACM CHIL: Conference on Healthcare, Inference, and Learning. pp 95-104. 2021.
[ published paper | arXiv preprint ]
conference

Joint segmentation of Multiple Sclerosis lesions and brain anatomy in MRI scans of any contrast and resolution with CNNs.
B. Billot, S. Cerri, K. v. Leemput, A. V. Dalca J. E. Iglesias
ISBI: International Symposium on Biomedical Imaging. pp. 1971-1974. 2021.
[ published paper | Oral Presentation ]
journal

A Deep Learning Toolbox for Automatic Segmentation of Subcortical Limbic Structures from MRI Images.
D. N. Greve, B. Billot, D. Cordero, A. Hoopes, M. Hoffmann, A.V. Dalca, B. Fischl, J. E. Iglesias, J. C. Augustinack
NeuroImage. 244. 118610. 2021.
[ published paper ]
journal

MRI Radiomic signature of white matter hyperintensities is associated with clinical phenotypes.
M. Bretzner, AK Bonkhoff, MD Schirmer, S Hong, A. V. Dalca, KL Donahue et al (55 authors)
Frontiers Neuroscience. 15(691244). pp 1-11. 2021.
[ published paper ]
journal

Excessive White Matter Hyperintensity Increases Susceptibility to Poor Functional Outcomes After Acute Ischemic Stroke
S. Hong, Anne-K. Giese, M. D. Schirmer, A. K. Bonkhoff, M. Bretzner, P. Rist, A.V. Dalca, et al (56 authors)
Frontiers in Neurology. 12(7000616). pp 1-10. 2021.
[ Paper link ]
journal

Outcome after acute ischemic stroke is linked to sex-specific lesion patterns.
A. K. Bonkhoff, M. D. Schirmer, M. Bretzner, S. Hong, R. W. Regenhardt, M. Brudfors, K. L. Donahue, M. J. Nardin, A. V. Dalca, et al (62 authors)
Nature Communications. 12(3289). pp 1-14. 2021.
[ published paper ]
journal

Reliability and sensitivity of two whole-brain segmentation approaches included in FreeSurfer - ASEG and SAMSEG.
D. Sederevicius, D. Vidal-Pineiro, O. Sorensen, K. van Leemput, J. E. Iglesias, A. V. Dalca, D. N. Greve, B. Fischl, A. Bjornerud, K. B. Walhovd, A. M. Fjell
Neuroimage. 237. Article 118113. 2021.
[ published paper ]
2020
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conference

A Learning Strategy for Contrast-agnostic MRI Segmentation.
B. Billot, D. Greve, K. Van Leemput, B. Fischl, J. E. Iglesias^‡, A. V. Dalca^‡
MIDL: Medical Imaging with Deep Learning. PMLR 121. pp 75-93. 2020.
[ arXiv preprint | Oral Presentation | Open Review ]
conference

Painting Many Pasts: Synthesizing Time Lapse Videos of Paintings
A. Zhao, G. Balakrishnan, K. M. Lewis, F. Durand, J. Guttag, A.V. Dalca.
CVPR: Computer Vision and Pattern Recognition. pp. 8435-8445. 2020.
[ published paper | arXiv preprint | video | website | engaget ]
conference

Fast Learning-based Registration of Sparse 3D Clinical Images
K. Lewis, N, Rost, J. Guttag, A.V. Dalca
ACM CHIL: Conference on Healthcare, Inference, and Learning. pp 90-98. 2020.
[ published paper | arXiv preprint ]
journal

Cortical surface registration using unsupervised learning.
J. Cheng, A.V. Dalca, B. Fischl^‡, L. Zollei^‡.
Neuroimage. 221. Article 117161. 2020.
[ published paper | arXiv preprint ]
journal

Deep-learning-based Optimization of the Under-sampling Pattern in MRI
C. Bahadir^‡, A.Q. Wang^‡, A.V. Dalca, M.R. Sabuncu.
IEEE TCP: Transactions on Computational Imaging. 6. pp. 1139-1152. 2020.
[ published paper | arXiv preprint ]
conference

Partial Volume Segmentation of Brain MRI Scans of any Resolution and Contrast.
B. Billot, E.D. Robinson, A.V. Dalca, J.E. Iglesias
MICCAI: Medical Image Computing and Computer Assisted Intervention. LNCS 12267. pp 177-187. 2020.
[ published paper | arXiv preprint | Early Accept ]
conference

Learning a Probabilistic Strategy for Computational Imaging Sensor Selection
H. Sun, A.V. Dalca, K. Bouman
IEEE ICCP: International Conference on Computational Photography. pp. 1-12. 2020.
[ published paper | arXiv preprint | code ]
conference

An Auto-Encoder Strategy for Adaptive Image Segmentation.
E. M. Yu, J. E. Iglesias, A. V. Dalca, M. R. Sabuncu
MIDL: Medical Imaging with Deep Learning. PMLR 121. pp 881-891. 2020.
[ Spotlight | arXiv preprint | Open Review ]
journal

White matter hyperintensity burden in acute stroke patients differs by ischemic stroke subtype
A.K. Giese, M.D. Schirmer, A.V. Dalca, R. Sridharan, K. Donahue, M. Nardin, R. Irie, et al (34 authors)
Neurology. 95 (1). pp e79-e88. 2020.
[ Paper link ]
conference

3D reconstruction and segmentation of dissection photographs for MRI-free neuropathology
H Tregidgo, A Casamitjana, C Latimer, M Kilgore, N Robinson, E Blackburn, K Van Leemput, B Fischl, A.V. Dalca, C MacDonald, D Keene, JE Iglesias
MICCAI: Medical Image Computing and Computer Assisted Intervention. LNCS 12265. pp. 204-214. 2020.
[ published paper | arXiv preprint ]
journal

Automated segmentation of the Hypothalamus and associated subunits in brain MRI.
B. Billot, M. Bocchetta, E. Todd, A. V. Dalca, J.D. Rohrer, J. E. Iglesias
NeuroImage. 223. Article 117287. 2020.
[ published paper ]
journal

Multi-atlas image registration of clinical data with automated quality assessment using ventricle segmentation
F. Dubost, M. de Bruijne, M. Nardin, A. V. Dalca, K.L. Donahue, A-K Giese, et al (13 authors)
MedIA: Medical Image Analysis. 63. pp 101698. 2020.
[ published paper | arXiv preprint ]
journal

Diffusion Weighted Imaging, MR Angiography and Baseline Data in a Systematic Multi-Center Analysis of 3301 MRI Scans of Ischemic Stroke Patients - Neuroradiological review within the MRI-GENIE study
M. Drake et al (41 authors)
Frontiers in Neurology. 11. pp 577. 2020.
[ paper ]
journal

Detailed phenotyping of posterior vs. Anterior circulation ischemic stroke: a multi-center MRI study
P. Frid et al (44 authors)
Journal of Neurology. 267(3) pp 649-658. 2020.
[ published paper ]
journal

Brain volume: An important determinant of functional outcome after acute ischemic stroke
M.D. Schirmer, K.L. Donahue, M.J. Nardin, A.V. Dalca, A.K. Giese, M.R. Etherton, et al (41 authors)
Mayo Clinic Proceedings. 95(5). pp 955-965. 2020.
[ published paper | arXiv preprint ]
2019
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conference

Learning Conditional Deformable Templates with Convolutional Networks
A.V. Dalca, M. Rakic, J. Guttag, M.R. Sabuncu.
NeurIPS: Advances in Neural Information Processing Systems. 32. pp 804-816, 2019.
[ published paper | arXiv preprint ]
journal

Unsupervised Learning for Probabilistic Diffeomorphic Registration for Images and Surfaces
A.V. Dalca, G. Balakrishnan, J. Guttag, M.R. Sabuncu.
MedIA: Medical Image Analysis. (57). pp 226-236, 2019.
[ published paper | arXiv preprint ]
conference

Unsupervised deep learning for Bayesian brain MRI segmentation
A.V. Dalca, E Yu, P Golland, B Fischl, M R. Sabuncu, J E. Iglesias
MICCAI: Medical Image Computing and Computer Assisted Intervention. LNCS 11766. pp 356-365. 2019.
[ published paper | arXiv preprint ]
conference

Data Augmentation Using Learned Transformations for One-Shot Medical Image Segmentation
A. Zhao, G. Balakrishnan, F. Durand, J. Guttag, A.V. Dalca.
CVPR: Computer Vision and Pattern Recognition. pp 8543-8553. 2019.
[ published paper | arXiv preprint | Oral Presentation - video | paper | MIT News ]
journal

VoxelMorph: A Learning Framework for Deformable Medical Image Registration
G. Balakrishnan, A. Zhao, M. R. Sabuncu, J. Guttag, A.V. Dalca.
IEEE TMI: Transactions on Medical Imaging. 38(8). pp 1788-1800. 2019.
[ published paper | arXiv preprint | paper ]
conference

Learning-based Optimization of the Under-sampling Pattern in MRI
C. Bahadir A.V. Dalca, M.R. Sabuncu.
IPMI: Information Processing and Medical Imaging. LNCS 11492. pp 780-792. 2019.
[ published paper | arXiv preprint ]
journal

Medical Image Imputation from Image Collections
A.V. Dalca, K.L. Bouman, W.T. Freeman, N.S. Rost, M.R. Sabuncu, P. Golland.
IEEE TMI: Transactions on Medical Imaging, 38 (2), pp 504-514. 2019.
[ published paper | arXiv preprint | paper ]
conference

Visual Deprojection: Probabilistic Recovery of Collapsed Dimensions in Images and Videos
G. Balakrishnan, A.V. Dalca, A. Zhao, J. Guttag, F. Durand, W. T. Freeman.
ICCV: International Conference in Computer Vision. pp 171-180. 2019.
[ published paper | arXiv preprint ]
journal

White Matter Hyperintensity Quantification in Large-Scale Clinical Acute Ischemic Stroke Cohorts
M.D. Schirmer, A.V. Dalca, R. Sridharan, A.K. Giese, K.L. Donahue, M.J. Nardin, et al (34 authors)
Neuroimage: Clinical. 23. Article 101884. 2019.
[ published paper | biorxiv preprint ]
journal

Trends and Focus of Machine Learning Applications for Health Research
B. Beaulieu-Jones, S. G. Finlayson, C. Chivers, I. Chen, M. McDermott, J. Kandola, A.V. Dalca, A. Beam, M. Fiterau, T. Naumann
JAMA network open. 2(10). Article e1914051. 2019.
[ paper ]
2018
▴
conference

Unsupervised Learning for Fast Probabilistic Diffeomorphic Registration
A.V. Dalca, G. Balakrishnan, J. Guttag, M.R. Sabuncu.
MICCAI: Medical Image Computing and Computer Assisted Intervention. LNCS 11070, pp 729-738. 2018.
[ paper | code | news article | arXiv preprint ]
[ Publication Impact (Young Scientist) Award 2023 | Finalist: Best paper (young scientist) award | Early accept | Oral Presentation | Best Poster at MLIM | Finalist: Publication Impact (Young Scientist) Award 2022 ]
conference

Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation.
A.V. Dalca, J. Guttag, M. R. Sabuncu.
CVPR: Computer Vision and Pattern Recognition. pp 9290-9299. 2018.
[ published paper | arXiv preprint | paper | code ]
conference

An Unsupervised Learning Model for Deformable Medical Image Registration.
G. Balakrishnan, A. Zhao, M. R. Sabuncu, J. Guttag, A.V. Dalca.
CVPR: Computer Vision and Pattern Recognition. pp 9252-9260. 2018.
[ published paper | arXiv preprint | paper | code | news articles: MIT News, Engaget, Forbes, ExtremeTech ]
conference

Gaussian Process Prior Variational Autoencoders.
F.P. Casale, A. V. Dalca, L. Saglietti, N. Fusi, J. Listgarten.
NeurIPS: Advances in Neural Information Processing Systems. 31. pp 10369-10380. 2018.
[ published paper | arXiv preprint | paper | supp. materials ]
conference

Synthesizing Images of Humans in Unseen Poses.
G. Balakrishnan, A. Zhao, A.V. Dalca, F. Durand, J. Guttag.
CVPR: Computer Vision and Pattern Recognition. pp 8340-8348. 2018.
[ published paper | arXiv preprint | paper | code | news article | Oral Presentation ]
journal

Reconstructing Video of Time-Varying Sources from Radio Interferometric Measurements
K.L. Bouman, M.D. Johnson, A.V. Dalca, A.A. Chael, F.Roelofs, S.S. Doeleman, W.T. Freeman.
IEEE TCI: Transactions on Computational Imaging. 4.4. pp. 512-527. 2018.
[ arXiv preprint | IEEE Early Access ]
2017 and earlier
▴
conference

Population Based Image Imputation.
A.V. Dalca, K.L. Bouman, W.T. Freeman, M.R. Sabuncu, N.S. Rost, P. Golland.
IPMI: Information Processing and Medical Imaging. LNCS 10265, pp 659-671. 2017.
[ published paper | paper | News article | Best poster award ]
conference

Frequency Diffeomorphisms for Efficient Image Registration.
M. Zhang, R. Liao, A.V. Dalca, E.A. Turk, J. Luo, E. Grant, P. Golland.
IPMI: Information Processing and Medical Imaging. LNCS 10265, pp 559-570. 2017.
[ published paper | paper | Oral Presentation ]
journal

Design and Rationale for Examining Neuroimaging Genetics in Ischemic Stroke: the MRI-GENIE Study.
A.K. Giese, M.D. Schirmer, K.L. Donahue, L. Cloonan, R. Irie, S. Winzeck, M.J. Bouts, E.C. McIntosh, S. J. Mocking, A.V. Dalca, et al.
Neurology: Genetics. 3(5). Article e180. 2017.
[ published paper | PMC paper ]
journal

Probabilistic Modeling of Imaging, Genetics and Diagnosis.
K.N. Batmanghelich, A.V. Dalca, G. Quon, M.R. Sabuncu, P. Golland.
IEEE TMI: Transactions on Medical Imaging, 35(7), pp 1765-79, 2016.
[ published paper | paper ]
conference

Predictive Modeling of Anatomy with Genetic and Clinical Data.
A.V. Dalca, R. Sridharan, M.R. Sabuncu, P. Golland.
MICCAI: Medical Image Computing and Computer Assisted Intervention, LNCS 9351, pp. 519-526, 2015.
[ published paper | arXiv preprint | paper | Poster | Video | news article ]
conference

Interactive Whole-Heart Segmentation in Congenital Heart Disease.
D. Pace, A.V. Dalca, T.Geva, A.J. Powell, M.H. Moghari, P. Golland.
MICCAI: Medical Image Computing and Computer Assisted Intervention, LNCS 9351, pp. 80-88, 2015.
[ published paper | paper | news article ]
conference

Segmentation of Cerebrovascular Pathologies in Stroke Patients with Spatial and Shape Priors.
A.V. Dalca, R. Sridharan, L. Cloonan, K. M. Fitzpatrick, A. Kanakis, K.L. Furie, J.Rosand, O.Wu, M.Sabuncu, N.S. Rost, P.Golland.
MICCAI: Medical Image Computing and Computer Assisted Intervention, LNCS 8674, pp. 773-780, 2014.
[ published paper | paper | Poster PDF | doi ]
conference

Joint Modeling of Imaging and Genetics.
K.N. Batmanghelich, A.V. Dalca, M.R. Sabuncu, P. Golland.
IPMI: Information Processing and Medical Imaging, LNCS 7917, pp. 766-777, 2013.
[ published paper | paper | Oral Presentation | doi ]
journal

On Post-glacial Sea-Level - III: Incorporating Sediment Redistribution.
A.V. Dalca, K.L.Ferrier, J.X.Mitrovica, J.T. Perron, G.A. Milne, J.R. Creveling.
Geophysical Journal International. 194(1). pp. 45-60. 2013.
[ paper | doi ]
conference

Segmentation of Nerve Bundles and Ganglia in Spine MRI using Particle Filters.
A.V. Dalca, G. Danagoulian, R. Kikinis, E. Schmidt, P. Golland.
MICCAI: Medical Image Computing and Computer Assisted Intervention, LNCS, vol. 6893, pp 537-545, 2011.
[ paper | doi | Pubmed | Poster PDF ]
journal

VARiD: A variation detection framework for color-space and letter-space platforms.
A.V. Dalca, S.M. Rumble, S. Levy and M. Brudno.
Bioinformatics,26: i343-i349, 2010.
[ paper | doi | Website | Pubmed | together with ISMB 2010: Oral Presentation ]
journal

Genome Variation Discovery with High Throughput Sequencing Data.
A.V. Dalca and M. Brudno.
Briefings in Bioinformatics, 11. p3-14, 2010.
[ paper | doi | Pubmed ]
journal

SHRiMP Accurate Mapping of Short Color-space Reads.
S.M. Rumble, P. Lacroute, A.V. Dalca, M. Fiume, A. Sidow, M. Brudno.
PLoS Computational Biology. 5(5). Article e1000386. 2009.
[ paper | Website | doi | Pubmed ]
conference

FRESCO: Flexible Alignment with Rectangle Scoring Schemes.
A.V. Dalca and M. Brudno.
Pacific Symposium on Biocomputing, 13. p3-14, 2008.
[ published paper | paper | Website | Pubmed | Oral Presentation ]

Peer Reviewed Workshop / short Publications

workshop

Empirical Analysis of a Segmentation Foundation Model in Prostate Imaging.
H. Kim, V. Butoi, A. V. Dalca, M. Sabuncu
MICCAI MedAGI: International Workshop on Foundation Models for General Medical AI. LNCS 14393. pp 140-150. 2023.
[ published paper | arXiv preprint ]
workshop

UniverSeg: Universal Medical Image Segmentation.
V. I. Butoi^‡, J.J.G. Ortiz ^‡, T. Ma, J. Guttag; M. Sabuncu, A. V. Dalca
Med NeurIPS: Medical Imaging meets NeurIPS. Extended Abstract. 2022.
[ arXiv preprint ]
workshop

Probabilistic Interactive Segmentation for any Medical Image.
H. Wong, J. Guttag, A. V. Dalca
Med NeurIPS: Medical Imaging meets NeurIPS. Extended Abstract. 2022.
workshop

Contrast Invariant Feature Representations for Medical Image Analysis.
Y.Z.R. Chua, A. V. Dalca
Med NeurIPS: Medical Imaging meets NeurIPS. Extended Abstract. 2022.
workshop

Region-of-Interest Adaptive Acquisition for Accelerated MRI.
Z. Wu, T. Yin, A. V. Dalca, K. Bouman
Med NeurIPS: Medical Imaging meets NeurIPS. Extended Abstract. 2022.
workshop

3D-StyleGAN: A Style-Based Generative Adversarial Network for Generative Modeling of Three-Dimensional Medical Images.
S. Hong, R. Marinescu, A. V. Dalca, A. K. Bonkhoff, M. Bretzner, N. S. Rost, P. Golland
MICCAI DGM: Generative Modeling of Three-Dimensional Medical Images. LNCS 13003. pp 24-34. Springer. 2021.
[ published paper | arXiv preprint ]
workshop

HyperRecon: Regularization-Agnostic CS-MRI Reconstruction with Hypernetworks.
A.Q. Wang, A.V. Dalca, M. R. Sabuncu
MICCAI MLMIR: Machine Learning for Medical Image Reconstruction. LNCS 12964. pp 3-13. Springer. 2021.
[ published paper | arXiv preprint ]
conference

Anatomical Predictions using Subject-Specific Medical Data.
M. Rakic, J. Guttag, A.V. Dalca.
MIDL: Medical Imaging with Deep Learning. Short Paper. 2020.
[ Open Review | arXiv preprint ]
workshop

Learning MRI contrast agnostic registration.
M. Hoffmann, B. Billot, J.E. Iglesias, B. Fischl, A.V. Dalca
MED NeurIPS: Medical Imaging Meets NeurIPS. Extended Abstract. 2020.
[ arXiv preprint | interactive video ]
workshop

Neural Network-based Reconstruction in Compressed Sensing MRI Without Fully-sampled Training Data.
A.Q. Wang, A.V. Dalca, M.R.Sabuncu.
MICCAI MLMIR: Machine Learning for Medical Image Reconstruction. LNCS 12450. pp 27-37. Springer. 2020.
[ published paper | arXiv preprint ]
workshop

Learning Conditional Deformable Shape Templates for Brain Anatomy.
E. Yu, A.V. Dalca, M.R.Sabuncu.
MICCAI MLMI: Machine Learning in Medical Imaging. LNCS 12436. Pp 353-362. Springer. 2020.
[ published paper ]
workshop

Unbiased atlas construction for neonatal cortical surfaces via unsupervised learning.
J. Cheng, A.V. Dalca, L. Zollei.
MICCAI PIPPI: Perinatal, Preterm and Paediatric Image Analysis. LNCS 12437. Pp 334-342. Springer. 2020.
[ published paper ]
workshop

Learning to Predict and Support for Clinical Risk Stratification
A. Raghu, K. Young, E. Pomerantsev, J. Guttag, A. V. Dalca C. Stultz
NeurIPS ML4H: Machine Learning for Health. Extended Abstract. 2020.
workshop

Few Labeled Atlases are Necessary for Deep-Learning-Based Segmentation
H. W. Lee, M. R. Sabuncu, A. V. Dalca
NeurIPS ML4H: Machine Learning for Health. 2019.
[ arXiv preprint ]
workshop

Unsupervised Medical Image Imputation via Variational Inference of Deep Subspaces
A.V. Dalca, J. Guttag, M. R. Sabuncu.
NeurIPS ML4H: Machine Learning for Health. 2018.
[ arXiv preprint ]
workshop

Atlas Construction and Improved Registration of Medical Images with CNN Frameworks
A.V. Dalca, G. Balakrishnan, J. Guttag, M. R. Sabuncu.
NeurIPS ML4H: Machine Learning for Health. 2018.
workshop

Improved Probabilistic Diffeomorphic Registration with CNNs
A.V. Dalca, G. Balakrishnan, J. Guttag, M. R. Sabuncu.
MED NeurIPS: Medical Imaging Meets NeurIPS. 2018.
[ paper | Oral Presentation ]
workshop

Fast Learning-based Registration of Sparse Clinical Images
K. Lewis, G. Balakrishnan, N, Rost, J. Guttag and A.V. Dalca
NeurIPS ML4H: Machine Learning for Health. 2018.
[ paper | Spotlight ]
workshop

Generative Models for Clinical Imaging Genetic Analysis
F. P. Casale, A.V. Dalca, N. Fusi and J. Listgarten
NeurIPS ML4H: Machine Learning for Health. 2018.
workshop

Iterative Segmentation from Limited Training Data: Applications to Congenital Heart Disease
D. Pace, A.V. Dalca, T.Brosch, T.Geva, A.J. Powell, J. Weese, M.H. Moghari, P. Golland.
MICCAI DLMIA: Deep Learning in Medical Image Analysis. LNCS 11045. pp. 334-342. 2018.
[ published paper | arXiv preprint ]
workshop

Spatial Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation
A.V. Dalca, J. Guttag, M. R. Sabuncu.
NeurIPS ML4H: Machine Learning for Health. 2017.
[ Spotlight ]
workshop

Patch-Based Discrete Registration of Clinical Brain Images.
A.V. Dalca, A. Bobu, N.S. Rost, P. Golland.
MICCAI PATCHMI: Patch-based Techniques in Medical Imaging, LNCS 9993, pp 60-67, 2016.
[ published paper | paper | code | Best paper award ]
workshop

tipiX: Rapid Visualization of Large Image Collections
A.V. Dalca, R. Sridharan, N.S. Rost, P. Golland.
MICCAI IMIC: Interactive Medical Image Computing Workshop, 2014.
[ paper | Video ]
[ Best paper award for impact and usability | Finalist CSAIL Amazing Research Highlight Competition | Oral Presentation ]
workshop

An interactive visualization tool for Nipype medical imaging pipelines
R. Sridharan, A.V. Dalca, P. Golland.
MICCAI IMIC: Interactive Medical Image Computing Workshop, 2014.
[ paper | Oral Presentation ]
workshop

Quantification and Analysis of Large Multimodal Clinical Image Studies: Application to Stroke
R. Sridharan^‡, A.V. Dalca^‡, K.M. Fitzpatrick, L. Cloonan, A. Kanakis, O. Wu, K.L. Furie, J. Rosand, N.S. Rost, P. Golland.
MICCAI MBIA: International Workshop on Multimodal Brain Image Analysis (MBIA). LNCS 8159. pp. 18–30. 2013.
[ paper | doi | ^‡ equal contribution | Oral Presentation ]

Theses

thesis

Genetic, Clinical and Population Priors for Brain Images
A.V. Dalca.
Ph.D. Thesis, Massachusetts Institute of Technology, 2016.
[ PDF ]
thesis

Segmentation of Nerve Bundles and Ganglia in Spine MRI using Particle Filters
A.V. Dalca
S.M. Thesis, Massachusetts Institute of Technology, 2012.
[ PDF | Morris Joseph Levin Award for best thesis presentation at Masterworks ]

Books and Proceedings

Uncertainty for Safe Utilization of Machine Learning in Medical Imaging, and Perinatal Imaging, Placental and Preterm Image Analysis
C.H. Sudre, R. Licandro, H., C.F. Baumgartner, A. Melbourne, A. V. Dalca, et al (Editors).
Springer. 2021.
[ Book link ]
Uncertainty for Safe Utilization of Machine Learning in Medical Imaging, and Graphs in Biomedical Image Analysis
C.H. Sudre, H. Fehri, H., T. Arbel, C.F. Baumgartner, A. V. Dalca, et al (Editors).
Springer. 2020.
[ Book link ]
NeurIPS Machine Learning for Health Workshop
A. V. Dalca, M. B.A. McDermott, E. Alsentzer, S. G. Finlayson, M. Oberst, F. Falck, C. Chivers, A. Beam, T. Naumann, B. Beaulieu-jones (Editors).
PMLR. 2020.
[ Proceedings | Introduction | citation bib ]
Uncertainty for Safe Utilization of Machine Learning in Medical Imaging and Clinical Image-Based Procedures
H. Greenspan, R. Tanno, M. Erdt, T. Arbel, C. Baumgartner, A. V. Dalca, et al (Editors).
Springer. 2019.
[ Book link ]
Graphs in Biomedical Image Analysis and Integrating Medical Imaging and Non-Imaging Modalities
D. Stoyanov, Z.Taylor, E. Ferrante, A. V. Dalca, et al (Editors).
Springer. 2018.
[ Book link ]
Imaging Genetics
A.V. Dalca, N.K. Batmanghelich, M.R. Sabuncu, L. Shen (Editors).
Elsevier. 2017.
[ Book link ]
Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics
J. Cardoso, T. Arbel, E. Ferrante, X. Pennec, A.V. Dalca, et al (Editors).
Springer. 2017.
[ Book link ]
Molecular Imaging, Reconstruction and Analysis of Moving Body Organs, Stroke Imaging and Treatment
J. Cardoso, T. Arbel, F. Gao, B. Kainz, T. van Walsum, K. Shi, K.K. Bhatia, R. Peter, T. Vercauteren, M. Reyes, A.V. Dalca, et al (Editors)
Springer. 2017.
[ Book link ]