Search Results for author: Malte Hoffmann

Found 12 papers, 3 papers with code

Registration by Regression (RbR): a framework for interpretable and flexible atlas registration

no code implementations25 Apr 2024 Karthik Gopinath, Xiaoling Hu, Malte Hoffmann, Oula Puonti, Juan Eugenio Iglesias

In human neuroimaging studies, atlas registration enables mapping MRI scans to a common coordinate frame, which is necessary to aggregate data from multiple subjects.

regression

Boosting Skull-Stripping Performance for Pediatric Brain Images

no code implementations26 Feb 2024 William Kelley, Nathan Ngo, Adrian V. Dalca, Bruce Fischl, Lilla Zöllei, Malte Hoffmann

With the emergence of multi-institutional pediatric data acquisition efforts to broaden the understanding of perinatal brain development, it is essential to develop robust and well-tested tools ready for the relevant data processing.

Skull Stripping

SE(3)-Equivariant and Noise-Invariant 3D Rigid Motion Tracking in Brain MRI

1 code implementation21 Dec 2023 Benjamin Billot, Neel Dey, Daniel Moyer, Malte Hoffmann, Esra Abaci Turk, Borjan Gagoski, Ellen Grant, Polina Golland

Here we propose EquiTrack, the first method that uses recent steerable SE(3)-equivariant CNNs (E-CNN) for motion tracking.

Time Series

Anatomy-aware and acquisition-agnostic joint registration with SynthMorph

no code implementations26 Jan 2023 Malte Hoffmann, Andrew Hoopes, Douglas N. Greve, Bruce Fischl, Adrian V. Dalca

Most affine methods are agnostic to anatomy, meaning the registration will be inaccurate if algorithms consider all structures in the image.

Affine Image Registration Anatomy +1

Data Consistent Deep Rigid MRI Motion Correction

1 code implementation25 Jan 2023 Nalini M. Singh, Neel Dey, Malte Hoffmann, Bruce Fischl, Elfar Adalsteinsson, Robert Frost, Adrian V. Dalca, Polina Golland

Motion artifacts are a pervasive problem in MRI, leading to misdiagnosis or mischaracterization in population-level imaging studies.

Image Reconstruction

Learning the Effect of Registration Hyperparameters with HyperMorph

no code implementations30 Mar 2022 Andrew Hoopes, Malte Hoffmann, Douglas N. Greve, Bruce Fischl, John Guttag, Adrian V. Dalca

We design a meta network, or hypernetwork, that predicts the parameters of a registration network for input hyperparameters, thereby comprising a single model that generates the optimal deformation field corresponding to given hyperparameter values.

Image Registration

SynthStrip: Skull-Stripping for Any Brain Image

no code implementations18 Mar 2022 Andrew Hoopes, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl, Malte Hoffmann

The removal of non-brain signal from magnetic resonance imaging (MRI) data, known as skull-stripping, is an integral component of many neuroimage analysis streams.

Skull Stripping

The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients

no code implementations13 Dec 2021 Bhakti Baheti, Satrajit Chakrabarty, Hamed Akbari, Michel Bilello, Benedikt Wiestler, Julian Schwarting, Evan Calabrese, Jeffrey Rudie, Syed Abidi, Mina Mousa, Javier Villanueva-Meyer, Brandon K. K. Fields, Florian Kofler, Russell Takeshi Shinohara, Juan Eugenio Iglesias, Tony C. W. Mok, Albert C. S. Chung, Marek Wodzinski, Artur Jurgas, Niccolo Marini, Manfredo Atzori, Henning Muller, Christoph Grobroehmer, Hanna Siebert, Lasse Hansen, Mattias P. Heinrich, Luca Canalini, Jan Klein, Annika Gerken, Stefan Heldmann, Alessa Hering, Horst K. Hahn, Mingyuan Meng, Lei Bi, Dagan Feng, Jinman Kim, Ramy A. Zeineldin, Mohamed E. Karar, Franziska Mathis-Ullrich, Oliver Burgert, Javid Abderezaei, Aymeric Pionteck, Agamdeep Chopra, Mehmet Kurt, Kewei Yan, Yonghong Yan, Zhe Tang, Jianqiang Ma, Sahar Almahfouz Nasser, Nikhil Cherian Kurian, Mohit Meena, Saqib Shamsi, Amit Sethi, Nicholas J. Tustison, Brian B. Avants, Philip Cook, James C. Gee, Lin Tian, Hastings Greer, Marc Niethammer, Andrew Hoopes, Malte Hoffmann, Adrian V. Dalca, Stergios Christodoulidis, Theo Estiene, Maria Vakalopoulou, Nikos Paragios, Daniel S. Marcus, Christos Davatzikos, Aristeidis Sotiras, Bjoern Menze, Spyridon Bakas, Diana Waldmannstetter

Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance.

Descriptive Image Registration +1

Rapid head-pose detection for automated slice prescription of fetal-brain MRI

no code implementations8 Oct 2021 Malte Hoffmann, Esra Abaci Turk, Borjan Gagoski, Leah Morgan, Paul Wighton, M. Dylan Tisdall, Martin Reuter, Elfar Adalsteinsson, P. Ellen Grant, Lawrence L. Wald, André J. W. van der Kouwe

In fetal-brain MRI, head-pose changes between prescription and acquisition present a challenge to obtaining the standard sagittal, coronal and axial views essential to clinical assessment.

HyperMorph: Amortized Hyperparameter Learning for Image Registration

1 code implementation4 Jan 2021 Andrew Hoopes, Malte Hoffmann, Bruce Fischl, John Guttag, Adrian V. Dalca

We present HyperMorph, a learning-based strategy for deformable image registration that removes the need to tune important registration hyperparameters during training.

Image Registration

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