Publications

2024

1. MRI2Qmap: compressed-sampled multiparametric quantitative MRI reconstruction using learned spatial priors from multimodal MRI datasets

   Mohammad Golbabaee, Matteo Cencini, Carolin Pirkl, and 3 more authors

   In 2024 ISMRM & ISMRT Annual Meeting & Exhibition. Selected as an Annual Meeting Program Committee (AMPC) Highlight paper (top 1%) , 2024

   Highlight Paper (top 1%) Bib

   Selected as an Annual Meeting Program Committee (AMPC) Highlight paper

   @inproceedings{golbabaee2024mri2qmap,
     title = {MRI2Qmap: compressed-sampled multiparametric quantitative MRI reconstruction using learned spatial priors from multimodal MRI datasets},
     author = {Golbabaee, Mohammad and Cencini, Matteo and Pirkl, Carolin and Menzel, Marion and Tosetti, Michela and Menze, Bjoern},
     booktitle = {2024 ISMRM \& ISMRT Annual Meeting \& Exhibition},
     year = {2024},
   }

2. Deep Image Priors for Magnetic Resonance Fingerprinting with Pretrained Bloch-Consistent Denoising Autoencoders

   Perla Mayo, Matteo Cencini, Ketan Fatania, and 5 more authors

   In 2024 IEEE International Symposium on Biomedical Imaging (ISBI), 2024

   Bib

   @inproceedings{mayo2024deep,
     title = {Deep Image Priors for Magnetic Resonance Fingerprinting with Pretrained Bloch-Consistent Denoising Autoencoders},
     author = {Mayo, Perla and Cencini, Matteo and Fatania, Ketan and Pirkl, Carolin M and Menzel, Marion I and Menze, Bjoern H and Tosetti, Michela and Golbabaee, Mohammad},
     booktitle = {2024 IEEE International Symposium on Biomedical Imaging (ISBI)},
     pages = {1--4},
     year = {2024},
     organization = {IEEE}
   }

3. StoDIP: Efficient 3D MRF image reconstruction with deep image priors and stochastic iterations

   Perla Mayo, Matteo Cencini, Carolin M Pirkl, and 4 more authors

   arXiv preprint arXiv:2408.02367, 2024

   Best Paper Award Bib

   Recognised as Best Paper Award at the 15th International Workshop in Machine Learning in Medical Imaging (MLMI) 2024

   @article{mayo2024stodip,
     title = {StoDIP: Efficient 3D MRF image reconstruction with deep image priors and stochastic iterations},
     author = {Mayo, Perla and Cencini, Matteo and Pirkl, Carolin M and Menzel, Marion I and Tosetti, Michela and Menze, Bjoern H and Golbabaee, Mohammad},
     journal = {arXiv preprint arXiv:2408.02367},
     year = {2024},
   }

2023

1. Nonlinear Equivariant Imaging: Learning Multi-Parametric Tissue Mapping without Ground Truth for Compressive Quantitative MRI

   Ketan Fatania, Kwai Y Chau, Carolin M Pirkl, and 2 more authors

   In 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), 2023

   Bib

   @inproceedings{fatania2023nonlinear,
     title = {Nonlinear Equivariant Imaging: Learning Multi-Parametric Tissue Mapping without Ground Truth for Compressive Quantitative MRI},
     author = {Fatania, Ketan and Chau, Kwai Y and Pirkl, Carolin M and Menzel, Marion I and Golbabaee, Mohammad},
     booktitle = {2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)},
     pages = {1--4},
     year = {2023},
     organization = {IEEE}
   }

2. Joint radial trajectory correction for accelerated T2* mapping on an MR-Linac

   Wajiha Bano, Will Holmes, Rosie Goodburn, and 6 more authors

   Medical Physics, 2023

   Bib

   @article{bano2023joint,
     title = {Joint radial trajectory correction for accelerated T2* mapping on an MR-Linac},
     author = {Bano, Wajiha and Holmes, Will and Goodburn, Rosie and Golbabaee, Mohammad and Gupta, Amit and Withey, Sam and Tree, Alison and Oelfke, Uwe and Wetscherek, Andreas},
     journal = {Medical Physics},
     volume = {50},
     number = {11},
     pages = {7027--7038},
     year = {2023},
     publisher = {Wiley Online Library}
   }

2022

1. Deep unrolling for magnetic resonance fingerprinting

   Dongdong Chen, Mike E Davies, and Mohammad Golbabaee

   In 2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI), 2022

   Bib

   @inproceedings{chen2022deep,
     title = {Deep unrolling for magnetic resonance fingerprinting},
     author = {Chen, Dongdong and Davies, Mike E and Golbabaee, Mohammad},
     booktitle = {2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI)},
     pages = {1--4},
     year = {2022},
     organization = {IEEE}
   }

2. A plug-and-play approach to multiparametric quantitative MRI: image reconstruction using pre-trained deep denoisers

   Ketan Fatania, Carolin M Pirkl, Marion I Menzel, and 2 more authors

   In 2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI), 2022

   Oral Bib

   Oral

   @inproceedings{fatania2022plug,
     title = {A plug-and-play approach to multiparametric quantitative MRI: image reconstruction using pre-trained deep denoisers},
     author = {Fatania, Ketan and Pirkl, Carolin M and Menzel, Marion I and Hall, Peter and Golbabaee, Mohammad},
     booktitle = {2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI)},
     pages = {1--4},
     year = {2022},
     organization = {IEEE},
   }

3. An off-the-grid approach to multi-compartment magnetic resonance fingerprinting

   Mohammad Golbabaee, and Clarice Poon

   Inverse Problems, 2022

   Bib

   @article{golbabaee2022off,
     title = {An off-the-grid approach to multi-compartment magnetic resonance fingerprinting},
     author = {Golbabaee, Mohammad and Poon, Clarice},
     journal = {Inverse Problems},
     volume = {38},
     number = {8},
     pages = {085002},
     year = {2022},
     publisher = {IOP Publishing}
   }

2021

1. Compressive MRI quantification using convex spatiotemporal priors and deep encoder-decoder networks

   Mohammad Golbabaee, Guido Buonincontri, Carolin M Pirkl, and 4 more authors

   Medical image analysis, 2021

   Bib

   @article{golbabaee2021compressive,
     title = {Compressive MRI quantification using convex spatiotemporal priors and deep encoder-decoder networks},
     author = {Golbabaee, Mohammad and Buonincontri, Guido and Pirkl, Carolin M and Menzel, Marion I and Menze, Bjoern H and Davies, Mike and G{\'o}mez, Pedro A},
     journal = {Medical image analysis},
     volume = {69},
     pages = {101945},
     year = {2021},
     publisher = {Elsevier}
   }

2. Accelerated 3D whole-brain T1, T2, and proton density mapping: feasibility for clinical glioma MR imaging

   Carolin M Pirkl, Laura Nunez-Gonzalez, Florian Kofler, and 8 more authors

   Neuroradiology, 2021

   Bib

   @article{pirkl2021accelerated,
     title = {Accelerated 3D whole-brain T1, T2, and proton density mapping: feasibility for clinical glioma MR imaging},
     author = {Pirkl, Carolin M and Nunez-Gonzalez, Laura and Kofler, Florian and Endt, Sebastian and Grundl, Lioba and Golbabaee, Mohammad and G{\'o}mez, Pedro A and Cencini, Matteo and Buonincontri, Guido and Schulte, Rolf F and others},
     journal = {Neuroradiology},
     pages = {1--21},
     year = {2021},
     publisher = {Springer}
   }

2020

1. Effects of spatial encoding strategies on 2D and 3D magnetic resonance fingerprinting

   Matteo Cencini, Pedro A Gómez, Mohammad Golbabaee, and 6 more authors

   Magnetic Resonance in Medicine, 2020

   Bib

   @article{cencini2020effects,
     title = {Effects of spatial encoding strategies on 2D and 3D magnetic resonance fingerprinting},
     author = {Cencini, Matteo and G{\'o}mez, Pedro A and Golbabaee, Mohammad and Schulte, Rolf F and Fallo, Giada and Peretti, Luca and Tosetti, Michela and Menze, Bjoern H and Buonincontri, Guido},
     journal = {Magnetic Resonance in Medicine},
     year = {2020},
     publisher = {Wiley}
   }

2. Neural network inference for three-dimensional quantitative transient-state imaging (QTI)

   Luca Pretti, Matteo Cencini, Mohammad Golbabaee, and 1 more author

   Magnetic Resonance in Medicine, 2020

   Bib

   @article{pretti2020neural,
     title = {Neural network inference for three-dimensional quantitative transient-state imaging (QTI)},
     author = {Pretti, Luca and Cencini, Matteo and Golbabaee, Mohammad and others},
     journal = {Magnetic Resonance in Medicine},
     year = {2020},
     publisher = {Wiley}
   }

3. Compressive mr fingerprinting reconstruction with neural proximal gradient iterations

   Dongdong Chen, Mike E Davies, and Mohammad Golbabaee

   In Medical Image Computing and Computer Assisted Intervention–MICCAI 2020: 23rd International Conference, Lima, Peru, October 4–8, 2020, Proceedings, Part II 23, 2020

   Oral Bib

   Oral

   @inproceedings{chen2020compressive,
     title = {Compressive mr fingerprinting reconstruction with neural proximal gradient iterations},
     author = {Chen, Dongdong and Davies, Mike E and Golbabaee, Mohammad},
     booktitle = {Medical Image Computing and Computer Assisted Intervention--MICCAI 2020: 23rd International Conference, Lima, Peru, October 4--8, 2020, Proceedings, Part II 23},
     pages = {13--22},
     year = {2020},
     organization = {Springer},
   }

4. Model-based super-resolution reconstruction of T2 maps

   Wajiha Bano, Gian Franco Piredda, Mike Davies, and 6 more authors

   Magnetic resonance in medicine, 2020

   Bib

   @article{bano2020model,
     title = {Model-based super-resolution reconstruction of T2 maps},
     author = {Bano, Wajiha and Piredda, Gian Franco and Davies, Mike and Marshall, Ian and Golbabaee, Mohammad and Meuli, Reto and Kober, Tobias and Thiran, Jean-Philippe and Hilbert, Tom},
     journal = {Magnetic resonance in medicine},
     volume = {83},
     number = {3},
     pages = {906--919},
     year = {2020},
     publisher = {Wiley Online Library}
   }

5. Rapid three-dimensional multiparametric MRI with quantitative transient-state imaging

   Pedro A Gómez, Matteo Cencini, Mohammad Golbabaee, and 8 more authors

   Scientific reports, 2020

   Bib

   @article{gomez2020rapid,
     title = {Rapid three-dimensional multiparametric MRI with quantitative transient-state imaging},
     author = {G{\'o}mez, Pedro A and Cencini, Matteo and Golbabaee, Mohammad and Schulte, Rolf F and Pirkl, Carolin and Horvath, Izabela and Fallo, Giada and Peretti, Luca and Tosetti, Michela and Menze, Bjoern H and others},
     journal = {Scientific reports},
     volume = {10},
     number = {1},
     pages = {13769},
     year = {2020},
     publisher = {Nature Publishing Group UK London}
   }

6. A temporal multiscale approach for MR Fingerprinting

   Samuel Cortinhas, Mohammad Golbabaee, and Matthias J Ehrhardt

   arXiv preprint arXiv:2010.03386, 2020

   Bib

   @article{cortinhas2020temporal,
     title = {A temporal multiscale approach for MR Fingerprinting},
     author = {Cortinhas, Samuel and Golbabaee, Mohammad and Ehrhardt, Matthias J},
     journal = {arXiv preprint arXiv:2010.03386},
     year = {2020}
   }

2019

1. Geometry of deep learning for magnetic resonance fingerprinting

   Mohammad Golbabaee, Dongdong Chen, Pedro A Gómez, and 2 more authors

   In ICASSP 2019-2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2019

   Oral

   Oral

2. Deep fully convolutional network for MR fingerprinting

   Dongdong Chen, Mohammad Golbabaee, Pedro A Gómez, and 2 more authors

   In Medical Imaging with Deep Learning, MIDL 2019: Extended Abstract Track, 2019
3. High-resolution Isotropic Whole Brain T2 Mapping with Model-based Super-resolution Reconstruction

   Wajiha Bano, Gian Franco Piredda, Michael Davies, and 6 more authors

   In ISMRM 27th Annual Meeting & Exhibition, 11-16 May 2019, 2019
4. Deep MR Fingerprinting with total-variation and low-rank subspace priors

   Mohammad Golbabaee, Carolin M Pirkl, Marion I Menzel, and 2 more authors

   2019

   Oral

   Oral

5. Multi-shot Echo Planar Imaging for accelerated Cartesian MR Fingerprinting: an alternative to conventional spiral MR Fingerprinting

   Arnold Julian Vinoj Benjamin, Pedro A Gómez, Mohammad Golbabaee, and 5 more authors

   Magnetic resonance imaging, 2019
6. Spatio-temporal regularization for deep MR Fingerprinting

   Mohammad Golbabaee, Dongdong Chen, Mike E Davies, and 2 more authors

   In Medical Imaging with Deep Learning, MIDL 2019: Extended Abstract Track, 2019
7. Multi-shot Echo Planar Imaging for accelerated Cartesian MR Fingerprinting: an alternative to conventional spiral MR Fingerprinting

   Arnold Julian Vinoj Benjamin, Pedro A Gómez, Mohammad Golbabaee, and 5 more authors

   Magnetic resonance imaging, 2019
8. A fully convolutional network for MR fingerprinting

   Dongdong Chen, Mohammad Golbabaee, Pedro A Gómez, and 2 more authors

   arXiv preprint arXiv:1911.09846, 2019
9. CoverBLIP: accelerated and scalable iterative matched-filtering for magnetic resonance fingerprint reconstruction

   Mohammad Golbabaee, Zhouye Chen, Yves Wiaux, and 1 more author

   Inverse Problems, 2019

   Bib

   @article{golbabaee2019coverblip,
     title = {CoverBLIP: accelerated and scalable iterative matched-filtering for magnetic resonance fingerprint reconstruction},
     author = {Golbabaee, Mohammad and Chen, Zhouye and Wiaux, Yves and Davies, Mike},
     journal = {Inverse Problems},
     volume = {36},
     number = {1},
     pages = {015003},
     year = {2019},
     publisher = {IOP Publishing}
   }