publications

2024

1. OHBM

   

   Physiopy: a Python suite for handling physiological data recorded in neuroimaging settings

   Roza G Bayrak, Catie Chang, Katherine Bottenhorn , and 26 more authors

   In Organization for Human Brain Mapping–OHBM 2024: 30th International Conference, Seoul, Korea, June 23 –- 27, 2024, Proceedings , 2024

   Poster
2. OHBM

   

   Thumbs up or down: Simple quality assessment tool for physiological signals

   Roza G Bayrak, Richard Song, Ruogi Yang , and 1 more author

   In Organization for Human Brain Mapping–OHBM 2024: 30th International Conference, Seoul, Korea, June 23 –- 27, 2024, Proceedings , 2024

   Poster
3. OHBM

   

   Physiological Signatures Across the Brain

   Roza G Bayrak, Nafis Ahmed, Mara Mather , and 2 more authors

   In Organization for Human Brain Mapping–OHBM 2024: 30th International Conference, Seoul, Korea, June 23 –- 27, 2024, Proceedings , 2024

   Poster

2023

1. NeurIPS

   

   Neurograph: Benchmarks for graph machine learning in brain connectomics

   Anwar Said, Roza G Bayrak, Tyler Derr , and 4 more authors

   Advances in Neural Information Processing Systems, 2023

   Abs arXiv Code

   

2. OSF Preprint

   

   Tracing peripheral physiology in low frequency fMRI dynamics

   Roza G Bayrak, Colin Hansen, Jorge Salas , and 5 more authors

   2023

   Abs HTML

   Many studies of the human brain using functional magnetic resonance imag-ing (fMRI) lack physiological measurements, which substantially impacts theinterpretation and richness of fMRI studies. Natural fluctuations in autonomicphysiology, such as breathing and heart rate, provide windows into critical func-tions including cognition, emotion, and health, and can heavily influence fMRIsignals. Here, we developedDeepPhysioRecon, a Long-Short-Term-Memory(LSTM)-based network that decodes continuous variations in respiration ampli-tude and heart rate directly from whole-brain fMRI dynamics. Through sys-tematic evaluations, we investigate the generalizability of this approach acrossdatasets and experimental conditions. We also demonstrate the importance ofincluding these measures in fMRI analyses. This work highlights the importanceof studying brain-body interactions, proposes a tool that may enhance the efficacyof fMRI as a biomarker, and provides widely applicable open-source software.

2022

1. PRIME Workshop

   

   Learning subject-specific functional parcellations from cortical surface measures

   Roza G Bayrak, Ilwoo Lyu, and Catie Chang

   In International Workshop on PRedictive Intelligence In MEdicine , 2022

   
2. MRI

   

   TractEM: evaluation of protocols for deterministic tractography white matter atlas

   Francois Rheault^*, Roza G Bayrak^*, Xuan Wang , and 8 more authors

   Magnetic Resonance Imaging, 2022

   

2021

1. Neuroimage

   

   Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?

   Kurt G Schilling, François Rheault, Laurent Petit , and 8 more authors

   Neuroimage, 2021

   
2. MICCAI

   

   From brain to body: learning low-frequency respiration and cardiac signals from fMRI dynamics

   Roza G Bayrak, Colin B Hansen, Jorge A Salas , and 4 more authors

   In Medical Image Computing and Computer Assisted Intervention–MICCAI 2021: 24th International Conference, Strasbourg, France, September 27–October 1, 2021, Proceedings, Part VII 24 , 2021

   
3. Neuroimage

   

   Reconstruction of respiratory variation signals from fMRI data

   Jorge A Salas, Roza G Bayrak, Yuankai Huo , and 1 more author

   Neuroimage, 2021

   

2020

1. MICCAI

   

   A deep pattern recognition approach for inferring respiratory volume fluctuations from fmri data

   Roza G Bayrak, Jorge A Salas, Yuankai Huo , and 1 more author

   In International Conference on Medical Image Computing and Computer-Assisted Intervention , 2020

   
2. IEEE VIS

   

   PRAGMA: Interactively Constructing Functional Brain Parcellations

   Roza G Bayrak^*, Nhung Hoang^*, Colin B Hansen , and 2 more authors

   In 2020 IEEE Visualization Conference (VIS) , 2020

   Abs HTML Video

   PRAGMA is an interactive tool for constructing scan-specific brain parcellations from mainstream atlases. Its interface incorporates five complementary visuals: (A) abstract view of the hierarchical clustering of the brain through a node-link diagram, (B1) similarity of fMRI signal time-courses represented with a line plot with a shaded confidence interval, (B2) homogeneity glyphs within nodes, (C1) functional connectivity depicted as a chord diagram and (C2) anatomical location of parcels viewed on an orthographic template.