Model-based physiological noise removal in fast fMRI
Recent improvements in the speed and sensitivity of fMRI acquisition techniques suggest that fast fMRI can be used to detect and precisely localize sub-second neural dynamics. This enhanced temporal resolution has enormous potential for neuroscientists. However, physiological noise poses a major cha...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-01-01
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| Series: | NeuroImage |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1053811919308225 |
| _version_ | 1828387256458543104 |
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| author | Uday Agrawal Emery N. Brown Laura D. Lewis |
| author_facet | Uday Agrawal Emery N. Brown Laura D. Lewis |
| author_sort | Uday Agrawal |
| collection | DOAJ |
| description | Recent improvements in the speed and sensitivity of fMRI acquisition techniques suggest that fast fMRI can be used to detect and precisely localize sub-second neural dynamics. This enhanced temporal resolution has enormous potential for neuroscientists. However, physiological noise poses a major challenge for the analysis of fast fMRI data. Physiological noise scales with sensitivity, and its autocorrelation structure is altered in rapidly sampled data, suggesting that new approaches are needed for physiological noise removal in fast fMRI. Existing strategies either rely on external physiological recordings, which can be noisy or difficult to collect, or employ data-driven approaches which make assumptions that may not hold true in fast fMRI. We created a statistical model of harmonic regression with autoregressive noise (HRAN) to estimate and remove cardiac and respiratory noise from the fMRI signal directly. This technique exploits the fact that cardiac and respiratory noise signals are fully sampled (rather than aliasing) when imaging at fast rates, allowing us to track and model physiology over time without requiring external physiological measurements. We then created a joint model of neural hemodynamics, and physiological and autocorrelated noise to more accurately remove noise. We first verified that HRAN accurately estimates cardiac and respiratory dynamics and that our model demonstrates goodness-of-fit in fast fMRI data. In task-driven data, we then demonstrated that HRAN is able to remove physiological noise while leaving the neural signal intact, thereby increasing detection of task-driven voxels. Finally, we established that in both simulations and fast fMRI data HRAN is able to improve statistical inferences as compared with gold-standard physiological noise removal techniques. In conclusion, we created a tool that harnesses the novel information in fast fMRI to remove physiological noise, enabling broader use of the technology to study human brain function. |
| first_indexed | 2024-12-10T05:52:19Z |
| format | Article |
| id | doaj.art-7fbdb3c7df7c418fafba858e92722c55 |
| institution | Directory Open Access Journal |
| issn | 1095-9572 |
| language | English |
| last_indexed | 2024-12-10T05:52:19Z |
| publishDate | 2020-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | NeuroImage |
| spelling | doaj.art-7fbdb3c7df7c418fafba858e92722c552022-12-22T02:00:01ZengElsevierNeuroImage1095-95722020-01-01205116231Model-based physiological noise removal in fast fMRIUday Agrawal0Emery N. Brown1Laura D. Lewis2Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USAHarvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USADepartment of Biomedical Engineering, Boston University, Boston, MA, USA; Corresponding author.Recent improvements in the speed and sensitivity of fMRI acquisition techniques suggest that fast fMRI can be used to detect and precisely localize sub-second neural dynamics. This enhanced temporal resolution has enormous potential for neuroscientists. However, physiological noise poses a major challenge for the analysis of fast fMRI data. Physiological noise scales with sensitivity, and its autocorrelation structure is altered in rapidly sampled data, suggesting that new approaches are needed for physiological noise removal in fast fMRI. Existing strategies either rely on external physiological recordings, which can be noisy or difficult to collect, or employ data-driven approaches which make assumptions that may not hold true in fast fMRI. We created a statistical model of harmonic regression with autoregressive noise (HRAN) to estimate and remove cardiac and respiratory noise from the fMRI signal directly. This technique exploits the fact that cardiac and respiratory noise signals are fully sampled (rather than aliasing) when imaging at fast rates, allowing us to track and model physiology over time without requiring external physiological measurements. We then created a joint model of neural hemodynamics, and physiological and autocorrelated noise to more accurately remove noise. We first verified that HRAN accurately estimates cardiac and respiratory dynamics and that our model demonstrates goodness-of-fit in fast fMRI data. In task-driven data, we then demonstrated that HRAN is able to remove physiological noise while leaving the neural signal intact, thereby increasing detection of task-driven voxels. Finally, we established that in both simulations and fast fMRI data HRAN is able to improve statistical inferences as compared with gold-standard physiological noise removal techniques. In conclusion, we created a tool that harnesses the novel information in fast fMRI to remove physiological noise, enabling broader use of the technology to study human brain function.http://www.sciencedirect.com/science/article/pii/S1053811919308225HRANFast fMRIPhysiological noiseAutocorrelationHarmonic regressionSimultaneous multislice (SMS) |
| spellingShingle | Uday Agrawal Emery N. Brown Laura D. Lewis Model-based physiological noise removal in fast fMRI NeuroImage HRAN Fast fMRI Physiological noise Autocorrelation Harmonic regression Simultaneous multislice (SMS) |
| title | Model-based physiological noise removal in fast fMRI |
| title_full | Model-based physiological noise removal in fast fMRI |
| title_fullStr | Model-based physiological noise removal in fast fMRI |
| title_full_unstemmed | Model-based physiological noise removal in fast fMRI |
| title_short | Model-based physiological noise removal in fast fMRI |
| title_sort | model based physiological noise removal in fast fmri |
| topic | HRAN Fast fMRI Physiological noise Autocorrelation Harmonic regression Simultaneous multislice (SMS) |
| url | http://www.sciencedirect.com/science/article/pii/S1053811919308225 |
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