Model‐based dynamic off‐resonance correction for improved accelerated fMRI in awake behaving nonhuman primates

Abstract

To estimate dynamic off-resonance due to vigorous body motion in accelerated fMRI of awake behaving nonhuman primates (NHPs) using the echo-planar imaging reference navigator, in order to attenuate the effects of timevarying off-resonance on the reconstruction. Methods:In NHP fMRI, the animal's head is usually head-posted, and the dynamic off-resonance is mainly caused by motion in body parts that are distant from the brain and have low spatial frequency. Hence, off-resonance at each frame can be approximated as a spatially linear perturbation of the off-resonance at a reference frame, and is manifested as a relative linear shift in k-space. Using GRAPPA operators, we estimated these shifts by comparing the navigator at each time frame with that at the reference frame. Estimated shifts were then used to correct the data at each frame. The proposed method was evaluated in phantom scans, simulations, and in vivo data. Results:The proposed method is shown to successfully estimate spatially low-order dynamic off-resonance perturbations, including induced linear offresonance perturbations in phantoms, and is able to correct retrospectively corrupted data in simulations. Finally, it is shown to reduce ghosting artifacts and geometric distortions by up to 20% in simultaneous multislice in vivo acquisitions in awake-behaving NHPs. Conclusion:A method is proposed that does not need sequence modification or extra acquisitions and makes accelerated awake behaving NHP imaging more robust and reliable, reducing the gap between what is possible with NHP protocols and state-of-the-art human imaging.

A frontopolar-temporal circuit determines the impact of social information in macaque decision making

“…T2 ∗ EPI images acquired during the experimental task were reconstructed using a custom offline reconstruction script, using techniques described previously. 49 Preprocessing of structural and functional images involved tools from the FMRIB Software Library (FSL), 50 MATLAB (R2022a, Mathworks), Advanced Normalisation Tools (ANTs; http://stnava.github.io/ANTs ), 45 and the Magnetic Resonance Comparative Anatomy Toolbox (MrCat; http://github.com/neuroecology/MrCat ).…”

Dynamic off-resonance correction improves functional image analysis in fMRI of awake behaving non-human primates

“…Single-band reference data and fully sampled calibration data were acquired along with the functional data as separate parts of the imaging sequence. Standard Nyquist ghost correction and dynamic zeroth-order B0 correction were applied on all reconstructions prior to off-resonance estimation and correction (Shahdloo et al, 2022).…”

“…Recently, we proposed a method to correct for these dynamic B0 changes (Shahdloo et al, 2022) by using the reference navigator data which are often available in most standard echo planar imaging (EPI) sequences used for fMRI data acquisition (Fig. 1a).…”

“… (a,b) EPI reference navigators in each frame are compared to a reference frame to estimate the dynamic linear off-resonance. These estimates are then used to correct the imaging data (Shahdloo et al, 2022). (c) This off-resonance correction method was validated in a decision-making task in awake NHPs, where the animals decide to act based on the number and colour of dots appearing on the screen, respond by touching a pad, and receive a liquid reward based on the response.…”

Dorsal Raphe Nucleus Controls Motivational State Transitions in Monkeys

“…Offline reconstruction of the raw functional data was performed following the dynamic off-resonance correction method developed by Shahdloo et al 80 . In summary, standard Nyquist ghost correction and dynamic zeroth-order B0 correction were applied first.…”