Optogenetic stimulation with BOLD-fMRI has been applied in studies of brain circuits, by selectiv... more Optogenetic stimulation with BOLD-fMRI has been applied in studies of brain circuits, by selectively exciting optical fluorophores with wavelength-specific light. However, the light used for stimulation may induce non-negligible heating effects. Because BOLD fMRI is mainly based on relatively long TE gradient-recalled echo acquisitions that are also suitable for measuring temperature changes with the proton resonance frequency (PRF) shift, we can monitor simultaneously the neural effects and laser-associated heating. We proposed a processing pipeline to calculate temperatures from BOLD images based on PRF shift thermometry and detect small temperature rises induced by laser-associated heating with general linear modeling.
PurposeTo calculate temperatures from T2*‐weighted images collected during optogenetic fMRI based... more PurposeTo calculate temperatures from T2*‐weighted images collected during optogenetic fMRI based on proton resonance frequency (PRF) shift thermometry, to monitor confounding heating effects and determine appropriate light parameters for optogenetic stimulation.MethodsfMRI is mainly based on long‐TE gradient‐recalled echo acquisitions that are also suitable for measuring small temperature changes via the PRF shift. A motion‐ and respiration‐robust processing pipeline was developed to calculate temperature changes based on the PRF shift directly from the T2*‐weighted images collected for fMRI with a two‐shot 2D gradient‐recalled echo‐EPI sequence at 9.4T. Optogenetic fMRI protocols which differed in stimulation durations (3, 6 and 9 s) within a total block duration of 30 s were applied in a squirrel monkey to validate the methods with blue and green light (20 Hz, 30 mW) delivery interleaved between periods. General linear modeling was performed on the resulting time series temperature maps to verify if light delivery with each protocol resulted in significant heating in the brain around the optical fiber.ResultsThe temperature SD was 0.05°C with the proposed imaging protocol and processing. Statistical analysis showed that the optogenetic stimulation protocol with a 3 s stimulation duration did not result in significant temperature rises. Significant temperature rises up to 0.13°C (p < 0. 05) were observed with 6 and 9 s stimulation durations for blue and green light.ConclusionThe proposed processing pipeline can be useful for the design of optogenetic stimulation protocols and for monitoring confounding heating effects.
A quadrature transmit/receive birdcage coil was optimized for squirrel monkey functional imaging ... more A quadrature transmit/receive birdcage coil was optimized for squirrel monkey functional imaging at the high field of 9.4 T. The coil length was chosen to gain maximum coil efficiency/signal-to-noise ratio (SNR) and meanwhile provide enough homogenous RF field in the whole brain area. Based on the numerical simulation results, a 16-rung high-pass birdcage coil with the optimal length of 9 cm was constructed and evaluated on phantom and in vivo experiments. Compared to a general-purpose non-optimized coil, it exhibits approximately 25% in vivo SNR improvement. In addition to the volume coil, details about how to design and construct the associated animal preparation system were provided.
Optogenetic stimulation combined with MRI detection of blood oxygenation level dependent (BOLD) e... more Optogenetic stimulation combined with MRI detection of blood oxygenation level dependent (BOLD) effects has been developed as a powerful tool to delineate brain circuits. Opsin targeting specific cell types induce neural activity when irradiated with light at a specific wavelength. We detected robust BOLD effects in secondary somatosensory cortex (S2) and downstream interconnected caudate putamen (CPu) of monkey brains from irradiation with low-intensity green light without exogenous green light specific opsin, suggesting hemodynamic changes can be stimulated without any associated neural activity.
RF shields are key components of volume coils, but they may cause imaging distortions and the sig... more RF shields are key components of volume coils, but they may cause imaging distortions and the significant heating. The effects of different shielding strategies were evaluated for a birdcage coil used to image animals at 9.4T. Three shields with various thicknesses and two shields with different slot patterns were comparatively investigated ed in terms of performance and temperature rise during fMRI acquisitions.
Intracortical microstimulation is one of the most common techniques used to activate cortical fun... more Intracortical microstimulation is one of the most common techniques used to activate cortical functional networks and probe causal connections. This study investigates whether BOLD signals can detect layer-specific functional circuit responses to electrical brain stimulation. We delivered electrical current to different layers of secondary somatosensory cortex (S2) and detected layer-specific BOLD activations. Effective functional connectivity analysis revealed different networks to different layers of S2 cortex.
Simultaneous imaging of brain and spinal cord regions potentially provides valuable information a... more Simultaneous imaging of brain and spinal cord regions potentially provides valuable information about how they work together and interact. However, to date, almost all studies have investigated these two highly interconnected systems separately, mainly because of a lack of adequate imaging coils. We designed a volume Tx and conformal receive array dedicated to simultaneous imaging of squirrel monkey brain and spinal cord at 9.4 T. The coil exhibits excellent SNR in both brain and spinal cord areas and can be used for studies investigating how the brain and spinal cord work together.
To image the pedunculopontine tegmental nucleus (PPN), a deep brain stimulation (DBS) target for ... more To image the pedunculopontine tegmental nucleus (PPN), a deep brain stimulation (DBS) target for Parkinson disease, using MRI with validated results. This study used the MP2RAGE sequence with high resolution and enhanced grey-white matter contrast on a 7-T ultra-high-field MRI system to image the PPN as well as a diffusion spectrum imaging method on a 3-T MRI system to reconstruct the main fibre systems surrounding the PPN. The coordinates of the rostral and caudal PPN poles of both sides were measured in relation to the third and fourth ventricular landmarks on the 7-T image. The boundary of the PPN was delineated, and showed morphology consistent with previous histological works. The main fibres around the PPN were reconstructed. The pole coordinate results combined with the fibre spatial relationships validate the imaging results. A practical protocol is provided to directly localise the PPN using MRI; the position and morphology of the PPN can be obtained and validated by locati...
A quadrature transmit/receive birdcage coil was optimized for squirrel monkey functional imaging ... more A quadrature transmit/receive birdcage coil was optimized for squirrel monkey functional imaging at the high field of 9.4 T. The coil length was chosen to gain maximum coil efficiency/signal-to-noise ratio (SNR) and meanwhile provide enough homogenous RF field in the whole brain area. Based on the numerical simulation results, a 16-rung high-pass birdcage coil with the optimal length of 9 cm was constructed and evaluated on phantom and in vivo experiments. Compared to a general-purpose non-optimized coil, it exhibits approximately 25% in vivo SNR improvement. In addition to the volume coil, details about how to design and construct the associated animal preparation system were provided.
Optogenetic stimulation with BOLD-fMRI has been applied in studies of brain circuits, by selectiv... more Optogenetic stimulation with BOLD-fMRI has been applied in studies of brain circuits, by selectively exciting optical fluorophores with wavelength-specific light. However, the light used for stimulation may induce non-negligible heating effects. Because BOLD fMRI is mainly based on relatively long TE gradient-recalled echo acquisitions that are also suitable for measuring temperature changes with the proton resonance frequency (PRF) shift, we can monitor simultaneously the neural effects and laser-associated heating. We proposed a processing pipeline to calculate temperatures from BOLD images based on PRF shift thermometry and detect small temperature rises induced by laser-associated heating with general linear modeling.
PurposeTo calculate temperatures from T2*‐weighted images collected during optogenetic fMRI based... more PurposeTo calculate temperatures from T2*‐weighted images collected during optogenetic fMRI based on proton resonance frequency (PRF) shift thermometry, to monitor confounding heating effects and determine appropriate light parameters for optogenetic stimulation.MethodsfMRI is mainly based on long‐TE gradient‐recalled echo acquisitions that are also suitable for measuring small temperature changes via the PRF shift. A motion‐ and respiration‐robust processing pipeline was developed to calculate temperature changes based on the PRF shift directly from the T2*‐weighted images collected for fMRI with a two‐shot 2D gradient‐recalled echo‐EPI sequence at 9.4T. Optogenetic fMRI protocols which differed in stimulation durations (3, 6 and 9 s) within a total block duration of 30 s were applied in a squirrel monkey to validate the methods with blue and green light (20 Hz, 30 mW) delivery interleaved between periods. General linear modeling was performed on the resulting time series temperature maps to verify if light delivery with each protocol resulted in significant heating in the brain around the optical fiber.ResultsThe temperature SD was 0.05°C with the proposed imaging protocol and processing. Statistical analysis showed that the optogenetic stimulation protocol with a 3 s stimulation duration did not result in significant temperature rises. Significant temperature rises up to 0.13°C (p < 0. 05) were observed with 6 and 9 s stimulation durations for blue and green light.ConclusionThe proposed processing pipeline can be useful for the design of optogenetic stimulation protocols and for monitoring confounding heating effects.
A quadrature transmit/receive birdcage coil was optimized for squirrel monkey functional imaging ... more A quadrature transmit/receive birdcage coil was optimized for squirrel monkey functional imaging at the high field of 9.4 T. The coil length was chosen to gain maximum coil efficiency/signal-to-noise ratio (SNR) and meanwhile provide enough homogenous RF field in the whole brain area. Based on the numerical simulation results, a 16-rung high-pass birdcage coil with the optimal length of 9 cm was constructed and evaluated on phantom and in vivo experiments. Compared to a general-purpose non-optimized coil, it exhibits approximately 25% in vivo SNR improvement. In addition to the volume coil, details about how to design and construct the associated animal preparation system were provided.
Optogenetic stimulation combined with MRI detection of blood oxygenation level dependent (BOLD) e... more Optogenetic stimulation combined with MRI detection of blood oxygenation level dependent (BOLD) effects has been developed as a powerful tool to delineate brain circuits. Opsin targeting specific cell types induce neural activity when irradiated with light at a specific wavelength. We detected robust BOLD effects in secondary somatosensory cortex (S2) and downstream interconnected caudate putamen (CPu) of monkey brains from irradiation with low-intensity green light without exogenous green light specific opsin, suggesting hemodynamic changes can be stimulated without any associated neural activity.
RF shields are key components of volume coils, but they may cause imaging distortions and the sig... more RF shields are key components of volume coils, but they may cause imaging distortions and the significant heating. The effects of different shielding strategies were evaluated for a birdcage coil used to image animals at 9.4T. Three shields with various thicknesses and two shields with different slot patterns were comparatively investigated ed in terms of performance and temperature rise during fMRI acquisitions.
Intracortical microstimulation is one of the most common techniques used to activate cortical fun... more Intracortical microstimulation is one of the most common techniques used to activate cortical functional networks and probe causal connections. This study investigates whether BOLD signals can detect layer-specific functional circuit responses to electrical brain stimulation. We delivered electrical current to different layers of secondary somatosensory cortex (S2) and detected layer-specific BOLD activations. Effective functional connectivity analysis revealed different networks to different layers of S2 cortex.
Simultaneous imaging of brain and spinal cord regions potentially provides valuable information a... more Simultaneous imaging of brain and spinal cord regions potentially provides valuable information about how they work together and interact. However, to date, almost all studies have investigated these two highly interconnected systems separately, mainly because of a lack of adequate imaging coils. We designed a volume Tx and conformal receive array dedicated to simultaneous imaging of squirrel monkey brain and spinal cord at 9.4 T. The coil exhibits excellent SNR in both brain and spinal cord areas and can be used for studies investigating how the brain and spinal cord work together.
To image the pedunculopontine tegmental nucleus (PPN), a deep brain stimulation (DBS) target for ... more To image the pedunculopontine tegmental nucleus (PPN), a deep brain stimulation (DBS) target for Parkinson disease, using MRI with validated results. This study used the MP2RAGE sequence with high resolution and enhanced grey-white matter contrast on a 7-T ultra-high-field MRI system to image the PPN as well as a diffusion spectrum imaging method on a 3-T MRI system to reconstruct the main fibre systems surrounding the PPN. The coordinates of the rostral and caudal PPN poles of both sides were measured in relation to the third and fourth ventricular landmarks on the 7-T image. The boundary of the PPN was delineated, and showed morphology consistent with previous histological works. The main fibres around the PPN were reconstructed. The pole coordinate results combined with the fibre spatial relationships validate the imaging results. A practical protocol is provided to directly localise the PPN using MRI; the position and morphology of the PPN can be obtained and validated by locati...
A quadrature transmit/receive birdcage coil was optimized for squirrel monkey functional imaging ... more A quadrature transmit/receive birdcage coil was optimized for squirrel monkey functional imaging at the high field of 9.4 T. The coil length was chosen to gain maximum coil efficiency/signal-to-noise ratio (SNR) and meanwhile provide enough homogenous RF field in the whole brain area. Based on the numerical simulation results, a 16-rung high-pass birdcage coil with the optimal length of 9 cm was constructed and evaluated on phantom and in vivo experiments. Compared to a general-purpose non-optimized coil, it exhibits approximately 25% in vivo SNR improvement. In addition to the volume coil, details about how to design and construct the associated animal preparation system were provided.
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