- Jonathan Westley Peirce
Alex Beckett currently works at the Helen Wills Neuroscience Institute, University of California, Berkeley. Alex does research in Neuroscience, Psychophysics and Cognitive Psychology. Their current project is 'MRI Corticography (MRCoG): Micro-scale Human Cortical Imaging'.
To image the activity and connections of the brain's cortex on a micro scale – with dramatically higher resolution than existing scanners
Research Item (11)
High isotropic resolution fMRI is challenging primarily due to long repetition times (TR) and insufficient SNR, especially at lower field strengths. Recently, Simultaneous Multi-Slice (SMS) imaging with blipped-CAIPI has substantially reduced scan time and improved SNR efficiency of fMRI. Similarly, super-resolution techniques utilizing sub- voxel spatial shifts in the slice direction have increased both resolution and SNR efficiency. Here we demonstrate the synergistic combination of SLIce Dithered Enhanced Resolution (SLIDER) and SMS for high-resolution, high-SNR whole brain fMRI in comparison to standard resolution fMRI data as well as high-resolution data. With SLIDER-SMS, high spatial frequency information is recovered (unaliased) even in absence of super-resolution deblurring algorithms. Additionally we find that BOLD CNR (as measured by t-value in a visual checkerboard paradigm) is improved by as much as 100% relative to traditionally acquired high- resolution data. Using this gain in CNR, we are able to obtain unprecedented nominally isotropic resolutions at 3 T (0.66 mm) and 7 T (0.45 mm).
Encoding higher spatial resolution in simultaneous multi-slice (SMS) EPI is highly dependent on gradient performance, high density receiver coil arrays and pulse sequence optimization. We simulate gradient amplitude and slew rate determination of EPI imaging performance in terms of minimum TE, echo spacing (ES) and spatial resolution. We discuss the effects of image zooming in pulse sequences that have been used for sub-millimeter resolutions and the trade-offs in using partial Fourier and parallel imaging to reduce TE, PSF and ES. Using optimizations for SMS EPI pulse sequences with available gradient and receiver hardware, experimental results in ultra-high resolution (UHR) (0.45–0.5mm isotropic) SMS-EPI fMRI and mapping ocular dominance columns (ODC) in human brain at 0.5 mm isotropic resolution are demonstrated. We discuss promising future directions of UHR fMRI.
- Aug 2015
Cerebrospinal fluid (CSF) dynamics have been mostly studied with cardiac-gated phase contrast MRI combining signal from many cardiac cycles to create cine-phase sampling of one time averaged cardiac cycle. The relative effects of cardiac and respiratory changes on CSF movement are not well understood. There is possible respiration driven movement of CSF in ventricles, cisterns, and subarachnoid spaces which has not been characterized with velocity measurements. To date, commonly used cine-phase contrast techniques of velocity imaging inherently cannot detect respiratory velocity changes since cardiac gated data acquired over several minutes randomizes respiratory phase contributions. We have developed an extremely fast, real-time and quantitative MRI technique to image CSF velocity in simultaneous multi-slice (SMS) echo planar imaging (EPI) acquisitions of 3 or 6 slice levels simultaneously over 30 seconds and observe 3D spatial distributions of CSF velocity. Measurements were made in 10 subjects utilizing a respiratory belt to record respiratory phases and visual cues to instruct subjects on breathing rates. A protocol is able to measure velocity within regions of brain and basal cisterns covered with 24 axial slices in 4 minutes, repeated for 3 velocity directions. These measurements were performed throughout the whole brain, rather than in selected line regions so that a global view of CSF dynamics could be visualized. Observations of cardiac and breathing-driven CSF dynamics show bidirectional respiratory motion occurs primarily along the central axis through the basal cisterns and intraventricular passageways and to a lesser extent in the peripheral Sylvian fissure with little CSF motion present in subarachnoid spaces. During inspiration phase, there is upward (inferior to superior direction) CSF movement into the cranial cavity and into the lateral ventricles and a reversed direction in expiration phase. Copyright © 2015. Published by Elsevier Inc.
Simultaneous multi-slice EPI has been combined with pulsed ASL to record several times more images than conventional EPI. Comparison of quantitative CBF maps and perfusion weighted images show good agreement to EPI. Comparisons to segmented 3D GRASE ASL shows differences in scan times and susceptibility artifacts with advantages of background suppression and higher SNR in 3D GRASE, while both achieve whole brain slice coverage.
A new highly efficient velocity imaging technique is developed with simultaneous multi-slice EPI and zoomed spatial resolution which enables real-time measurement of CSF and brain velocity. Application of this 7D imaging technique to normal subjects revealed respiratory synchronous motion modulating cardiac waveforms in brain parenchyma and CSF. The brain pulsations may play a role in clearance of interstitial fluid in the brain.
- Dec 2013
Simultaneous multi-slice (SMS) echo planar imaging (EPI) is incorporated into two-dimensional (2D) arterial spin labeling (ASL) imaging to produce more slices for measuring perfusion in a larger region of the brain than currently possible with multi-slice EPI. Pulsed ASL (PASL) preparations using FAIR and QUIPSS II techniques were combined with SMS-EPI. Testing was performed in four subjects at 3 Tesla. Multiband slice acceleration factors (MB) from MB-2 to MB-5 using 40 averages were evaluated. Comparisons were made quantitatively to PASL 2D EPI and qualitatively to PASL 3D GRASE. In the 12 slice data set, spatial SNR for the perfusion weighted images averaged across subjects was 3.28 and 3.44 for the two sequential MB-1 acquisitions as control comparison, 3.25 for MB-2 and 2.98 for MB-3. The temporal SNR averaged 1.01 and 0.99 for MB-1, 0.89 for MB-2, and 0.78 for MB-3. For whole-brain spatial coverage, the 20 slice data sets could be acquired in narrower time windows, from 874 ms using EPI (MB-1) down to 196 ms using MB-5. SMS-EPI ASL differed from 3D GRASE ASL, which can use background suppression and has less susceptibility artifact as a CPMG SE sequence. SMS-EPI has a major advantage over EPI-based ASL imaging by increasing slice coverage without lengthening the acquisition time window. Magn Reson Med, 2013. © 2013 Wiley Periodicals, Inc.
Functional magnetic resonance imaging (fMRI) offers a number of opportunities to non-invasively study the properties of the human visual system. Advances in scanner technology, particularly the development of high-field scanners, allow improvements in fMRI such as higher resolution and higher signal to noise ratio (SNR). We aimed to examine what these advances in scanner technology, combined with novel analysis techniques, can tell us about the processing of motion stimuli in the human visual cortex. In Chapter 3 we investigated whether high-resolution fMRI allows us to directly study motion-selective responses in MT+. We used event-related and adaptation methods to examine selectivity for coherent motion and selectivity for direction of motion, and examined the potential limitations of these techniques. One particular analysis technique that has been developed in recent years uses multivariate methods to classify patterns of activity from visual cortex. In Chapter 4 we investigated these methods for classifying direction of motion, particularly whether successful classification responses are based on fine-scale information such as the arrangement of direction-selective columns, or a global signal at a coarser scale. In Chapter 5 we investigated multivariate classification of non-translational motion (e.g. rotation) to see how this compared to the classification of translational motion. The processing of such stimuli have been suggested to be free from the large-scale signals that may be involved in other stimuli, and therefore a more powerful tool for studying the neural architecture of visual cortex. Chapter 6 investigated the processing of plaid motion stimuli, specifically ’pattern’ motion selectivity in MT+ as opposed to ’component’ motion selectivity. These experiments highlight the usefulness of multivariate methods even if the scale of the signal is unknown.
The primary somatosensory cortex (S1) can be subdivided cytoarchitectonically into four distinct Brodmann areas (3a, 3b, 1, and 2), but these areas have never been successfully delineated in vivo in single human subjects. Here, we demonstrate the functional parcellation of four areas of S1 in individual human subjects based on high-resolution functional MRI measurements made at 7 T using vibrotactile stimulation. By stimulating four sites along the length of the index finger, we were able to identify and locate map reversals of the base to tip representation of the index finger in S1. We suggest that these reversals correspond to the areal borders between the mirrored representations in the four Brodmann areas, as predicted from electrophysiology measurements in nonhuman primates. In all subjects, maps were highly reproducible across scanning sessions and stable over weeks. In four of the six subjects scanned, four, mirrored, within-finger somatotopic maps defining the extent of the Brodmann areas could be directly observed on the cortical surface. In addition, by using multivariate classification analysis, the location of stimulation on the index finger (four distinct sites) could be decoded with a mean accuracy of 65% across subjects. Our measurements thus show that within-finger topography is present at the millimeter scale in the cortex and is highly reproducible. The ability to identify functional areas of S1 in vivo in individual subjects will provide a framework for investigating more complex aspects of tactile representation in S1.
Previous studies have demonstrated that the perceived direction of motion of a visual stimulus can be decoded from the pattern of functional magnetic resonance imaging (fMRI) responses in occipital cortex using multivariate analysis methods (Kamitani and Tong, 2006). One possible mechanism for this is a difference in the sampling of direction selective cortical columns between voxels, implying that information at a level smaller than the voxel size might be accessible with fMRI. Alternatively, multivariate analysis methods might be driven by the organization of neurons into clusters or even orderly maps at a much larger scale. To assess the possible sources of the direction selectivity observed in fMRI data, we tested how classification accuracy varied across different visual areas and subsets of voxels for classification of motion-direction. To enable high spatial resolution functional MRI measurements (1.5mm isotropic voxels), data were collected at 7T. To test whether information about the direction of motion is represented at the scale of retinotopic maps, we looked at classification performance after combining data across different voxels within visual areas (V1-3 and MT+/V5) before training the multivariate classifier. A recent study has shown that orientation biases in V1 are both necessary and sufficient to explain classification of stimulus orientation (Freeman et al., 2011). Here, we combined voxels with similar visual field preference as determined in separate retinotopy measurements and observed that classification accuracy was preserved when averaging in this 'retinotopically restricted' way, compared to random averaging of voxels. This insensitivity to averaging of voxels (with similar visual angle preference) across substantial distances in cortical space suggests that there are large-scale biases at the level of retinotopic maps underlying our ability to classify direction of motion.
Previous studies have demonstrated that the perceived direction of motion of a visual stimulus can be decoded from the pattern of fMRI responses in occipital cortex (Kamitani and Tong, 2006). One possible mechanism for this is a difference in the sampling of direction selective columns between voxels, implying that sub-voxel information may be accessible with fMRI. To assess the possible sources of this direction-selectivity, we tested how classification accuracy varied across different visual areas and subsets of voxels for 8-way direction classification. Functional imaging data were collected using 3D-gradient-echo EPI at 7T (Achieva, Philips; SPMMR Centre, Nottingham) using 1.5 mm isotropic voxels, (volume TR 2s). In one set of analyses we tested how classification accuracy varied with the number of voxels used. We used a ‘searchlight’ technique that performs classification based on a spherically defined subsets of voxels (Kriegeskorte et al., 2006) and found classification performance above chance across several visual areas (V1–V4, V5/hMT+) and in areas of the intraparietal sulcus, with a range of searchlight sizes (radius 7.5–10.5 mm). In the second set of analyses, we looked at classification performance after combining data across different voxels within visual areas (with similar visual angle preference from retinotopy) before classifier training. Preserved classification accuracy when averaging in this way, compared to random averaging of voxels, suggests that there may be large-scale biases at the level of retinotopic maps underlying some part of our results (see also Freeman et al., 2010).
- Jul 2010
To investigate the independent role of spatial frequency on component motion integration. Two Type II plaids were presented at varying spatial frequencies. The velocity vectors of the underlying components were constructed so that predicted speed and direction from the components; the Intersection of Constraints; the vector average; and distortion products, remained constant for each of the two plaids across spatial frequency. Perceived direction was measured using a method of adjustment. Perceived direction changed as a function of spatial frequency, approaching the pattern direction only at spatial frequencies greater than 0.5cpd. Spatial frequency has an independent effect on the component integration stage that determines perceived pattern motion direction. The results appear to reflect the resolution of orientation for recombination of the components at low spatial frequencies. These results have implications for motion modelling and possible clinical applications.