Jonathan R. Polimeni

The organization of the human cerebral cortex estimated by intrinsic functional connectivity

Information processing in the cerebral cortex involves interactions among distributed areas. Anatomical connectivity suggests that certain areas form local hierarchical relations such as within the visual system. Other connectivity patterns, particularly among association areas, suggest the presence of large-scale circuits without clear hierarchical relations. In this study the organization of networks in the human cerebrum was explored using resting-state functional connectivity MRI. Data from 1,000 subjects were registered using surface-based alignment. A clustering approach was employed to identify and replicate networks of functionally coupled regions across the cerebral cortex. The results revealed local networks confined to sensory and motor cortices as well as distributed networks of association regions. Within the sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas. In association cortex, the connectivity patterns often showed abrupt transitions between network boundaries. Focused analyses were performed to better understand properties of network connectivity. A canonical sensory-motor pathway involving primary visual area, putative middle temporal area complex (MT+), lateral intraparietal area, and frontal eye field was analyzed to explore how interactions might arise within and between networks. Results showed that adjacent regions of the MT+ complex demonstrate differential connectivity consistent with a hierarchical pathway that spans networks. The functional connectivity of parietal and prefrontal association cortices was next explored. Distinct connectivity profiles of neighboring regions suggest they participate in distributed networks that, while showing evidence for interactions, are embedded within largely parallel, interdigitated circuits. We conclude by discussing the organization of these large-scale cerebral networks in relation to monkey anatomy and their potential evolutionary expansion in humans to support cognition.

The minimal preprocessing pipelines for the Human Connectome Project

The Human Connectome Project (HCP) faces the challenging task of bringing multiple magnetic resonance imaging (MRI) modalities together in a common automated preprocessing framework across a large cohort of subjects. The MRI data acquired by the HCP differ in many ways from data acquired on conventional 3 Tesla scanners and often require newly developed preprocessing methods. We describe the minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space. These pipelines are specially designed to capitalize on the high quality data offered by the HCP. The final standard space makes use of a recently introduced CIFTI file format and the associated grayordinate spatial coordinate system. This allows for combined cortical surface and subcortical volume analyses while reducing the storage and processing requirements for high spatial and temporal resolution data. Here, we provide the minimum image acquisition requirements for the HCP minimal preprocessing pipelines and additional advice for investigators interested in replicating the HCPs acquisition protocols or using these pipelines. Finally, we discuss some potential future improvements to the pipelines.

Blipped-controlled aliasing in parallel imaging for simultaneous multislice echo planar imaging with reduced g-factor penalty

Simultaneous multislice Echo Planar Imaging (EPI) acquisition using parallel imaging can decrease the acquisition time for diffusion imaging and allow full‐brain, high‐resolution functional MRI (fMRI) acquisitions at a reduced repetition time (TR). However, the unaliasing of simultaneously acquired, closely spaced slices can be difficult, leading to a high g‐factor penalty. We introduce a method to create interslice image shifts in the phase encoding direction to increase the distance between aliasing pixels. The shift between the slices is induced using sign‐ and amplitude‐modulated slice‐select gradient blips simultaneous with the EPI phase encoding blips. This achieves the desired shifts but avoids an undesired “tilted voxel” blurring artifact associated with previous methods. We validate the method in 3× slice‐accelerated spin‐echo and gradient‐echo EPI at 3 T and 7 T using 32‐channel radio frequency (RF) coil brain arrays. The Monte‐Carlo simulated average g‐factor penalty of the 3‐fold slice‐accelerated acquisition with interslice shifts is <1% at 3 T (compared with 32% without slice shift). Combining 3× slice acceleration with 2× inplane acceleration, the g‐factor penalty becomes 19% at 3 T and 10% at 7 T (compared with 41% and 23% without slice shift). We demonstrate the potential of the method for accelerating diffusion imaging by comparing the fiber orientation uncertainty, where the 3‐fold faster acquisition showed no noticeable degradation. Magn Reson Med, 2012.

Laminar analysis of 7 T BOLD using an imposed spatial activation pattern in human V1

With sufficient image encoding, high-resolution fMRI studies are limited by the biological point-spread of the hemodynamic signal. The extent of this spread is determined by the local vascular distribution and by the spatial specificity of blood flow regulation, as well as by measurement parameters that (i) alter the relative sensitivity of the acquisition to activation-induced hemodynamic changes and (ii) determine the image contrast as a function of vessel size. In particular, large draining vessels on the cortical surface are a major contributor to both the BOLD signal change and to the spatial bias of the BOLD activation away from the site of neuronal activity. In this work, we introduce a laminar surface-based analysis method and study the relationship between spatial localization and activation strength as a function of laminar depth by acquiring 1mm isotropic, single-shot EPI at 7 T and sampling the BOLD signal exclusively from the superficial, middle, or deep cortical laminae. We show that highly-accelerated EPI can limit image distortions to the point where a boundary-based registration algorithm accurately aligns the EPI data to the surface reconstruction. The spatial spread of the BOLD response tangential to the cortical surface was analyzed as a function of cortical depth using our surface-based analysis. Although sampling near the pial surface provided the highest signal strength, it also introduced the most spatial error. Thus, avoiding surface laminae improved spatial localization by about 40% at a cost of 36% in z-statistic, implying that optimal spatial resolution in functional imaging of the cortex can be achieved using anatomically-informed spatial sampling to avoid large pial vessels.

96‐Channel receive‐only head coil for 3 Tesla: Design optimization and evaluation

The benefits and challenges of highly parallel array coils for head imaging were investigated through the development of a 3T receive‐only phased‐array head coil with 96 receive elements constructed on a close‐fitting helmet‐shaped former. We evaluated several designs for the coil elements and matching circuitry, with particular attention to sources of signal‐to‐noise ratio (SNR) loss, including various sources of coil loading and coupling between the array elements. The SNR and noise amplification (g‐factor) in accelerated imaging were quantitatively evaluated in phantom and human imaging and compared to a 32‐channel array built on an identical helmet‐shaped former and to a larger commercial 12‐channel head coil. The 96‐channel coil provided substantial SNR gains in the distal cortex compared to the 12‐ and 32‐channel coils. The central SNR for the 96‐channel coil was similar to the 32‐channel coil for optimum SNR combination and 20% lower for root‐sum‐of‐squares combination. There was a significant reduction in the maximum g‐factor for 96 channels compared to 32; for example, the 96‐channel maximum g‐factor was 65% of the 32‐channel value for acceleration rate 4. The performance of the array is demonstrated in highly accelerated brain images. Magn Reson Med, 2009.

Accurate prediction of V1 location from cortical folds in a surface coordinate system

Previous studies demonstrated substantial variability of the location of primary visual cortex (V1) in stereotaxic coordinates when linear volume-based registration is used to match volumetric image intensities [Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., and Zilles, K. (2000). Brodmanns areas 17 and 18 brought into stereotaxic space-where and how variable? Neuroimage, 11(1):66-84]. However, other qualitative reports of V1 location [Smith, G. (1904). The morphology of the occipital region of the cerebral hemisphere in man and the apes. Anatomischer Anzeiger, 24:436-451; Stensaas, S.S., Eddington, D.K., and Dobelle, W.H. (1974). The topography and variability of the primary visual cortex in man. J Neurosurg, 40(6):747-755; Rademacher, J., Caviness, V.S., Steinmetz, H., and Galaburda, A.M. (1993). Topographical variation of the human primary cortices: implications for neuroimaging, brain mapping, and neurobiology. Cereb Cortex, 3(4):313-329] suggested a consistent relationship between V1 and the surrounding cortical folds. Here, the relationship between folds and the location of V1 is quantified using surface-based analysis to generate a probabilistic atlas of human V1. High-resolution (about 200 microm) magnetic resonance imaging (MRI) at 7 T of ex vivo human cerebral hemispheres allowed identification of the full area via the stria of Gennari: a myeloarchitectonic feature specific to V1. Separate, whole-brain scans were acquired using MRI at 1.5 T to allow segmentation and mesh reconstruction of the cortical gray matter. For each individual, V1 was manually identified in the high-resolution volume and projected onto the cortical surface. Surface-based intersubject registration [Fischl, B., Sereno, M.I., Tootell, R.B., and Dale, A.M. (1999b). High-resolution intersubject averaging and a coordinate system for the cortical surface. Hum Brain Mapp, 8(4):272-84] was performed to align the primary cortical folds of individual hemispheres to those of a reference template representing the average folding pattern. An atlas of V1 location was constructed by computing the probability of V1 inclusion for each cortical location in the template space. This probabilistic atlas of V1 exhibits low prediction error compared to previous V1 probabilistic atlases built in volumetric coordinates. The increased predictability observed under surface-based registration suggests that the location of V1 is more accurately predicted by the cortical folds than by the shape of the brain embedded in the volume of the skull. In addition, the high quality of this atlas provides direct evidence that surface-based intersubject registration methods are superior to volume-based methods at superimposing functional areas of cortex and therefore are better suited to support multisubject averaging for functional imaging experiments targeting the cerebral cortex.

Slice-Selective RF pulses for In-vivo B1+ Inhomogeneity Mitigation at 7 Tesla using Parallel RF Excitation with a 16-Element Coil

Slice‐selective RF waveforms that mitigate severe B  1+ inhomogeneity at 7 Tesla using parallel excitation were designed and validated in a water phantom and human studies on six subjects using a 16‐element degenerate stripline array coil driven with a butler matrix to utilize the eight most favorable birdcage modes. The parallel RF waveform design applied magnitude least‐squares (MLS) criteria with an optimized k‐space excitation trajectory to significantly improve profile uniformity compared to conventional least‐squares (LS) designs. Parallel excitation RF pulses designed to excite a uniform in‐plane flip angle (FA) with slice selection in the z‐direction were demonstrated and compared with conventional sinc‐pulse excitation and RF shimming. In all cases, the parallel RF excitation significantly mitigated the effects of inhomogeneous B  1+ on the excitation FA. The optimized parallel RF pulses for human B  1+ mitigation were only 67% longer than a conventional sinc‐based excitation, but significantly outperformed RF shimming. For example the standard deviations (SDs) of the in‐plane FA (averaged over six human studies) were 16.7% for conventional sinc excitation, 13.3% for RF shimming, and 7.6% for parallel excitation. This work demonstrates that excitations with parallel RF systems can provide slice selection with spatially uniform FAs at high field strengths with only a small pulse‐duration penalty. Magn Reson Med 60:1422–1432, 2008.

A 128-channel receive-only cardiac coil for highly accelerated cardiac MRI at 3 Tesla

A 128‐channel receive‐only array coil is described and tested for cardiac imaging at 3T. The coil is closely contoured to the body with a “clam‐shell” geometry with 68 posterior and 60 anterior elements, each 75 mm in diameter, and arranged in a continuous overlapped array of hexagonal symmetry to minimize nearest neighbor coupling. Signal‐to‐noise ratio (SNR) and noise amplification for parallel imaging (G‐factor) were evaluated in phantom and volunteer experiments. These results were compared to those of commercially available 24‐channel and 32‐channel coils in routine use for cardiac imaging. The in vivo measurements with the 128‐channel coil resulted in SNR gains compared to the 24‐channel coil (up to 2.2‐fold in the apex). The 128‐ and 32‐channel coils showed similar SNR in the heart, likely dominated by the similar element diameters of these coils. The maximum G‐factor values were up to seven times better for a seven‐fold acceleration factor (R = 7) compared to the 24‐channel coil and up to two‐fold improved compared to the 32‐channel coil. The ability of the 128‐channel coil to facilitate highly accelerated cardiac imaging was demonstrated in four volunteers using acceleration factors up to seven‐fold (R = 7) in a single spatial dimension. Magn Reson Med 59:1431–1439, 2008.

T2* mapping and B0 orientation-dependence at 7 T reveal cyto- and myeloarchitecture organization of the human cortex

Ultra-high field MRI (≥ 7 T) has recently shown great sensitivity to depict patterns of tissue microarchitecture. Moreover, recent studies have demonstrated a dependency between T₂* and orientation of white matter fibers with respect to the main magnetic field B₀. In this study we probed the potential of T₂* mapping at 7 T to provide new markers of cortical architecture. We acquired multi-echo measurements at 7 T and mapped T₂* over the entire cortex of eight healthy individuals using surface-based analysis. B₀ dependence was tested by computing the angle θ(z) between the normal of the surface and the direction of B₀, then fitting T₂*(θ(z)) using model from the literature. Average T₂* in the cortex was 32.20 +/- 1.35 ms. Patterns of lower T₂* were detected in the sensorimotor, visual and auditory cortices, likely reflecting higher myelin content. Significantly lower T₂* was detected in the left hemisphere of the auditory region (p<0.005), suggesting higher myelin content, in accordance with previous investigations. B₀ orientation dependence was detected in some areas of the cortex, the strongest being in the primary motor cortex (∆R₂*=4.10 Hz). This study demonstrates that quantitative T₂* measures at 7 T MRI can reveal patterns of cytoarchitectural organization of the human cortex in vivo and that B₀ orientation dependence can probe the coherency and orientation of gray matter fibers in the cortex, shedding light into the potential use of this type of contrast to characterize cyto-/myeloarchitecture and to understand the pathophysiology of diseases associated with changes in iron and/or myelin concentration.

Functional magnetic resonance imaging detection of vascular reactivity in cerebral amyloid angiopathy.

In addition to its role in hemorrhagic stroke, advanced cerebral amyloid angiopathy (CAA) is also associated with ischemic lesions and vascular cognitive impairment. We used functional magnetic resonance imaging (MRI) techniques to identify CAA‐associated vascular dysfunction.