Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project
Open accessAbstract
The Human Connectome Project (HCP) relies primarily on three complementary magnetic resonance (MR) methods. These are: 1) resting state functional MR imaging (rfMRI) which uses correlations in the temporal fluctuations in an fMRI time series to deduce 'functional connectivity'; 2) diffusion imaging (dMRI), which provides the input for tractography algorithms used for the reconstruction of the complex axonal fiber architecture; and 3) task based fMRI (tfMRI), which is employed to identify functional parcellation in the human brain in order to assist analyses of data obtained with the first two methods. We describe technical improvements and optimization of these methods as well as instrumental choices that impact speed of acquisition of fMRI and dMRI images at 3T, leading to whole brain coverage with 2 mm isotropic resolution in 0.7 s for fMRI, and 1.25 mm isotropic resolution dMRI data for tractography analysis with three-fold reduction in total dMRI data acquisition time. Ongoing technical developments and optimization for acquisition of similar data at 7 T magnetic field are also presented, targeting higher spatial resolution, enhanced specificity of functional imaging signals, mitigation of the inhomogeneous radio frequency (RF) fields, and reduced power deposition. Results demonstrate that overall, these approaches represent a significant advance in MR imaging of the human brain to investigate brain function and structure.
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Work over two years to improve the 3T scanning protocols led to major progress in all four MR imaging modalities.
“A two-year effort to develop and refine the scanning protocols for the 3T Connectome Scanner has yielded important advances in each of the four MR-based imaging modalities (Ugurbil et al., 2013).”
From The WU-Minn Human Connectome Project: An overview (2013) · cites this paper as Ugurbil et al., 2013
Theory suggests that 100 mT/m helps diffusion imaging substantially more than 40 mT/m, but less than the 300 mT/m system used by MGH/UCLA.
“This specifically benefits diffusion imaging, and on theoretical grounds (Ugurbil et al., 2013) it should provide significant gains over the standard 40 mT/m though not as much as the 300 mT/m customized gradients used by the MGH/UCLA HCP consortium.”
From The WU-Minn Human Connectome Project: An overview (2013) · cites this paper as Ugurbil et al., 2013
Choosing the best multiband factor and other sequence settings involves complex trade-offs and required extensive pilot work.
“The optimal multiband factor and other pulse sequence parameters depend on a complex set of trade-offs that entailed extensive piloting and analysis (Ugurbil et al., 2013; Smith et al. 2013; Sotiropoulos et al., 2013c).”
From The WU-Minn Human Connectome Project: An overview (2013) · cites this paper as Ugurbil et al., 2013
With the WU-Minn diffusion method and b-values, 100 mT/m captures much of the benefit that 300 mT/m could offer.
“For the specific method and diffusion weighting (b values) chosen in the WU-Minn consortium, 100 mT/m maximal gradient strength provides much of the gain that would be available at 300 mT/m (Ugurbil et al. 2013); the relative merit of each depends on the method and b- values employed.”
From The WU-Minn Human Connectome Project: An overview (2013) · cites this paper as Ugurbil et al. 2013
Together with 1.25 mm isotropic resolution, this gives unusually good 3T whole-brain diffusion data.
“Combined with the spatial resolution of 1.25 mm isotropic, this yields exceptional data quality for in vivo whole brain diffusion imaging at 3T (Sotiropoulos et al., 2013c; Ugurbil et al., 2013).”
From The WU-Minn Human Connectome Project: An overview (2013) · cites this paper as Ugurbil et al., 2013
The standard reconstruction was substantially improved to raise data quality, particularly for dMRI, and to shorten reconstruction time for HCP's large datasets.
“Major improvements to the standard reconstruction process have been made in order to improve the data quality (especially for dMRI, Sotiropoulos et al. 2013c) and to reduce the reconstruction time for the very large HCP datasets (Ugurbil et al., 2013).”
From The WU-Minn Human Connectome Project: An overview (2013) · cites this paper as Ugurbil et al., 2013
Initial findings suggest whole-brain isotropic resolution near 1 mm is achievable with a TR near 2 s.
“Despite this, early results (see Ugurbil et al 2013) indicate that ~ 1mm isotropic resolutions over the whole brain are feasible with a TR of around 2 s.”
From The WU-Minn Human Connectome Project: An overview (2013) · cites this paper as Ugurbil et al 2013
Even with voxels about eight times smaller, functional contrast-to-noise holds up because image SNR and BOLD contrast rise.
“The functional contrast to noise at such high resolutions is not compromised, despite the ~ 8 times smaller voxel size, because of the aforementioned increases in image SNR and BOLD based contrast (Ugurbil et al., 2013).”
From The WU-Minn Human Connectome Project: An overview (2013) · cites this paper as Ugurbil et al., 2013
Signal-to-noise for subcortical regions is generally weaker than for cerebral and cerebellar cortical regions, largely because of their buried location relative to the 32-channel head coil.
“However, the SNR for subcortical regions is generally weaker than for cerebral and cerebellar cortical regions, in large part because of their buried location relative to the 32-channel head coil (Ugurbil et al, 2013).”
From The WU-Minn Human Connectome Project: An overview (2013) · cites this paper as Ugurbil et al, 2013
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Signal and noise characteristics of Hahn SE and GE BOLD fMRI at 7 T in humans
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Self-citationLayer-specific fMRI reflects different neuronal computations at different depths in human V1
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Initial results of cardiac imaging at 7 tesla
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Spatially Regularized Compressed Sensing for High Angular Resolution Diffusion Imaging
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Multi‐contrast reconstruction with Bayesian compressed sensing
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Self-citationHigh‐resolution fMRI using multislice partial k‐space GR‐EPI with cubic voxels
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Evaluation of highly accelerated simultaneous multi-slice EPI for fMRI
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Self-citationIn vivo magnetic resonance imaging and spectroscopy of humans with a 4 t whole‐body magnet
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Real‐time optical motion correction for diffusion tensor imaging
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REAL-TIME ECHO-PLANAR IMAGING BY NMR
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Cortex-based independent component analysis of fMRI time series
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Mapping Connections in Humans and Non-Human Primates
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Self-citationReduction of transmitter B1 inhomogeneity with transmit SENSE slice‐select pulses
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Simultaneous echo refocusing in EPI
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Self-citationDifferentiation of somatosensory cortices by high-resolution fMRI at 7 T
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Self-citationAccelerated volumetric MRI with a SENSE/GRAPPA combination
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Whole-body MR imaging and spectroscopy with a 4-T system.
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Self-citationAccelerated diffusion spectrum imaging with compressed sensing using adaptive dictionaries
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Head motion detection using FID navigators
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Self-citationThe road to functional imaging and ultrahigh fields
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Self-citationBroadband slab selection with B mitigation at 7T via parallel spectral‐spatial excitation
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Whole brain, high resolution spin-echo resting state fMRI using PINS multiplexing at 7T
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Self-citationSparse Multi-Shell Diffusion Imaging
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Self-citationJoint design of spoke trajectories and RF pulses for parallel excitation
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Self-citationLocal SAR reduction in parallel excitation based on channel‐dependent Tikhonov parameters
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Magnetic Resonance Field Strength Effects on Diffusion Measures and Brain Connectivity Networks
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Self-citationTheoretical and Numerical Aspects of Transmit SENSE
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Parametric Dictionary Learning for Modeling EAP and ODF in Diffusion MRI
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Optimal Design of Multiple Q-shells experiments for Diffusion MRI
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Self-citationCompressed Sensing for Accelerated EAP Recovery in Diffusion MRI
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How does DWI correlate with white matter structures?
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Practical considerations for the design of sparse-spokes pulses
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Accelerated Diffusion Spectrum Imaging with Compressed Sensing Using Adaptive Dictionaries
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Estimation of the CSA‐ODF using Bayesian compressed sensing of multi‐shell HARDI
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Accelerated diffusion spectrum imaging with compressed sensing using adaptive dictionaries
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Nonnegative Definite EAP and ODF Estimation via a Unified Multi-shell HARDI Reconstruction
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Spherical Polar Fourier EAP and odf reconstruction via compressed sensing in diffusion mri
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Research works printed but not linked: 6
- Auerbach EJ Xu J Yacoub E Moeller S Uğurbil K 2013 Reducing power in multi-banded RF pulses by time shifting Magn Reson Med In Press PMC3769699 23468087
- Caruyer E Cheng J Lenglet C Sapiro G Jiang T Deriche R 2012 Optimal Design of Multiple Q-shells experiments for Diffusion MRI Proceedings of MICCAI 2012 workshop on Computational Diffusion MRI Toronto
- Duarte-Carvajalino JM Lenglet C Ugurbil K Moeller S Carin L Sapiro G 2012 A Framework for Multi-task Bayesian Compressive Sensing of Diffusion-Weighted MRI Proceedings of MICCAI 2012 workshop on Computational Diffusion MRI Nice, France Oct 5 2012
- Kamath A Aganj I Xu J Yacoub E Ugurbil K Sapiro G Lenglet C 2012 Generalized Constant Solid Angle ODF and Optimal Acquisition Protocol for Fiber Orientation Mapping Proceedings of MICCAI 2012 workshop on Computational Diffusion MRI Nice, France Oct 5 2012
- Setsompop K Gagoski BA Polimeni JR Witzel T Wedeen VJ Wald LL 2012 Blipped-controlled aliasing in parallel imaging for simultaneous multislice echo planar imaging with reduced g-factor penalty Magn Reson Med 67 1210 1224 21858868 PMC3323676
- Wu X Schmitter S Auerbach AJ Moeller S Ugurbil K Van de Moortele PF 2013b Simultaneous multi-slice parallel RF excitation with independent slice-specific transmit B1 homogenization Proc Int Soc Mag Reson Med 21 74 PMC3884042 23801410
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Human Connectome Project informatics: Quality control, database services, and data visualization
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Evaluation and statistical inference for human connectomes
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- Authors
- Uğurbil, K., Xu, J., Auerbach, E. J., Moeller, S., Vu, A. T., Duarte-Carvajalino, J. M., Lenglet, C., Wu, X., Schmitter, S., Van de Moortele, P. F., Strupp, J., Sapiro, G., De Martino, F., Wang, D., Harel, N., Garwood, M., Chen, L., Feinberg, D. A., Smith, S. M., Miller, K. L., Sotiropoulos, S. N., Jbabdi, S., Andersson, J. L. R., Behrens, T. E. J., Glasser, M. F., Van Essen, D. C., & Yacoub, E.
- Affiliations
- University of Minnesota (US)
- Advanced MRI Technologies (United States) (US)
- University of Oxford (GB)
- Wellcome Centre for Human Neuroimaging (GB)
- Washington University in St. Louis (US)
- ORCID
- Xu, Junqian
- Auerbach, Edward J.
- Moeller, Steen
- Vu, An T.
- Lenglet, Christophe
- Wu, Xiaoping
- Schmitter, Sebastian
- Strupp, John
- Sapiro, Guillermo
- Harel, Noam
- Garwood, Michael
- Chen, Liyong
- Smith, Stephen M.
- Miller, Karla L.
- Sotiropoulos, Stamatios N.
- Andersson, Jesper L.R.
- Behrens, Timothy E.J.
- Glasser, Matthew F.
- Yacoub, Essa
- Venue
- NeuroImage
- Publisher
- Elsevier BV
- Published
- 2013-10
- Volume
- 80
- Pages
- 80-104
- ISSN
- 1053-8119 (ISSN-L)
- PMC
- PMC3740184
- OpenAlex
- W1993053013
- Cited by
- 812
- References
- 158
- Citations by year
- 2026: 43 · 2025: 55 · 2024: 63 · 2023: 53 · 2022: 76 · 2021: 87 · 2020: 59 · 2019: 66 · 2018: 76 · 2017: 69 · 2016: 64 · 2015: 51 · 2014: 33 · 2013: 15 · 2012: 1
- FWCI
- 41.83
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- NeuroImage (publishedVersion)
- PubMed (publishedVersion)
- Research Publications (Maastricht University) (publishedVersion)
- PubMed Central (acceptedVersion)
- UniTERAMO Research Catalog (University of Teramo) (submittedVersion)
- Research Publications (Maastricht University) (submittedVersion)
- Funders
- Human Connectome Project
- National Institutes of Health (1U54MH091657)
- Biotechnology Research Center (BTRC)
- NIBIB (P41 EB015894)
- NINDS Institutional Center (P30 NS076408)
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
- Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
- Keywords
- Human Connectome Project, resting-state fMRI, diffusion MRI, tractography, task-based fMRI, functional connectivity, accelerated MRI, isotropic resolution, 7T MRI, 3T MRI, radiofrequency field inhomogeneity, power deposition, RF pulse design, whole-brain imaging
- MeSH terms
- Animals, Brain, Humans, Image Enhancement, Models, Anatomic, Models, Neurological, Nerve Net, Diffusion Magnetic Resonance Imaging, Spatio-Temporal Analysis, Connectome
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