Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project

Abstract

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 3 Tesla, leading to whole brain coverage with 2 mm isotropic resolution in 0.7 second for fMRI, and 1.25 mm isotropic resolution dMRI data for tractography analysis with three-fold reduction in total data acquisition time. Ongoing technical developments and optimization for acquisition of similar data at 7 Tesla magnetic field are also presented, targeting higher resolution, specificity of functional imaging signals, mitigation of the inhomogeneous radio frequency (RF) fields and 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.

Auditory and visual connectivity gradients in frontoparietal cortex

“…Diffusion MRI (dMRI) data from the Human Connectome Project were obtained using a Siemens “Connectome Skyra” 3.0 Tesla MRI scanner using a 32‐channel receive head‐coil, and a customized SC72 gradient insert [Uğurbil et al, 2013]. Diffusion weighted MRI images were obtained using a spin‐echo echoplanar imaging (EPI) sequence with whole‐brain coverage (TR/TE = 5,520/89.5; 111 ascending slices with thickness 1.25 mm, voxel size 1.25 × 1.25 × 1.25 mm, flip angle 78°, field of view 210 × 180 mm, matrix 168 × 144, with a multiband acceleration factor of 3).…”

High‐resolution gradient‐recalled echo imaging at 9.4T using 16‐channel parallel transmit simultaneous multislice spokes excitations with slice‐by‐slice flip angle homogenization

“…Simultaneous multislice (SMS) imaging allows the signals from simultaneously excited slices to be separated using parallel imaging techniques 30, 31, 32, 33, 34. SMS has in recent years received considerable attention, especially for its ability to significantly accelerate blood‐oxygen‐level dependent and diffusion‐weighted echo planar imaging acquisitions 35, 36, 37, where SMS and in‐plane accelerations [e.g., SENSE 38 or generalized autocalibrating partially parallel acquisitions (GRAPPA) 39] work in synergy to reduce scan time as well as reduce artifacts such as geometric distortion and T 2 ‐blurring caused by long readout time. The application of SMS is also rapidly extending to the clinical domain for anatomical T 2 ‐ and ${\mathrm{normalT}}_2^{*}$‐weighted imaging and below the neck.…”

Two‐dimensional‐NGC‐SENSE‐GRAPPA for fast, ghosting‐robust reconstruction of in‐plane and slice‐accelerated blipped‐CAIPI echo planar imaging

“…This ensures that the correction is dominated by the slice that is closest to the coil to alleviate the problem to an extent 27.…”

“…Parameters were: SMS factor 3, in‐plane acceleration factor 2, FOV 210 mm, matrix 140, 81 27 slices of 1.5 mm, TE = 60 ms, echo spacing 0.36 ms, 32 channels, CAIPI FOV/2.…”