Simultaneous echo refocusing in EPI

Single-shot T2 mapping via multi-echo-train multiple overlapping-echo detachment planar imaging and multitask deep learning

BACKGROUND

Quantitative magnetic resonance imaging provides robust biomarkers in clinics. Nevertheless, the lengthy scan time reduces imaging throughput and increases the susceptibility of imaging results to motion. In this context, a single-shot T₂ mapping method based on multiple overlapping-echo detachment (MOLED) planar imaging was presented, but the relatively small echo time range limits its accuracy, especially in tissues with large T₂ .

PURPOSE

In this work we proposed a novel single-shot method, Multi-Echo-Train Multiple OverLapping-Echo Detachment (METMOLED) planar imaging, to accommodate a large range of T₂ quantification without additional measurements to rectify signal degeneration arisen from refocusing pulse imperfection.

METHODS

Multiple echo-train techniques were integrated into the MOLED sequence to capture larger TE information. Maps of T₂ , B₁ , and spin density were reconstructed synchronously from acquired METMOLED data via multitask deep learning. A typical U-Net was trained with 3000/600 synthetic data with geometric/brain patterns to learn the mapping relationship between METMOLED signals and quantitative maps. The refocusing pulse imperfection was settled through the inherent information of METMOLED data and auxiliary tasks.

RESULTS

Experimental results on the digital brain (structural similarity (SSIM) index = 0.975/0.991/0.988 for MOLED/METMOLED-2/METMOLED-3, hyphenated number denotes the number of echo-trains), physical phantom (the slope of linear fitting with reference T₂ map = 1.047/1.017/1.006 for MOLED/METMOLED-2/METMOLED-3), and human brain (Pearson's correlation coefficient (PCC) = 0.9581/0.9760/0.9900 for MOLED/METMOLED-2/METMOLED-3) demonstrated that the METMOLED improved the quantitative accuracy and the tissue details in contrast to the MOLED. These improvements were more pronounced in tissues with large T₂ and in application scenarios with high temporal resolution (PCC = 0.8692/0.9465/0.9743 for MOLED/METMOLED-2/METMOLED-3). Moreover, the METMOLED could rectify the signal deviations induced by the non-ideal slice profiles of refocusing pulses without additional measurements. A preliminary measurement also demonstrated that the METMOLED is highly repeatable (mean coefficient of variation (CV) = 1.65%).

CONCLUSIONS

METMOLED breaks the restriction of echo-train length to TE and implements unbiased T₂ estimates in an extensive range. Furthermore, it corrects the effect of refocusing pulse inaccuracy without additional measurements or signal post-processing, thus retaining its single-shot characteristic. This technique would be beneficial for accurate T₂ quantification.

SLOW: A novel spectral editing method for whole-brain MRSI at ultra high magnetic field

PURPOSE

At ultra-high field (UHF), B₁ ⁺ -inhomogeneities and high specific absorption rate (SAR) of adiabatic slice-selective RF-pulses make spatial resolved spectral-editing extremely challenging with the conventional MEGA-approach. The purpose of the study was to develop a whole-brain resolved spectral-editing MRSI at UHF (UHF, B₀  ≥ 7T) within clinical acceptable measurement-time and minimal chemical-shift-displacement-artifacts (CSDA) allowing for simultaneous GABA/Glx-, 2HG-, and PE-editing on a clinical approved 7T-scanner.

METHODS

Slice-selective adiabatic refocusing RF-pulses (2π-SSAP) dominate the SAR to the patient in (semi)LASER based MEGA-editing sequences, causing large CSDA and long measurement times to fulfill SAR requirements, even using SAR-minimized GOIA-pulses. Therefore, a novel type of spectral-editing, called SLOW-editing, using two different pairs of phase-compensated chemical-shift selective adiabatic refocusing-pulses (2π-CSAP) with different refocusing bandwidths were investigated to overcome these problems.

RESULTS

Compared to conventional echo-planar spectroscopic imaging (EPSI) and MEGA-editing, SLOW-editing shows robust refocusing and editing performance despite to B₁ ⁺ -inhomogeneity, and robustness to B₀ -inhomogeneities (0.2 ppm ≥ ΔB₀  ≥ -0.2 ppm). The narrow bandwidth (∼0.6-0.8 kHz) CSAP reduces the SAR by 92%, RF peak power by 84%, in-excitation slab CSDA by 77%, and has no in-plane CSDA. Furthermore, the CSAP implicitly dephases water, lipid and all the other signals outside of range (≥ 4.6 ppm and ≤1.4 ppm), resulting in additional water and lipid suppression (factors ≥ 1000s) at zero SAR-cost, and no spectral aliasing artifacts.

CONCLUSION

A new spectral-editing has been developed that is especially suitable for UHF, and was successfully applied for 2HG, GABA+, PE, and Glx-editing within 10 min clinical acceptable measurement time.

A simultaneous multi-slice T2 mapping framework based on overlapping-echo detachment planar imaging and deep learning reconstruction

PURPOSE

Quantitative MRI (qMRI) is of great importance to clinical medicine and scientific research. However, most qMRI techniques are time-consuming and sensitive to motion, especially when a large 3D volume is imaged. To accelerate the acquisition, a framework is proposed to realize reliable simultaneous multi-slice T₂ mapping.

METHODS

The simultaneous multi-slice T₂ mapping framework is based on overlapping-echo detachment (OLED) planar imaging (dubbed SMS-OLED). Multi-slice overlapping-echo signals were generated by multiple excitation pulses together with echo-shifting gradients. The signals were excited and acquired with a single-channel coil. U-Net was used to reconstruct T₂ maps from the acquired overlapping-echo image.

RESULTS

Single-shot double-slice and two-shot triple-slice SMS-OLED scan schemes were designed according to the framework for evaluation. Simulations, water phantom, and in vivo rat brain experiments were carried out. Overlapping-echo signals were acquired, and T₂ maps were reconstructed and compared with references. The results demonstrate the superior performance of our method.

CONCLUSION

Two slices of T₂ maps can be obtained in a single shot within hundreds of milliseconds. Higher quality multi-slice T₂ maps can be obtained via multiple shots. SMS-OLED provides a lower specific absorption rate scheme compared with conventional SMS methods with a coil with only a single receiver channel. The new method is of potential in dynamic qMRI and functional qMRI where temporal resolution is vital.

The Human Connectome Project: A retrospective

The Human Connectome Project (HCP) was launched in 2010 as an ambitious effort to accelerate advances in human neuroimaging, particularly for measures of brain connectivity; apply these advances to study a large number of healthy young adults; and freely share the data and tools with the scientific community. NIH awarded grants to two consortia; this retrospective focuses on the "WU-Minn-Ox" HCP consortium centered at Washington University, the University of Minnesota, and University of Oxford. In just over 6 years, the WU-Minn-Ox consortium succeeded in its core objectives by: 1) improving MR scanner hardware, pulse sequence design, and image reconstruction methods, 2) acquiring and analyzing multimodal MRI and MEG data of unprecedented quality together with behavioral measures from more than 1100 HCP participants, and 3) freely sharing the data (via the ConnectomeDB database) and associated analysis and visualization tools. To date, more than 27 Petabytes of data have been shared, and 1538 papers acknowledging HCP data use have been published. The "HCP-style" neuroimaging paradigm has emerged as a set of best-practice strategies for optimizing data acquisition and analysis. This article reviews the history of the HCP, including comments on key events and decisions associated with major project components. We discuss several scientific advances using HCP data, including improved cortical parcellations, analyses of connectivity based on functional and diffusion MRI, and analyses of brain-behavior relationships. We also touch upon our efforts to develop and share a variety of associated data processing and analysis tools along with detailed documentation, tutorials, and an educational course to train the next generation of neuroimagers. We conclude with a look forward at opportunities and challenges facing the human neuroimaging field from the perspective of the HCP consortium.

Accelerated diffusion and relaxation-diffusion MRI using time-division multiplexing EPI

PURPOSE

To develop a time-division multiplexing echo-planar imaging (TDM-EPI) sequence for approximately two- to threefold acceleration when acquiring joint relaxation-diffusion MRI data with multiple TEs.

METHODS

The proposed TDM-EPI sequence interleaves excitation and data collection for up to 3 separate slices at different TEs and uses echo-shifting gradients to disentangle the overlapping echo signals during the readout period. By properly arranging the sequence event blocks for each slice and adjusting the echo-shifting gradients, diffusion-weighted images from separate slices can be acquired. Therefore, we present 2 variants of the sequence. A single-TE TDM-EPI is presented to demonstrate the concept. Next, a multi-TE TDM-EPI is presented to highlight the advantages of the TDM approach for relaxation-diffusion imaging. These sequences were evaluated on a 3 Tesla scanner with a water phantom and in vivo human brain data.

RESULTS

The single-TE TDM-EPI sequence can simultaneously acquire 2 slices with a maximum b value of 3000 s/mm² and 2.5 mm isotropic resolution using interleaved readout windows with TE ≈ 78 ms. With the same b value and resolution, the multi-TE TDM-EPI sequence can simultaneously acquire 2 or 3 separate slices using interleaved readout sections with shortest TE ≈ 70 ms and ΔTE ≈ 30 ms. Phantom and in vivo experiments have shown that the proposed TDM-EPI sequences can provide similar image quality and diffusion measures as conventional EPI readouts with multiple echoes but can reduce the overall relaxation-diffusion protocol scan time by approximately two- to threefold.

CONCLUSION

TDM-EPI is a novel approach to acquire diffusion imaging data at multiple TEs. This enables a significant reduction in acquisition time for relaxation-diffusion MRI experiments but without compromising image quality and diffusion measurements, thus removing a significant barrier to the adoption of relaxation-diffusion MRI in clinical research studies of neurological and mental disorders.

Does the increased motion probing gradient directional diffusion tensor imaging of lumbar nerves using multi-band SENSE improve the visualization and accuracy of FA values?

PURPOSE

Diffusion tensor imaging (DTI) is useful to evaluate lumbar nerves visually and quantitatively. Multi-band sensitivity encoding (MB-SENSE) is a technique to reduce the scan time. This study aimed to investigate if super-multi-gradient DTI with multi-band sensitivity encoding (MB-SENSE) is better in evaluating lumbar nerves than the conventional method.

METHODS

The participants were 12 healthy volunteers (mean age 33.6 years). In all subjects, DTI was performed using echo planar imaging with different motion probing gradient (MPG) directions (15 without MB, and 15, 32, 64, and 128 with MB) and the lumbar nerve roots were visualized with tractography. In the five groups, we evaluated the resultant DTI both visually and quantitatively. For visual measures, we counted the number of fluffs and disruptions of the nerve fibers. For quantitative measures, the fractional anisotropy (FA) and standard deviation of the fractional anisotropy (FA-SD) values at two regions (proximal and distal) of the lumbar nerve roots were quantified and compared.

RESULTS

Among the five groups, the number of fluffs decreased as the number of MPG directions increased. However, the number of disruptions showed no significant differences. The FA-SD values decreased as the number of MPG directions increased, indicating that the signal variation was reduced with multi-gradient directional DTI.

CONCLUSION

High-resolution multi-directional DTI with MB-SENSE may be useful to visualize nerve entrapments and may allow for more accurate DTI parameter quantification with opportunities for clinical diagnostic applications.

Generalized simultaneous multi-orientation 2D imaging

PURPOSE

Flexibility in slice prescription is critical for precise motion monitoring during MR-guided therapies. Adding more slices to improve spatial coverage during rapid 2D cine imaging often hampers temporal resolution. This work describes a framework to simultaneously acquire multiple arbitrarily oriented slices which share a common frequency encoding axis. This framework allows for higher frame rates for a given number of slices compared to conventional interleaved-slice multi-orientation cine imaging.

THEORY AND METHODS

A framework to calculate zeroth gradient moments to be played out between sequentially excited slices with multiple orientations is described here. Experiments were performed in phantom, and in vivo in the head/neck and abdomen of patients.

RESULTS

Images arbitrarily rotated relative to one another were successfully obtained in phantom and in vivo. Simultaneous multi-orientation (SMO) images were also acquired with additional in-plane acceleration to demonstrate the capability of this method to rapidly image objects moving with physiological motion.

CONCLUSIONS

The technical feasibility of the generalized SMO imaging framework was tested in this study. It shows promise for continued development for motion monitoring during MR-guided therapies.

Robust Single-Shot T2 Mapping via Multiple Overlapping-Echo Acquisition and Deep Neural Network

Quantitative magnetic resonance imaging (MRI) is of great value to both clinical diagnosis and scientific research. However, most MRI experiments remain qualitative, especially dynamic MRI, because repeated sampling with variable weighting parameter makes quantitative imaging time-consuming and sensitive to motion artifacts. A single-shot quantitative T₂ mapping method based on multiple overlapping-echo acquisition (dubbed MOLED-4) was proposed to obtain reliable T₂ mapping in milliseconds. Different from traditional MRI acceleration methods, such as compressed sensing and parallel imaging, MOLED-4 accelerates quantitative T₂ mapping via synchronized multisampling and then deep learning to map the complex nonlinear relationship that is difficult to solve by traditional optimization-based methods. The results of simulation, phantom, and in vivo human brain experiments show the great performance of the proposed method. The principle of MOLED-4 may be extended to other ultrafast quantitative parameter mappings and potentially lead to new dynamic MRI with high efficiency to catch quantitative variation of tissue properties.

The quest for high spatial resolution diffusion-weighted imaging of the human brain in vivo

Diffusion-weighted imaging, a contrast unique to MRI, is used for assessment of tissue microstructure in vivo. However, this exquisite sensitivity to finer scales far above imaging resolution comes at the cost of vulnerability to errors caused by sources of motion other than diffusion motion. Addressing the issue of motion has traditionally limited diffusion-weighted imaging to a few acquisition techniques and, as a consequence, to poorer spatial resolution than other MRI applications. Advances in MRI imaging methodology have allowed diffusion-weighted MRI to push to ever higher spatial resolution. In this review we focus on the pulse sequences and associated techniques under development that have pushed the limits of image quality and spatial resolution in diffusion-weighted MRI.

Mapping whole brain connectivity changes: The potential impact of different surgical resection approaches for temporal lobe epilepsy

In neurosurgery there are several situations that require transgression of the temporal cortex. For example, a subset of patients with temporal lobe epilepsy require surgical resection (most typically, en-bloc anterior temporal lobectomy). This procedure is the gold standard to alleviate seizures but is associated with chronic cognitive deficits. In recent years there have been multiple attempts to find the optimum balance between minimising the size of resection in order to preserve cognitive function, while still ensuring seizure freedom. Some attempts involve reducing the distance that the resection stretches back from the temporal pole, whilst others try to preserve one or more of the temporal gyri. More recent advanced surgical techniques (selective amygdalo-hippocamptectomies) try to remove the least amount of tissue by going under (sub-temporal), over (trans-Sylvian) or through the temporal lobe (middle-temporal), which have been related to better cognitive outcomes. Previous comparisons of these surgical techniques focus on comparing seizure freedom or behaviour post-surgery, however there have been no systematic studies showing the effect of surgery on white matter connectivity. The main aim of this study, therefore, was to perform systematic 'pseudo-neurosurgery' based on existing resection methods on healthy neuroimaging data and measuring the effect on long-range connectivity. We use anatomical connectivity maps (ACM) to determine long-range disconnection, which is complementary to existing measures of local integrity such as fractional anisotropy or mean diffusivity. ACMs were generated for each diffusion scan in order to compare whole-brain connectivity with an 'ideal resection', nine anterior temporal lobectomy and three selective approaches. For en-bloc resections, as distance from the temporal pole increased, reduction in connectivity was evident within the arcuate fasciculus, inferior longitudinal fasciculus, inferior fronto-occipital fasciculus, and the uncinate fasciculus. Increasing the height of resections dorsally reduced connectivity within the uncinate fasciculus. Sub-temporal amygdalohippocampectomy resections were associated with connectivity patterns most similar to the 'ideal' baseline resection, compared to trans-Sylvian and middle-temporal approaches. In conclusion, we showed the utility of ACM in assessing long-range disconnections/disruptions during temporal lobe resections, where we identified the sub-temporal resection as the least disruptive to long-range connectivity which may explain its better cognitive outcome. These results have a direct impact on understanding the amount and/or type of cognitive deficit post-surgery, which may not be obtainable using local measures of white matter integrity.

Accelerating multi-slice spatiotemporally encoded MRI with simultaneous echo refocusing

Single-shot spatiotemporally encoded (SPEN) ultrafast magnetic resonance imaging (MRI) is of great value to both scientific research and clinical application owing to its capability for delivering MR images with greater robustness to magnetic field inhomogeneity and chemical-shift displacement effects than conventional methods like EPI due to high effective phase-encoded bandwidth. Many SPEN MRI methods have been developed, among which multi-slice SPEN MRI arises as a promising supplement to ultrafast multi-slice sampling. In this work, we propose a new multi-slice SPEN MRI method, termed multi-echo segmented SPEN (ME-SeSPEN) method, which produces multiple images within a single train of echoes and successively samples widely separated slices. The resulting images were reconstructed using de-convolution super-resolved algorithm. The robustness and efficiency of the proposed method were demonstrated by phantom, lemon and in vivo experiments in comparison with spin-echo EPI, spin-echo simultaneous echo refocusing (SER), and segmented SPEN (SeSPEN) MRI. The results indicate that the new method effectively shortens the sampling time (20% reduction practically in comparison with SeSPEN when two slices are simultaneously sampled). ME-SeSPEN also reduces eddy current effects while maintaining the benefits of SPEN MRI, such as similar robustness to field inhomogeneity, spatial resolution and signal-to-noise ratio to SeSPEN MRI. The new method will promote the versatility of multi-slice MRI in practical applications.

Selective and coherent activity increases due to stimulation indicate functional distinctions between episodic memory networks

Posterior-medial and anterior-temporal cortical networks interact with the hippocampus and are thought to distinctly support episodic memory. We causally tested this putative distinction by determining whether targeted noninvasive stimulation could selectively affect neural signals of memory formation within the posterior-medial network. Stimulation enhanced the posterior-medial network's evoked response to stimuli during memory formation, and this activity increase was coherent throughout the network. In contrast, there was no increase in anterior-temporal network activity due to stimulation. In addition, control stimulation of an out-of-network prefrontal cortex location in a separate group of subjects did not influence memory-related activity in either network. The posterior-medial network is therefore a functional unit for memory processing that is distinct from the anterior-temporal network. These findings suggest that targeted stimulation can lead to network-specific increases in excitability during memory formation and hold promise for efforts to fine-tune network involvement in episodic memory via brain stimulation.

A systematic evaluation of intraoperative white matter tract shift in pediatric epilepsy surgery using high-field MRI and probabilistic high angular resolution diffusion imaging tractography

OBJECTIVE Characterization of intraoperative white matter tract (WMT) shift has the potential to compensate for neuronavigation inaccuracies using preoperative brain imaging. This study aimed to quantify and characterize intraoperative WMT shift from the global hemispheric to the regional tract-based scale and to investigate the impact of intraoperative factors (IOFs). METHODS High angular resolution diffusion imaging (HARDI) diffusion-weighted data were acquired over 5 consecutive perioperative time points (MR₁ to MR₅) in 16 epilepsy patients (8 male; mean age 9.8 years, range 3.8-15.8 years) using diagnostic and intraoperative 3-T MRI scanners. MR₁ was the preoperative planning scan. MR₂ was the first intraoperative scan acquired with the patient's head fixed in the surgical position. MR₃ was the second intraoperative scan acquired following craniotomy and durotomy, prior to lesion resection. MR₄ was the last intraoperative scan acquired following lesion resection, prior to wound closure. MR₅ was a postoperative scan acquired at the 3-month follow-up visit. Ten association WMT/WMT segments and 1 projection WMT were generated via a probabilistic tractography algorithm from each MRI scan. Image registration was performed through pairwise MRI alignments using the skull segmentation. The MR₁ and MR₂ pairing represented the first surgical stage. The MR₂ and MR₃ pairing represented the second surgical stage. The MR₃ and MR₄ (or MR₅) pairing represented the third surgical stage. The WMT shift was quantified by measuring displacements between a pair of WMT centerlines. Linear mixed-effects regression analyses were carried out for 6 IOFs: head rotation, craniotomy size, durotomy size, resected lesion volume, presence of brain edema, and CSF loss via ventricular penetration. RESULTS The average WMT shift in the operative hemisphere was 2.37 mm (range 1.92-3.03 mm) during the first surgical stage, 2.19 mm (range 1.90-3.65 mm) during the second surgical stage, and 2.92 mm (range 2.19-4.32 mm) during the third surgical stage. Greater WMT shift occurred in the operative than the nonoperative hemisphere, in the WMTs adjacent to the surgical lesion rather than those remote to it, and in the superficial rather than the deep segment of the pyramidal tract. Durotomy size and resection size were significant, independent IOFs affecting WMT shift. The presence of brain edema was a marginally significant IOF. Craniotomy size, degree of head rotation, and ventricular penetration were not significant IOFs affecting WMT shift. CONCLUSIONS WMT shift occurs noticeably in tracts adjacent to the surgical lesions, and those motor tracts superficially placed in the operative hemisphere. Intraoperative probabilistic HARDI tractography following craniotomy, durotomy, and lesion resection may compensate for intraoperative WMT shift and improve neuronavigation accuracy.

Multiplexed MRI methods for rapid estimation of global cerebral metabolic rate of oxygen consumption

The global cerebral metabolic rate of oxygen (CMRO₂), which reflects metabolic activity of the brain under various physiologic conditions, can be quantified using a method, referred to as 'OxFlow', which simultaneously measures hemoglobin oxygen saturation in a draining vein (Y_v) and total cerebral blood flow (tCBF). Conventional OxFlow (Conv-OxFlow) entails four interleaves incorporated in a single pulse sequence - two for phase-contrast based measurement of tCBF in the supplying arteries of the neck, and two to measure the intra- to extravascular phase difference in the superior sagittal sinus to derive Y_v [Jain et al., JCBFM 2010]. However, this approach limits achievable temporal resolution thus precluding capture of rapid changes of brain metabolic states such as the response to apneic stimuli. Here, we developed a time-efficient, multiplexed OxFlow method and evaluated its potential for measuring dynamic alterations in global CMRO₂ during a breath-hold challenge. Two different implementations of multiplexed OxFlow were investigated: 1) simultaneous-echo-refocusing based OxFlow (SER-OxFlow) and 2) simultaneous-multi-slice imaging-based dual-band OxFlow (DB-OxFlow). The two sequences were implemented on 3T scanners (Siemens TIM Trio and Prisma) and their performance was evaluated in comparison to Conv-OxFlow in ten healthy subjects for baseline CMRO₂ quantification. Comparison of measured parameters (Y_v, tCBF, CMRO₂) revealed no significant bias of SER-OxFlow and DB-OxFlow, with respect to the reference Conv-OxFlow while improving temporal resolution two-fold (12.5 versus 25s). Further acceleration shortened scan time to 8 and 6s for SER and DB-OxFlow, respectively, for time-resolved CMRO₂ measurement. The two sequences were able of capturing smooth transitions of Y_v, tCBF, and CMRO₂ over the time course consisting of 30s of normal breathing, 30s of volitional apnea, and 90s of recovery. While both SER- and DB-OxFlow techniques provide significantly improved temporal resolution (by a factor of 3 - 4 relative to Conv-OxFlow), DB-OxFlow was found to be superior for the study of short physiologic stimuli.

A Hitchhiker's Guide to Functional Magnetic Resonance Imaging

Functional Magnetic Resonance Imaging (fMRI) studies have become increasingly popular both with clinicians and researchers as they are capable of providing unique insights into brain functions. However, multiple technical considerations (ranging from specifics of paradigm design to imaging artifacts, complex protocol definition, and multitude of processing and methods of analysis, as well as intrinsic methodological limitations) must be considered and addressed in order to optimize fMRI analysis and to arrive at the most accurate and grounded interpretation of the data. In practice, the researcher/clinician must choose, from many available options, the most suitable software tool for each stage of the fMRI analysis pipeline. Herein we provide a straightforward guide designed to address, for each of the major stages, the techniques, and tools involved in the process. We have developed this guide both to help those new to the technique to overcome the most critical difficulties in its use, as well as to serve as a resource for the neuroimaging community.

MRI reconstruction of multi-image acquisitions using a rank regularizer with data reordering

PURPOSE

To improve rank constrained reconstructions for undersampled multi-image MRI acquisitions.

METHODS

Motivated by the recent developments in low-rank matrix completion theory and its applicability to rapid dynamic MRI, a new reordering-based rank constrained reconstruction of undersampled multi-image data that uses prior image information is proposed. Instead of directly minimizing the nuclear norm of a matrix of estimated images, the nuclear norm of reordered matrix values is minimized. The reordering is based on the prior image estimates. The method is tested on brain diffusion imaging data and dynamic contrast enhanced myocardial perfusion data.

RESULTS

Good quality images from data undersampled by a factor of three for diffusion imaging and by a factor of 3.5 for dynamic cardiac perfusion imaging with respiratory motion were obtained. Reordering gave visually improved image quality over standard nuclear norm minimization reconstructions. Root mean squared errors with respect to ground truth images were improved by ∼18% and ∼16% with reordering for diffusion and perfusion applications, respectively.

CONCLUSIONS

The reordered low-rank constraint is a way to inject prior image information that offers improvements over a standard low-rank constraint for undersampled multi-image MRI reconstructions.

Rapid multi-orientation quantitative susceptibility mapping

Three-dimensional gradient echo (GRE) is the main workhorse sequence used for susceptibility weighted imaging (SWI), quantitative susceptibility mapping (QSM), and susceptibility tensor imaging (STI). Achieving optimal phase signal-to-noise ratio requires late echo times, thus necessitating a long repetition time (TR). Combined with the large encoding burden of whole-brain coverage with high resolution, this leads to increased scan time. Further, the dipole kernel relating the tissue phase to the underlying susceptibility distribution undersamples the frequency content of the susceptibility map. Scans at multiple head orientations along with calculation of susceptibility through multi-orientation sampling (COSMOS) are one way to effectively mitigate this issue. Additionally, STI requires a minimum of 6 head orientations to solve for the independent tensor elements in each voxel. The requirements of high-resolution imaging with long TR at multiple orientations substantially lengthen the acquisition of COSMOS and STI. The goal of this work is to dramatically speed up susceptibility mapping at multiple head orientations. We demonstrate highly efficient acquisition using 3D-GRE with Wave-CAIPI and dramatically reduce the acquisition time of these protocols. Using R=15-fold acceleration with Wave-CAIPI permits acquisition per head orientation in 90s at 1.1mm isotropic resolution, and 5:35min at 0.5mm isotropic resolution. Since Wave-CAIPI fully harnesses the 3D spatial encoding capability of receive arrays, the maximum g-factor noise amplification remains below 1.30 at 3T and 1.12 at 7T. This allows a 30-min exam for STI with 12 orientations, thus paving the way to its clinical application.

Evaluation of 2D multiband EPI imaging for high-resolution, whole-brain, task-based fMRI studies at 3T: Sensitivity and slice leakage artifacts

Functional magnetic resonance imaging (fMRI) studies that require high-resolution whole-brain coverage have long scan times that are primarily driven by the large number of thin slices acquired. Two-dimensional multiband echo-planar imaging (EPI) sequences accelerate the data acquisition along the slice direction and therefore represent an attractive approach to such studies by improving the temporal resolution without sacrificing spatial resolution. In this work, a 2D multiband EPI sequence was optimized for 1.5 mm isotropic whole-brain acquisitions at 3 T with 10 healthy volunteers imaged while performing simultaneous visual and motor tasks. The performance of the sequence was evaluated in terms of BOLD sensitivity and false-positive activation at multiband (MB) factors of 1, 2, 4, and 6, combined with in-plane GRAPPA acceleration of 2 × (GRAPPA 2), and the two reconstruction approaches of Slice-GRAPPA and Split Slice-GRAPPA. Sensitivity results demonstrate significant gains in temporal signal-to-noise ratio (tSNR) and t-score statistics for MB 2, 4, and 6 compared to MB 1. The MB factor for optimal sensitivity varied depending on anatomical location and reconstruction method. When using Slice-GRAPPA reconstruction, evidence of false-positive activation due to signal leakage between simultaneously excited slices was seen in one instance, 35 instances, and 70 instances over the ten volunteers for the respective accelerations of MB 2 × GRAPPA 2, MB 4 × GRAPPA 2, and MB 6 × GRAPPA 2. The use of Split Slice-GRAPPA reconstruction suppressed the prevalence of false positives significantly, to 1 instance, 5 instances, and 5 instances for the same respective acceleration factors. Imaging protocols using an acceleration factor of MB 2 × GRAPPA 2 can be confidently used for high-resolution whole-brain imaging to improve BOLD sensitivity with very low probability for false-positive activation due to slice leakage. Imaging protocols using higher acceleration factors (MB 3 or MB 4 × GRAPPA 2) can likely provide even greater gains in sensitivity but should be carefully optimized to minimize the possibility of false activations.

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MB factors 1, 2, 4, and 6 and two reconstructions were evaluated for fMRI performance.

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MB accelerations 2, 4, and 6 improved BOLD sensitivity metrics over MB 1.

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False-positive activation due to signal leakage was seen at high accelerations.

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Use of Split Slice-GRAPPA reconstruction significantly reduces false positives.

Simultaneous multislice (SMS) imaging techniques

Simultaneous multislice imaging (SMS) using parallel image reconstruction has rapidly advanced to become a major imaging technique. The primary benefit is an acceleration in data acquisition that is equal to the number of simultaneously excited slices. Unlike in‐plane parallel imaging this can have only a marginal intrinsic signal‐to‐noise ratio penalty, and the full acceleration is attainable at fixed echo time, as is required for many echo planar imaging applications. Furthermore, for some implementations SMS techniques can reduce radiofrequency (RF) power deposition. In this review the current state of the art of SMS imaging is presented. In the Introduction, a historical overview is given of the history of SMS excitation in MRI. The following section on RF pulses gives both the theoretical background and practical application. The section on encoding and reconstruction shows how the collapsed multislice images can be disentangled by means of the transmitter pulse phase, gradient pulses, and most importantly using multichannel receiver coils. The relationship between classic parallel imaging techniques and SMS reconstruction methods is explored. The subsequent section describes the practical implementation, including the acquisition of reference data, and slice cross‐talk. Published applications of SMS imaging are then reviewed, and the article concludes with an outlook and perspective of SMS imaging. Magn Reson Med 75:63–81, 2016. © 2015 The Authors. Magnetic Resonance in Medicine Published by Wiley Periodicals, Inc. on behalf of International Society of Medicine in Resonance.

Evaluation of highly accelerated simultaneous multi-slice EPI for fMRI

Echo planar imaging (EPI) is the MRI technique that is most widely used for blood oxygen level-dependent (BOLD) functional MRI (fMRI). Recent advances in EPI speed have been made possible with simultaneous multi-slice (SMS) methods which combine acceleration factors M from multiband (MB) radiofrequency pulses and S from simultaneous image refocusing (SIR) to acquire a total of N=S×M images in one echo train, providing up to N times speed-up in total acquisition time over conventional EPI. We evaluated accelerations as high as N=48 using different combinations of S and M which allow for whole brain imaging in as little as 100ms at 3T with a 32 channel head coil. The various combinations of acceleration parameters were evaluated by tSNR as well as BOLD contrast-to-noise ratio (CNR) and information content from checkerboard and movie clips in fMRI experiments. We found that at low acceleration factors (N≤6), setting S=1 and varying M alone yielded the best results in all evaluation metrics, while at acceleration N=8 the results were mixed using both S=1 and S=2 sequences. At higher acceleration factors (N>8), using S=2 yielded maximal BOLD CNR and information content as measured by classification of movie clip frames. Importantly, we found significantly greater BOLD information content using relatively fast TRs in the range of 300ms-600ms compared to a TR of 2s, suggesting that faster TRs capture more information per unit time in task based fMRI.

Multimodal neuroimaging in humans at 9.4 T: a technological breakthrough towards an advanced metabolic imaging scanner

The aim of this paper is twofold: firstly, to explore the potential of simultaneously acquiring multimodal MR-PET-EEG data in a human 9.4 T scanner to provide a platform for metabolic brain imaging. Secondly, to demonstrate that the three modalities are complementary, with MRI providing excellent structural and functional imaging, PET providing quantitative molecular imaging, and EEG providing superior temporal resolution. A 9.4 T MRI scanner equipped with a PET insert and a commercially available EEG device was used to acquire in vivo proton-based images, spectra, and sodium- and oxygen-based images with MRI, EEG signals from a human subject in a static 9.4 T magnetic field, and demonstrate hybrid MR-PET capability in a rat model. High-resolution images of the in vivo human brain with an isotropic resolution of 0.5 mm and post-mortem brain images of the cerebellum with an isotropic resolution of 320 µm are presented. A (1)H spectrum was also acquired from 2 × 2 × 2 mm voxel in the brain allowing 12 metabolites to be identified. Imaging based on sodium and oxygen is demonstrated with isotropic resolutions of 2 and 5 mm, respectively. Auditory evoked potentials measured in a static field of 9.4 T are shown. Finally, hybrid MR-PET capability at 9.4 T in the human scanner is demonstrated in a rat model. Initial progress on the road to 9.4 T multimodal MR-PET-EEG is illustrated. Ultra-high resolution structural imaging, high-resolution images of the sodium distribution and proof-of-principle (17)O data are clearly demonstrated. Further, simultaneous MR-PET data are presented without artefacts and EEG data successfully corrected for the cardioballistic artefact at 9.4 T are presented.

Interslice leakage artifact reduction technique for simultaneous multislice acquisitions

PURPOSE

Controlled aliasing techniques for simultaneously acquired echo-planar imaging slices have been shown to significantly increase the temporal efficiency for both diffusion-weighted imaging and functional magnetic resonance imaging studies. The "slice-GRAPPA" (SG) method has been widely used to reconstruct such data. We investigate robust optimization techniques for SG to ensure image reconstruction accuracy through a reduction of leakage artifacts.

METHODS

Split SG is proposed as an alternative kernel optimization method. The performance of Split SG is compared to standard SG using data collected on a spherical phantom and in vivo on two subjects at 3 T. Slice-accelerated and nonaccelerated data were collected for a spin-echo diffusion-weighted acquisition. Signal leakage metrics and time-series SNR were used to quantify the performance of the kernel fitting approaches.

RESULTS

The Split SG optimization strategy significantly reduces leakage artifacts for both phantom and in vivo acquisitions. In addition, a significant boost in time-series SNR for in vivo diffusion-weighted acquisitions with in-plane 2× and slice 3× accelerations was observed with the Split SG approach.

CONCLUSION

By minimizing the influence of leakage artifacts during the training of SG kernels, we have significantly improved reconstruction accuracy. Our robust kernel fitting strategy should enable better reconstruction accuracy and higher slice-acceleration across many applications.

Interleaved diffusion-weighted improved by adaptive partial-Fourier and multiband multiplexed sensitivity-encoding reconstruction

PURPOSE

We report a series of techniques to reliably eliminate artifacts in interleaved echo-planar imaging (EPI) based diffusion-weighted imaging (DWI).

METHODS

First, we integrate the previously reported multiplexed sensitivity encoding (MUSE) algorithm with a new adaptive Homodyne partial-Fourier reconstruction algorithm, so that images reconstructed from interleaved partial-Fourier DWI data are free from artifacts even in the presence of either (a) motion-induced k-space energy peak displacement, or (b) susceptibility field gradient induced fast phase changes. Second, we generalize the previously reported single-band MUSE framework to multiband MUSE, so that both through-plane and in-plane aliasing artifacts in multiband multishot interleaved DWI data can be effectively eliminated.

RESULTS

The new adaptive Homodyne-MUSE reconstruction algorithm reliably produces high-quality and high-resolution DWI, eliminating residual artifacts in images reconstructed with previously reported methods. Furthermore, the generalized MUSE algorithm is compatible with multiband and high-throughput DWI.

CONCLUSION

The integration of the multiband and adaptive Homodyne-MUSE algorithms significantly improves the spatial-resolution, image quality, and scan throughput of interleaved DWI. We expect that the reported reconstruction framework will play an important role in enabling high-resolution DWI for both neuroscience research and clinical uses.

Simultaneous functional MRI acquisition of distributed brain regions with high temporal resolution using a 2D-selective radiofrequency excitation

PURPOSE

To perform simultaneous functional MRI of multiple, distributed brain regions at high temporal resolution using a 2D-selective radiofrequency (2DRF) excitation.

METHODS

A tailored 2DRF excitation is used to excite several, small regions-of-interest distributed in the brain. They are acquired in a single projection image with an appropriately chosen orientation such that the different regions-of-interest can be discriminated by their position in the projection plane. Thus, they are excited and acquired simultaneously with a temporal resolution comparable to that of a single-slice measurement. The feasibility of this approach for functional neuroimaging (in-plane resolution 2 × 2 mm(2) ) at high temporal resolution (80 ms) is demonstrated in healthy volunteers for regions-of-interest in the visual and motor system using checkerboard and finger tapping block-design paradigms.

RESULTS

Task-related brain activation could be observed in both the visual and the motor system simultaneously with a high temporal resolution. For an onset shift of 240 ms for half of the checkerboard, a delay of the hemodynamic response in the corresponding hemisphere of the visual cortex could be detected.

CONCLUSION

Limiting the excited magnetization to the desired target regions with a 2DRF excitation reduces the imaging sampling requirements which can improve the temporal resolution significantly.

Simultaneous Multi-Slice fMRI using spiral trajectories

Parallel imaging methods using multi-coil receiver arrays have been shown to be effective for increasing MRI acquisition speed. However parallel imaging methods for fMRI with 2D sequences show only limited improvements in temporal resolution because of the long echo times needed for BOLD contrast. Recently, Simultaneous Multi-Slice (SMS) imaging techniques have been shown to increase fMRI temporal resolution by factors of four and higher. In SMS fMRI multiple slices can be acquired simultaneously using Echo Planar Imaging (EPI) and the overlapping slices are un-aliased using a parallel imaging reconstruction with multiple receivers. The slice separation can be further improved using the "blipped-CAIPI" EPI sequence that provides a more efficient sampling of the SMS 3D k-space. In this paper a blipped-spiral SMS sequence for ultra-fast fMRI is presented. The blipped-spiral sequence combines the sampling efficiency of spiral trajectories with the SMS encoding concept used in blipped-CAIPI EPI. We show that blipped spiral acquisition can achieve almost whole brain coverage at 3mm isotropic resolution in 168 ms. It is also demonstrated that the high temporal resolution allows for dynamic BOLD lag time measurement using visual/motor and retinotopic mapping paradigms. The local BOLD lag time within the visual cortex following the retinotopic mapping stimulation of expanding flickering rings is directly measured and easily translated into an eccentricity map of the cortex.

Fast dictionary-based reconstruction for diffusion spectrum imaging

Diffusion spectrum imaging reveals detailed local diffusion properties at the expense of substantially long imaging times. It is possible to accelerate acquisition by undersampling in q-space, followed by image reconstruction that exploits prior knowledge on the diffusion probability density functions (pdfs). Previously proposed methods impose this prior in the form of sparsity under wavelet and total variation transforms, or under adaptive dictionaries that are trained on example datasets to maximize the sparsity of the representation. These compressed sensing (CS) methods require full-brain processing times on the order of hours using MATLAB running on a workstation. This work presents two dictionary-based reconstruction techniques that use analytical solutions, and are two orders of magnitude faster than the previously proposed dictionary-based CS approach. The first method generates a dictionary from the training data using principal component analysis (PCA), and performs the reconstruction in the PCA space. The second proposed method applies reconstruction using pseudoinverse with Tikhonov regularization with respect to a dictionary. This dictionary can either be obtained using the K-SVD algorithm, or it can simply be the training dataset of pdfs without any training. All of the proposed methods achieve reconstruction times on the order of seconds per imaging slice, and have reconstruction quality comparable to that of dictionary-based CS algorithm.

Slice accelerated gradient-echo spin-echo dynamic susceptibility contrast imaging with blipped CAIPI for increased slice coverage

PURPOSE

To improve slice coverage of gradient echo spin echo (GESE) sequences for dynamic susceptibility contrast (DSC) MRI using a simultaneous-multiple-slice (SMS) method.

METHODS

Data were acquired on 3 Tesla (T) MR scanners with a 32-channel head coil. To evaluate use of SMS for DSC, an SMS GESE sequence with two-fold slice coverage and same temporal sampling was compared with a standard GESE sequence, both with 2× in-plane acceleration. A signal to noise ratio (SNR) comparison was performed on one healthy subject. Additionally, data with Gadolinium injection were collected on three patients with glioblastoma using both sequences, and perfusion analysis was performed on healthy tissues as well as on tumor.

RESULTS

Retained SNR of SMS DSC is 90% for a gradient echo (GE) and 99% for a spin echo (SE) acquisition, compared with a standard acquisition without slice acceleration. Comparing cerebral blood volume maps, it was observed that the results of standard and SMS acquisitions are comparable for both GE and SE images.

CONCLUSION

Two-fold slice accelerated DSC MRI achieves similar SNR and perfusion metrics as a standard acquisition, while allowing a significant increase in slice coverage of the brain. The results also point to a possibility to improve temporal sampling rate, while retaining the same slice coverage.

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

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.

Boosting BOLD fMRI by K-space density weighted echo planar imaging

Functional magnetic resonance imaging (fMRI) has become a powerful and influential method to non-invasively study neuronal brain activity. For this purpose, the blood oxygenation level-dependent (BOLD) effect is most widely used. T₂* weighted echo planar imaging (EPI) is BOLD sensitive and the prevailing fMRI acquisition technique. Here, we present an alternative to its standard Cartesian recordings, i.e. k-space density weighted EPI, which is expected to increase the signal-to-noise ratio in fMRI data. Based on in vitro and in vivo pilot measurements, we show that fMRI by k-space density weighted EPI is feasible and that this new acquisition technique in fact boosted spatial and temporal SNR as well as the detection of local fMRI activations. Spatial resolution, spatial response function and echo time were identical for density weighted and conventional Cartesian EPI. The signal-to-noise ratio gain of density weighting can improve activation detection and has the potential to further increase the sensitivity of fMRI investigations.

Evaluation of slice accelerations using multiband echo planar imaging at 3 T

We evaluate residual aliasing among simultaneously excited and acquired slices in slice accelerated multiband (MB) echo planar imaging (EPI). No in-plane accelerations were used in order to maximize and evaluate achievable slice acceleration factors at 3 T. We propose a novel leakage (L-) factor to quantify the effects of signal leakage between simultaneously acquired slices. With a standard 32-channel receiver coil at 3 T, we demonstrate that slice acceleration factors of up to eight (MB=8) with blipped controlled aliasing in parallel imaging (CAIPI), in the absence of in-plane accelerations, can be used routinely with acceptable image quality and integrity for whole brain imaging. Spectral analyses of single-shot fMRI time series demonstrate that temporal fluctuations due to both neuronal and physiological sources were distinguishable and comparable up to slice-acceleration factors of nine (MB=9). The increased temporal efficiency could be employed to achieve, within a given acquisition period, higher spatial resolution, increased fMRI statistical power, multiple TEs, faster sampling of temporal events in a resting state fMRI time series, increased sampling of q-space in diffusion imaging, or more quiet time during a scan.

Slice accelerated diffusion-weighted imaging at ultra-high field strength

PURPOSE

Diffusion magnetic resonance imaging (dMRI) data with very high isotropic resolution can be obtained at 7T. However, for extensive brain coverage, a large number of slices is required, resulting in long acquisition times (TAs). Recording multiple slices simultaneously (SMS) promises to reduce the TA.

METHODS

A combination of zoomed and parallel imaging is used to achieve high isotropic resolution dMRI data with a low level of distortions at 7T. The blipped-CAIPI (controlled aliasing in parallel imaging) approach is used to acquire several slices simultaneously. Due to their high radiofrequency (RF) power deposition and ensuing specific absorption rate (SAR) constraints, the commonly used multiband (MB) RF pulses for SMS imaging are inefficient at 7T and entail long repetition times, counteracting the usefulness of SMS acquisitions. To address this issue, low SAR multislice Power Independent of Number of Slices RF pulses are employed.

RESULTS

In vivo dMRI results with and without SMS acceleration are presented at different isotropic spatial resolutions at ultra high field strength. The datasets are recorded at a high angular resolution to detect fiber crossings.

CONCLUSION

From the results and compared with earlier studies at these resolutions, it can be seen that scan time is significantly reduced, while image quality is preserved.

Pushing the limits of in vivo diffusion MRI for the Human Connectome Project

Perhaps more than any other "-omics" endeavor, the accuracy and level of detail obtained from mapping the major connection pathways in the living human brain with diffusion MRI depend on the capabilities of the imaging technology used. The current tools are remarkable; allowing the formation of an "image" of the water diffusion probability distribution in regions of complex crossing fibers at each of half a million voxels in the brain. Nonetheless our ability to map the connection pathways is limited by the image sensitivity and resolution, and also the contrast and resolution in encoding of the diffusion probability distribution. The goal of our Human Connectome Project (HCP) is to address these limiting factors by re-engineering the scanner from the ground up to optimize the high b-value, high angular resolution diffusion imaging needed for sensitive and accurate mapping of the brain's structural connections. Our efforts were directed based on the relative contributions of each scanner component. The gradient subsection was a major focus since gradient amplitude is central to determining the diffusion contrast, the amount of T2 signal loss, and the blurring of the water PDF over the course of the diffusion time. By implementing a novel 4-port drive geometry and optimizing size and linearity for the brain, we demonstrate a whole-body sized scanner with G(max) = 300 mT/m on each axis capable of the sustained duty cycle needed for diffusion imaging. The system is capable of slewing the gradient at a rate of 200 T/m/s as needed for the EPI image encoding. In order to enhance the efficiency of the diffusion sequence we implemented a FOV shifting approach to Simultaneous MultiSlice (SMS) EPI capable of unaliasing 3 slices excited simultaneously with a modest g-factor penalty allowing us to diffusion encode whole brain volumes with low TR and TE. Finally we combine the multi-slice approach with a compressive sampling reconstruction to sufficiently undersample q-space to achieve a DSI scan in less than 5 min. To augment this accelerated imaging approach we developed a 64-channel, tight-fitting brain array coil and show its performance benefit compared to a commercial 32-channel coil at all locations in the brain for these accelerated acquisitions. The technical challenges of developing the over-all system are discussed as well as results from SNR comparisons, ODF metrics and fiber tracking comparisons. The ultra-high gradients yielded substantial and immediate gains in the sensitivity through reduction of TE and improved signal detection and increased efficiency of the DSI or HARDI acquisition, accuracy and resolution of diffusion tractography, as defined by identification of known structure and fiber crossing.

Resting-state fMRI in the Human Connectome Project

Resting-state functional magnetic resonance imaging (rfMRI) allows one to study functional connectivity in the brain by acquiring fMRI data while subjects lie inactive in the MRI scanner, and taking advantage of the fact that functionally related brain regions spontaneously co-activate. rfMRI is one of the two primary data modalities being acquired for the Human Connectome Project (the other being diffusion MRI). A key objective is to generate a detailed in vivo mapping of functional connectivity in a large cohort of healthy adults (over 1000 subjects), and to make these datasets freely available for use by the neuroimaging community. In each subject we acquire a total of 1h of whole-brain rfMRI data at 3 T, with a spatial resolution of 2×2×2 mm and a temporal resolution of 0.7s, capitalizing on recent developments in slice-accelerated echo-planar imaging. We will also scan a subset of the cohort at higher field strength and resolution. In this paper we outline the work behind, and rationale for, decisions taken regarding the rfMRI data acquisition protocol and pre-processing pipelines, and present some initial results showing data quality and example functional connectivity analyses.

Evaluation of fiber tracking from subsampled q-space data in diffusion spectrum imaging

Diffusion spectrum imaging (DSI) is capable of resolving crossing and touching fiber bundles in a given voxel. Acquisition of DSI data involves sampling large number of points in the q-space which significantly increases scan times. The scan times can be reduced by exploiting the symmetry of the q-space. In this study the fiber pathways for five (fornix, cingulum, superior longitudinal fasciculus, corticospinal tract, and crossing fibers in the centrum semiovale region) fiber bundles derived using three subsampled data sets of different sizes derived from the 257 samples in the q-space are compared. The coefficient of variation of the ratio of the number of fiber pathways for each subsample data set to the original data points, averaged over all the 10 subjects, was used for quantitatively investigating the effect of subsampling on the tractography. The effect of threshold angles on tractography is also investigated. The effect of subsampling on the orientation distribution function (ODF) was quantitatively evaluated using both scalar and vector measures derived from the ODF. A streamline tractography method that improves the curvature problem and reduces the local truncation error to further improve the mapping of fiber pathways is adapted. Analysis of the fiber pathways in ten normal subjects, based on qualitative and quantitative methods, shows that the 129 and 198 q-space points provide very similar result with angle of threshold between 41° and 45°. Based on the scan time advantage, 129 subsampled points appear to be adequate for tractography.

Ultra-fast MRI of the human brain with simultaneous multi-slice imaging

The recent advancement of simultaneous multi-slice imaging using multiband excitation has dramatically reduced the scan time of the brain. The evolution of this parallel imaging technique began over a decade ago and through recent sequence improvements has reduced the acquisition time of multi-slice EPI by over ten fold. This technique has recently become extremely useful for (i) functional MRI studies improving the statistical definition of neuronal networks, and (ii) diffusion based fiber tractography to visualize structural connections in the human brain. Several applications and evaluations are underway which show promise for this family of fast imaging sequences.

Constrained source space imaging: application to fast, region-based functional MRI

A new technique called constrained source space imaging is introduced that holds promise for ultrafast acquisition of functional magnetic resonance imaging data. A sparse set of arbitrarily positioned, coarse voxels is first localized using radiofrequency selective excitation, from which magnetization signals are separated using only the spatial sensitivities of multichannel receiver coils, without the need for k-space encoding using imaging gradients. This method permits very fast acquisitions of targeted magnetization without complex or time-consuming image reconstruction techniques. Furthermore, because the data acquisition is performed without imaging gradients, T2* decays can be densely sampled and processed for contrast enhancement to improve functional magnetic resonance imaging data quality. Here, the constrained source space imaging technique is validated in proof-of-concept form, for a simple functional magnetic resonance imaging motor task using a prototype dual-band stimulated echo acquisition mode excitation to image four voxels at TR = 250 ms. Results demonstrate good voxel signal separation and good characterization of hemodynamic responses in primary motor cortices (M1) and supplementary motor areas through T2* fitting of the measured signals. With further refinement, the constrained source space imaging method has potential utility in a priori ROI-based functional magnetic resonance imaging experiments with TR values under 100 ms. Rapid, multivoxel measurements of other sources of MR signal contrast are also possible.

Generalized INverse imaging (GIN): ultrafast fMRI with physiological noise correction

An ultrafast functional magnetic resonance imaging (fMRI) technique, called generalized inverse imaging (GIN), is proposed, which combines inverse imaging with a phase constraint-leading to a less underdetermined reconstruction-and physiological noise correction. A single 3D echo planar imaging (EPI) prescan is sufficient to obtain the necessary coil sensitivity information and reference images that are used to reconstruct standard images, so that standard analysis methods are applicable. A moving dots stimulus paradigm was chosen to assess the performance of GIN. We find that the spatial localization of activation for GIN is comparable to an EPI protocol and that maximum z-scores increase significantly. The high temporal resolution of GIN (50 ms) and the acquisition of the phase information enable unaliased sampling and regression of physiological signals. Using the phase time courses obtained from the 32 channels of the receiver coils as nuisance regressors in a general linear model results in significant improvement of the functional activation, rendering the acquisition of external physiological signals unnecessary. The proposed physiological noise correction can in principle be used for other fMRI protocols, such as simultaneous multislice acquisitions, which acquire the phase information sufficiently fast and sample physiological signals unaliased.

Diffusion spectrum MRI using body-centered-cubic and half-sphere sampling schemes

The optimum sequence parameters of diffusion spectrum MRI (DSI) on clinical scanners were investigated previously. However, the scan time of approximately 30 min is still too long for patient studies. Additionally, relatively large sampling interval in the diffusion-encoding space may cause aliasing artifact in the probability density function when Fourier transform is undertaken, leading to estimation error in fiber orientations. Therefore, this study proposed a non-Cartesian sampling scheme, body-centered-cubic (BCC), to avoid the aliasing artifact as compared to the conventional Cartesian grid sampling scheme (GRID). Furthermore, the accuracy of DSI with the use of half-sphere sampling schemes, i.e. GRID102 and BCC91, was investigated by comparing to their full-sphere sampling schemes, GRID203 and BCC181, respectively. In results, smaller deviation angle and lower angular dispersion were obtained by using the BCC sampling scheme. The half-sphere sampling schemes yielded angular precision and accuracy comparable to the full-sphere sampling schemes. The optimum b(max) was approximately 4750 s/mm(2) for GRID and 4500 s/mm(2) for BCC. In conclusion, the BCC sampling scheme could be implemented as a useful alternative to the GRID sampling scheme. Combination of BCC and half-sphere sampling schemes, that is BCC91, may potentially reduce the scan time of DSI from 30 min to approximately 14 min while maintaining its precision and accuracy.

Signal fluctuations in fMRI data acquired with 2D-EPI and 3D-EPI at 7 Tesla

Segmented three-dimensional echo planar imaging (3D-EPI) provides higher image signal-to-noise ratio (SNR) than standard single-shot two-dimensional echo planar imaging (2D-EPI), but is more sensitive to physiological noise. The aim of this study was to compare physiological noise removal efficiency in single-shot 2D-EPI and segmented 3D-EPI acquired at 7 Tesla. Two approaches were investigated based either on physiological regressors (PR) derived from cardiac and respiratory phases, or on principal component analysis (PCA) using additional resting-state data. Results show that, prior to physiological noise removal, 2D-EPI data had higher temporal SNR (tSNR), while spatial SNR was higher in 3D-EPI. Blood oxygen level dependent (BOLD) sensitivity was similar for both methods. The PR-based approach allowed characterization of relative contributions from different noise sources, confirming significant increases in physiological noise from 2D to 3D prior to correction. Both physiological noise removal approaches produced significant increases in tSNR and BOLD sensitivity, and these increases were larger for 3D-EPI, resulting in higher BOLD sensitivity in the 3D-EPI than in the 2D-EPI data. The PCA-based approach was the most effective correction method, yielding higher tSNR values for 3D-EPI than for 2D-EPI postcorrection.

The future of the human connectome

The opportunity to explore the human connectome using cutting-edge neuroimaging methods has elicited widespread interest. How far will the field be able to progress in deciphering long-distance connectivity patterns and in relating differences in connectivity to phenotypic characteristics in health and disease? We discuss the daunting nature of this challenge in relation to specific complexities of brain circuitry and known limitations of in vivo imaging methods. We also discuss the excellent prospects for continuing improvements in data acquisition and analysis. Accordingly, we are optimistic that major insights will emerge from human connectomics in the coming decade.