3D EPI Research Articles

Collapsed fat navigators for brain 3D rigid body motion

PurposeTo acquire high-resolution 3D multi-slab echo planar imaging data without motion artifacts, using collapsed fat navigators. MethodsA fat navigator module (collapsed FatNav) was added to a diffusion-weighted 3D multi-slab echo planar imaging (DW 3D-MS EPI) sequence, comprising three orthogonal echo planar imaging readouts to track rigid body head motion in the image domain and performing prospective motion correction. The stability, resolution and accuracy of the navigator were investigated on phantoms and healthy volunteers. ResultsThe experiments on phantoms and volunteers show that the navigator, depicting projections of the subcutaneous fat in of the head, is capable of correcting for head motion with insignificant bias compared to motion estimates derived from the water-signaling DWI images. Despite that this projection technique implies a non-sparse image appearance, collapsed FatNav data could be highly accelerated with parallel imaging, allowing three orthogonal 2D EPI readouts in about 6ms. ConclusionBy utilizing signal from the leading fat saturation RF pulse of the diffusion sequence, only the readout portion of the navigator needs to be added, resulting in a scan time penalty of only about 5%. Motion can be detected and corrected for with a 5–10Hz update frequency when combined with a sequence like the DW 3D-MS EPI.

Prospective motion correction of 3D echo-planar imaging data for functional MRI using optical tracking

We evaluated the performance of an optical camera based prospective motion correction (PMC) system in improving the quality of 3D echo-planar imaging functional MRI data. An optical camera and external marker were used to dynamically track the head movement of subjects during fMRI scanning. PMC was performed by using the motion information to dynamically update the sequence's RF excitation and gradient waveforms such that the field-of-view was realigned to match the subject's head movement. Task-free fMRI experiments on five healthy volunteers followed a 2×2×3 factorial design with the following factors: PMC on or off; 3.0mm or 1.5mm isotropic resolution; and no, slow, or fast head movements. Visual and motor fMRI experiments were additionally performed on one of the volunteers at 1.5mm resolution comparing PMC on vs PMC off for no and slow head movements. Metrics were developed to quantify the amount of motion as it occurred relative to k-space data acquisition. The motion quantification metric collapsed the very rich camera tracking data into one scalar value for each image volume that was strongly predictive of motion-induced artifacts. The PMC system did not introduce extraneous artifacts for the no motion conditions and improved the time series temporal signal-to-noise by 30% to 40% for all combinations of low/high resolution and slow/fast head movement relative to the standard acquisition with no prospective correction. The numbers of activated voxels (p<0.001, uncorrected) in both task-based experiments were comparable for the no motion cases and increased by 78% and 330%, respectively, for PMC on versus PMC off in the slow motion cases. The PMC system is a robust solution to decrease the motion sensitivity of multi-shot 3D EPI sequences and thereby overcome one of the main roadblocks to their widespread use in fMRI studies.

Sparsely sampled MR navigators as a practical tool for quality control and correction of head motion in simultaneous PET/MR.

We present a study using MR navigators sampled between other protocolled MR sequences during PET/MR brain scanning, to make motion-QC and motion correction (MC) feasible in clinical simultaneous PET/MR, obviating the need for special MR sequences with interleaved (dense) navigators. During 30 min [11C]-PiB (453±148 MBq) PET listmode scans of 29 patients on the Siemens mMR, a set of 10 3D navigator volumes was acquired (2D EPI 3.0x3.0x3.0 mm3 voxels, 64x64 matrix, 36 slices, TE 30 ms, TR 3,000 ms) in between other scheduled MR acquisitions at 6 time points. The rigid motion between navigators was calculated (all motions given are for a point in the cortex 6 cm from the scanners cFOV). The 3 patients with largest motion (11, 8 and 8 mm) and the only 2 PiB-positive patients with motion > 4 mm (8 and 6 mm motion) were reconstructed into 6 frames with frames being split at the midpoint between navigator start times (framing [mean±SD]: 259±8, 306±8, 191±2, 342±2, 546±1, 157±19 seconds) and then averaged to one image after MC. A blinded evaluation comparing non-MC and MC PiB images was performed by a nuclear medicine physician. The average maximum motion magnitude was 3.9±2.4 mm (1 to 11 mm). The visual evaluation of the 5 MC patients rated 3/5 non-MC images blurred (average score: 3.4±0.5 on a scale of 1-5) and 0/5 MC images blurred (score: 4.0±0.0) with no correlation between motion magnitude and rating. A slight, overall decrease in blurring and an increase in image quality rating with MC was found, but with no impact on clinical outcome. The effect of MC is limited with PiB, but with other tracers (e.g. FDG), longer scans, smaller ROIs or larger motion magnitudes, navigators are easily used for motion-QC and MC in clinical practice.

A study-specific fMRI normalization approach that operates directly on high resolution functional EPI data at 7 Tesla

Due to the availability of ultra-high field scanners and novel imaging methods, high resolution, whole brain functional MR imaging (fMRI) has become increasingly feasible. However, it is common to use extensive spatial smoothing to account for inter-subject anatomical variation when pooling over subjects. This reduces the spatial details of group level functional activation considerably, even when the original data was acquired with high resolution. In our study we used an accelerated 3D EPI sequence at 7Tesla to acquire whole brain fMRI data with an isotropic spatial resolution of 1.1mm which shows clear gray/white matter contrast due to the stronger T1 weighting of 3D EPI. To benefit from the high spatial resolution on the group level, we develop a study specific, high resolution anatomical template which is facilitated by the good anatomical contrast that is present in the average functional EPI images. Different template generations with increasing accuracy were created by using a hierarchical linear and stepwise non-linear registration approach. As the template is based on the functional data themselves no additional co-registration step with the usual T1-weighted anatomical data is necessary which eliminates a potential source of misalignment. To test the improvement of functional localization and spatial details we performed a group level analysis of a finger tapping experiment in eight subjects. The most accurate template shows better spatial localization – such as a separation of somatosensory and motor areas and of single digit activation – compared to the simple linear registration. The number of activated voxels is increased by a factor of 1.2, 2.5, and 3.1 for somatosensory, supplementary motor area, and dentate nucleus, respectively, for the functional contrast between left versus right hand. Similarly, the number of activated voxels is increased 1.4- and 2.4-fold for right little versus right index finger and left little versus left index finger, respectively. The Euclidian distance between the activation (center of gravity) of the respective fingers was found to be 13.90mm using the most accurate template.

Improved temporal resolution for functional studies with reduced number of segments with three‐dimensional echo planar imaging

To introduce a new k-space traversal strategy for segmented three-dimensional echo planar imaging (3D EPI) that encodes two partitions per radiofrequency excitation, effectively reducing the number excitations used to acquire a 3D EPI dataset by half. The strategy was evaluated in the context of functional MRI applications for: image quality compared with segmented 3D EPI, temporal signal-to-noise ratio (tSNR) (the ability to detect resting state networks compared with multislice two-dimensional (2D) EPI and segmented 3D EPI, and temporal resolution (the ability to separate cardiac- and respiration-related fluctuations from the desired blood oxygen level-dependent signal of interest). Whole brain images with a nominal voxel size of 2 mm isotropic could be acquired with a temporal resolution under half a second using traditional parallel imaging acceleration up to 4× in the partition-encode direction and using novel data acquisition speed-up of 2× with a 32-channel coil. With 8× data acquisition speed-up in the partition-encode direction, 3D reduced excitations (RE)-EPI produced acceptable image quality without introduction of noticeable additional artifacts. Due to increased tSNR and better characterization of physiological fluctuations, the new strategy allowed detection of more resting state networks compared with multislice 2D-EPI and segmented 3D EPI. 3D RE-EPI resulted in significant increases in temporal resolution for whole brain acquisitions and in improved physiological noise characterization compared with 2D-EPI and segmented 3D EPI.

Toward real‐time availability of 3D temperature maps created with temporally constrained reconstruction

To extend the previously developed temporally constrained reconstruction (TCR) algorithm to allow for real-time availability of three-dimensional (3D) temperature maps capable of monitoring MR-guided high intensity focused ultrasound applications. A real-time TCR (RT-TCR) algorithm is developed that only uses current and previously acquired undersampled k-space data from a 3D segmented EPI pulse sequence, with the image reconstruction done in a graphics processing unit implementation to overcome computation burden. Simulated and experimental data sets of HIFU heating are used to evaluate the performance of the RT-TCR algorithm. The simulation studies demonstrate that the RT-TCR algorithm has subsecond reconstruction time and can accurately measure HIFU-induced temperature rises of 20°C in 15 s for 3D volumes of 16 slices (RMSE = 0.1°C), 24 slices (RMSE = 0.2°C), and 32 slices (RMSE = 0.3°C). Experimental results in ex vivo porcine muscle demonstrate that the RT-TCR approach can reconstruct temperature maps with 192 × 162 × 66 mm 3D volume coverage, 1.5 × 1.5 × 3.0 mm resolution, and 1.2-s scan time with an accuracy of ±0.5°C. The RT-TCR algorithm offers an approach to obtaining large coverage 3D temperature maps in real-time for monitoring MR-guided high intensity focused ultrasound treatments.

Comparison of 2D and 3D single-shot ASL perfusion fMRI sequences

Arterial spin labeling (ASL) can be implemented by combining different labeling schemes and readout sequences. In this study, the performance of 2D and 3D single-shot pulsed-continuous ASL (pCASL) sequences was assessed in a group of young healthy volunteers undergoing a baseline perfusion and a functional study with a sensory-motor activation paradigm. The evaluated sequences were 2D echo-planar imaging (2D EPI), 3D single-shot fast spin-echo with in-plane spiral readout (3D FSE spiral), and 3D single-shot gradient-and-spin-echo (3D GRASE). The 3D sequences were implemented with and without the addition of an optimized background suppression (BS) scheme. Labeling efficiency, signal-to-noise ratio (SNR), and gray matter (GM) to white matter (WM) contrast ratio were assessed in baseline perfusion measurements. 3D acquisitions without BS yielded 2-fold increments in spatial SNR, but no change in temporal SNR. The addition of BS to the 3D sequences yielded a 3-fold temporal SNR increase compared to the unsuppressed sequences. 2D EPI provided better GM-to-WM contrast ratio than the 3D sequences. The analysis of functional data at the subject level showed a 3-fold increase in statistical power for the BS 3D sequences, although the improvement was attenuated at the group level. 3D without BS did not increase the maximum t-values, however, it yielded larger activation clusters than 2D. These results demonstrate that BS 3D single-shot imaging sequences improve the performance of pCASL in baseline and activation studies, particularly for individual subject analyses where the improvement in temporal SNR translates into markedly enhanced power for task activation detection.

Multishot versus Single-Shot Pulse Sequences in Very High Field fMRI: A Comparison Using Retinotopic Mapping

High-resolution functional MRI is a leading application for very high field (7 Tesla) human MR imaging. Though higher field strengths promise improvements in signal-to-noise ratios (SNR) and BOLD contrast relative to fMRI at 3 Tesla, these benefits may be partially offset by accompanying increases in geometric distortion and other off-resonance effects. Such effects may be especially pronounced with the single-shot EPI pulse sequences typically used for fMRI at standard field strengths. As an alternative, one might consider multishot pulse sequences, which may lead to somewhat lower temporal SNR than standard EPI, but which are also often substantially less susceptible to off-resonance effects. Here we consider retinotopic mapping of human visual cortex as a practical test case by which to compare examples of these sequence types for high-resolution fMRI at 7 Tesla. We performed polar angle retinotopic mapping at each of 3 isotropic resolutions (2.0, 1.7, and 1.1 mm) using both accelerated single-shot 2D EPI and accelerated multishot 3D gradient-echo pulse sequences. We found that single-shot EPI indeed led to greater temporal SNR and contrast-to-noise ratios (CNR) than the multishot sequences. However, additional distortion correction in postprocessing was required in order to fully realize these advantages, particularly at higher resolutions. The retinotopic maps produced by both sequence types were qualitatively comparable, and showed equivalent test/retest reliability. Thus, when surface-based analyses are planned, or in other circumstances where geometric distortion is of particular concern, multishot pulse sequences could provide a viable alternative to single-shot EPI.

Robust and Fast Whole Brain Mapping of the RF Transmit Field B1 at 7T

In-vivo whole brain mapping of the radio frequency transmit field B1 + is a key aspect of recent method developments in ultra high field MRI. We present an optimized method for fast and robust in-vivo whole-brain B1 + mapping at 7T. The method is based on the acquisition of stimulated and spin echo 3D EPI images and was originally developed at 3T. We further optimized the method for use at 7T. Our optimization significantly improved the robustness of the method against large B1 + deviations and off-resonance effects present at 7T. The mean accuracy and precision of the optimized method across the brain was high with a bias less than 2.6 percent unit (p.u.) and random error less than 0.7 p.u. respectively.

3D cardiac navigation with rapid multi shot EPI

Summary To assess a rapid 3D multishot EPI acquisition as an improved cardiac respiratory navigator. Background 3D EPI navigators are a robust real-time brain navigation tool [1], they allow rapid online reconstruction and image registration (< 80 ms). A thoracic EPI volume can be acquired in 200 ms, thus allowing real-time navigation. An analysis of the EPI navigators’ stability and variance when registering the heart is presented. Methods

The PRESTO technique for fMRI

In the early days of BOLD fMRI, the acquisition of T(2)(*) weighted data was greatly facilitated by rapid scan techniques such as EPI. The latter, however, was only available on a few MRI systems that were equipped with specialized hardware that allowed rapid switching of the imaging gradients. For this reason, soon after the invention of fMRI, the scan technique PRESTO was developed to make rapid T(2)(*) weighted scanning available on standard clinical scanners. This method combined echo shifting, which allows for echo times longer than the sequence repetition time, with acquisition of multiple k-space lines per excitation. These two concepts were combined in order to achieve a method fast enough for fMRI, while maintaining a sufficiently long echo time for optimal contrast. PRESTO has been primarily used for 3D scanning, which minimized the contribution of large vessels due to inflow effects. Although PRESTO is still being used today, its appeal has lessened somewhat due to increased gradient performance of modern MRI scanners. Compared to 2D EPI, PRESTO may have somewhat reduced temporal stability, which is a disadvantage for fMRI that may not outweigh the advantage of reduced inflow effects provided by 3D scanning. In this overview, the history of the development of the PRESTO is presented, followed by a qualitative comparison with EPI.

Combined Endocardial and Epicardial Catheter Ablation in Arrhythmogenic Right Ventricular Dysplasia Incorporating Scar Dechanneling Technique

Ventricular tachycardia (VT) ablation in patients with arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) has a low success rate. A more extensive epicardial (Epi) arrhythmogenic substrate could explain the low efficacy. We report the results of combined endocardial (Endo) and Epi VT ablation and conducting channel (CC) elimination. Eleven consecutive patients with ARVD/C were included in the study. A high-density 3D Endo (321±93 sites mapped) and Epi (302±158 sites mapped) electroanatomical voltage map was obtained during sinus rhythm to define scar areas (<1.5 mV) and CCs inside the scars, between scars, or between the tricuspid annulus and a scar. The end point of the ablation procedure was the elimination of all identified CCs (scar dechanneling) and the abolition of all inducible VTs. The mean procedure and fluoroscopy time were 177±63 minutes and 20±8 minutes, respectively. Epi scar area was larger in all cases (26±18 versus 94±45 cm(2), P<0.01). The combined Endo and Epi VT ablation eliminated all clinical and induced VTs, and the addition of scar dechanneling resulted in noninducibility in all cases. Seven patients continued on sotalol. During a median follow-up of 11 months (6-24 months), only 1 (9%) patient had a VT recurrence. There was a single major bleeding event that did not preclude a successful procedure. Combined Endo and Epi mapping reveals a wider Epi VT substrate in patients with ARVD/C with clinical VTs. As a first-line therapy, combined Endo and Epi VT ablation incorporating scar dechanneling achieves a very good short- and midterm success rate.

Rapid full‐brain fMRI with an accelerated multi shot 3D EPI sequence using both UNFOLD and GRAPPA

The desire to understand complex mental processes using functional MRI drives development of imaging techniques that scan the whole human brain at a high spatial and temporal resolution. In this work, an accelerated multishot three-dimensional echo-planar imaging sequence is proposed to increase the temporal resolution of these studies. A combination of two modern acceleration techniques, UNFOLD and GRAPPA is used in the secondary phase encoding direction to reduce the scan time effectively. The sequence (repetition time of 1.02 s) was compared with standard two-dimensional echo-planar imaging (3 s) and multishot three-dimensional echo-planar imaging (3 s) sequences with both block design and event-related functional MRI paradigms. With the same experimental setup and imaging time, the temporal resolution improvement with our sequence yields similar activation regions in the block design functional MRI paradigm with slightly increased t-scores. Moreover, additional information on the timing of rapid dynamic changes was extracted from accelerated images for the case of the event related complex mental paradigm.

Cardiac-induced physiological noise in 3D gradient echo brain imaging: Effect of k-space sampling scheme

The physiological noise in 3D image acquisition is shown to depend strongly on the sampling scheme. Five sampling schemes are considered: Linear, Centric, Segmented, Random and Tuned. Tuned acquisition means that data acquisition at k-space positions k and − k are separated with a specific time interval. We model physiological noise as a periodic temporal oscillation with arbitrary spatial amplitude in the physical object and develop a general framework to describe how this is rendered in the reconstructed image. Reconstructed noise can be decomposed in one component that is in phase with the signal (parallel) and one that is 90° out of phase (orthogonal). Only the former has a significant influence on the magnitude of the signal. The study focuses on fMRI using 3D EPI. Each k-space plane is acquired in a single shot in a time much shorter than the period of the physiological noise. The above mentioned sampling schemes are applied in the slow k-space direction and noise propagates almost exclusively in this direction. The problem then, is effectively one-dimensional. Numerical simulations and analytical expressions are presented. 3D noise measurements and 2D measurements with high temporal resolution are conducted. The measurements are performed under breath-hold to isolate the effect of cardiac-induced pulsatile motion. We compare the time-course stability of the sampling schemes and the extent to which noise propagates from a localized source into other parts of the imaging volume. Tuned and Linear acquisitions perform better than Centric, Segmented and Random.

Diffusion imaging of whole, post-mortem human brains on a clinical MRI scanner

Diffusion imaging of post mortem brains has great potential both as a reference for brain specimens that undergo sectioning, and as a link between in vivo diffusion studies and “gold standard” histology/dissection. While there is a relatively mature literature on post mortem diffusion imaging of animals, human brains have proven more challenging due to their incompatibility with high-performance scanners. This study presents a method for post mortem diffusion imaging of whole, human brains using a clinical 3-Tesla scanner with a 3D segmented EPI spin-echo sequence. Results in eleven brains at 0.94×0.94×0.94mm resolution are presented, and in a single brain at 0.73×0.73×0.73mm resolution. Region-of-interest analysis of diffusion tensor parameters indicate that these properties are altered compared to in vivo (reduced diffusivity and anisotropy), with significant dependence on post mortem interval (time from death to fixation). Despite these alterations, diffusion tractography of several major tracts is successfully demonstrated at both resolutions. We also report novel findings of cortical anisotropy and partial volume effects.

Improvement of accuracy of diffusion MRI using real‐time self‐gated data acquisition

Diffusion-weighted and diffusion tensor MR imaging (DWI, DTI) techniques are generally performed with signal averaging of multiple measurements to improve the signal-to-noise ratio (SNR) and the accuracy of the diffusion measurement. Any discrepancy in the images between different averages causes errors which reduce the accuracy of the diffusion MRI measurements. In this report, a motion artifact reduction scheme with a real-time self-gated (RTSG) data acquisition for diffusion MRI using two-dimensional echo planar imaging (2D EPI) is described. A subject's translational and rotational motions during application of the diffusion gradients induce an additional phase term and a shift of the echo-peak position in the k-space, respectively. These motions also reduce the magnitude of the echo-peak. Based on these properties, we present a new scheme which monitors the position and the magnitude of the largest echo-peak in the k-space. The position and the magnitude of each average is compared to those of early averaging shot to determine if the differences are within or beyond the given threshold values. Motion corrupted data are reacquired in real time. Our preliminary results using RTSG indicate an improvement of both SNR and the accuracy of diffusion MRI measurements.

High resolution diffusion-weighted imaging in fixed human brain using diffusion-weighted steady state free precession

High resolution diffusion tensor imaging and tractography of ex vivo brain specimens has the potential to reveal detailed fibre architecture not visible on in vivo images. Previous ex vivo diffusion imaging experiments have focused on animal brains or small sections of human tissue since the unfavourable properties of fixed tissue (including short T2 and low diffusion rates) demand the use of very powerful gradient coils that are too small to accommodate a whole, human brain. This study proposes the use of diffusion-weighted steady-state free precession (DW-SSFP) as a method of extending the benefits of ex vivo DTI and tractography to whole, human, fixed brains on a clinical 3 T scanner. DW-SSFP is a highly efficient pulse sequence; however, its complicated signal dependence precludes the use of standard diffusion tensor analysis and tractography. In this study, a method is presented for modelling anisotropy in the context of DW-SSFP. Markov Chain Monte Carlo sampling is used to estimate the posterior distributions of model parameters and it is shown that it is possible to estimate a tight distribution on the principal axis of diffusion at each voxel using DW-SSFP. Voxel-wise estimates are used to perform tractography in a whole, fixed human brain. A direct comparison between 3D diffusion-weighted spin echo EPI and 3D DW-SSFP-EPI reveals that the orientation of the principal diffusion axis can be inferred on with a higher degree of certainty using a 3D DW-SSFP-EPI even with a 68% shorter acquisition time.

Reciprocal Effects of Antidepressant Treatment on Activity and Connectivity of the Mood Regulating Circuit: An fMRI Study

Reciprocal Effects of Antidepressant Treatment on Activity and Connectivity of the Mood Regulating Circuit: An fMRI Study

The effects of brain tissue decomposition on diffusion tensor imaging and tractography

There have been numerous high resolution diffusion tensor imaging studies in fixed animal brains, but relatively few studies in human brains. While animal tissues are generally fixed pre-mortem or directly postmortem, this is not possible for human tissue, therefore there is always some delay between death and tissue fixation. The elapsed time between death and tissue fixation, the postmortem interval (PMI), will most likely adversely affect the tissue's diffusion properties. We studied the effects of PMI on the diffusion properties of rodent brain. Eight mice were euthanized and the brains (kept in the skull) were placed in formalin at PMIs of 0, 1, 4 and 14 days. Post fixation they were placed in a solution of GdDTPA and phosphate buffered saline. Brains were scanned with a 3D EPI DTI sequence at 4.7T. DTI data were processed to generate apparent diffusion coefficient (ADC) and fractional anisotropy (FA) maps. DTI tractography was also performed. The temporal changes in regional ADC and FA values were analyzed statistically using a one-way ANOVA, followed by individual Student's T-tests. Regional FA and ADC of gray and white matter decreased significantly with time (p<0.05). DTI tractography showed a decrease in the number and coherence of reconstructed fiber pathways between PMIs 0 and 14. Elapsed time between death and tissue fixation has a major effect upon the brain's diffusion properties and should be born in mind when interpreting fixed brain DTI.

High‐resolution DTI with 2D interleaved multislice reduced FOV single‐shot diffusion‐weighted EPI (2D ss‐rFOV‐DWEPI)

Diffusion tensor MRI (DTI), using single-shot 2D diffusion weighted-EPI (2D ss-DWEPI), is limited to intracranial (i.c.) applications far from the sinuses and bony structures, due to the severe geometric distortions caused by significant magnetic field inhomogeneities at or near the tissue-air or tissue-bone interfaces. Reducing these distortions in single-shot EPI by shortening the readout period generally requires a reduced field of view (and the potential of wraparound artifact) in the phase-encoding direction and/or reduced spatial resolution. To resolve the problem, a novel 2D reduced FOV single-shot diffusion-weighted EPI (2D ss-rFOV-DWEPI) pulse sequence applicable for high resolution diffusion-weighted MRI of local anatomic regions, such as brainstem, cervical spinal cord, and optic nerve, has been developed. In the proposed technique, time-efficient interleaved acquisition of multiple slices with a limited FOV was achieved by applying an even number of refocusing 180 degrees pulses with the slice-selection gradient applied in the phase-encoding direction. The two refocusing pulses used for each slice acquisition were separated by a short time interval (typically less than 45 ms) required for the 2D EPI echotrain acquisition. The new technique can be useful for high resolution DTI of various anatomies, such as localized brain structures, cervical spinal cord, optic nerve, heart, or other extra-cerebral organ, where conventional 2D ss-DWEPI is limited in usage due to the severity of image distortions.