2D multislice and 3D MRI sequences are often equally sensitive

A novel network architecture combining central-peripheral deviation with image-based convolutional neural networks for diffusion tensor imaging studies

Brain imaging research is a very challenging topic due to complex structure and lack of explicitly identifiable features in the image. With the advancement of magnetic resonance imaging (MRI) technologies, such as diffusion tensor imaging (DTI), developing classification methods to improve clinical diagnosis is crucial. This paper proposes a classification method for DTI data based on a novel neural network strategy that combines a convolutional neural network (CNN) with a multilayer neural network using central-peripheral deviation (CPD), which reflects diffusion dynamics in the white matter by spatially evaluating the deviation of diffusion coefficients between the inner and outer parts of the brain. In our method, a multilayer perceptron (MLP) using CPD is combined with the final layers for classification after reducing the dimensions of images in the convolutional layers of the neural network architecture. In terms of training loss and the classification error, the proposed classification method improves the existing image classification with CNN. For real data analysis, we demonstrate how to process raw DTI image data sets obtained from a traumatic brain injury study (MagNeTS) and a brain atlas construction study (ICBM), and apply the proposed approach to the data, successfully improving classification performance with two age groups.

Neuromelanin accumulation in patients with schizophrenia: A systematic review and meta-analysis

Although schizophrenia is associated with increased presynaptic dopamine function in the striatum, it remains unclear if neuromelanin levels, which are thought to serve as a biomarker for midbrain dopamine neuron function, are increased in patients with schizophrenia. We conducted a systematic review and meta-analysis of magnetic resonance imaging (MRI) and postmortem studies comparing neuromelanin (NM) levels between patients with schizophrenia and healthy controls (HCs). Standard mean differences were calculated to assess group differences in NM accumulation levels between patients with schizophrenia and HCs. This study included 7 articles in total. Five studies employed NM-sensitive MRI (NM-MRI) and two were postmortem brain studies. The patient group (n = 163) showed higher NM levels in the substantia nigra (SN) than HCs (n = 228) in both the analysis of the seven studies and the subgroup analysis of the 5 NM-MRI studies. This analysis suggest increased NM levels in the SN may be a potential biomarker for stratifying schizophrenia, warranting further research that accounts for the heterogeneity of this disorder.

Fast 3D MR elastography of the whole brain using spiral staircase: Data acquisition, image reconstruction, and joint deblurring

PURPOSE

To address the need for a method to acquire 3D data for MR elastography (MRE) of the whole brain with substantially improved spatial resolution, high SNR, and reduced acquisition time compared with conventional methods.

METHODS

We combined a novel 3D spiral staircase data-acquisition method with a spoiled gradient-echo pulse sequence and MRE motion-encoding gradients (MEGs). The spiral-out acquisition permitted use of longer-duration motion-encoding gradients (ie, over two full oscillatory cycles) to enhance displacement SNR, while still maintaining a reasonably short TE for good phase-SNR. Through-plane parallel imaging with low noise penalties was implemented to accelerate acquisition along the slice direction. Shared anatomical information was exploited in the deblurring procedure to further boost SNR for stiffness inversion.

RESULTS

In vivo and phantom experiments demonstrated the feasibility of the proposed method in producing brain MRE results comparable to the spin-echo-based approaches, both qualitatively and quantitatively. High-resolution (2-mm isotropic) brain MRE data were acquired in 5 minutes using our method with good SNR. Joint deblurring with shared anatomical information produced SNR-enhanced images, leading to upward stiffness estimation.

CONCLUSION

A novel 3D gradient-echo-based approach has been designed and implemented, and shown to have promising potential for fast and high-resolution in vivo MRE of the whole brain.

3D MRI in Musculoskeletal Oncology

Advances in magnetic resonance imaging (MRI) technology now enable the feasible three-dimensional (3D) acquisition of images. With respect to the imaging of musculoskeletal (MSK) tumors, literature is beginning to accumulate on the use of 3D MRI acquisition for tumor detection and characterization. The benefits of 3D MRI, including general advantages, such as decreased acquisition time, isotropic resolution, and increased image quality, are not only inherently useful for tumor imaging, but they also contribute to the feasibility of more specialized tumor-imaging techniques, such as whole-body MRI, and are reviewed here. Disadvantages of 3D acquisition, such as motion artifact and equipment requirements, do exist and are also discussed. Although further study is needed, 3D MRI acquisition will likely prove increasingly useful in the evaluation of patients with tumors of the MSK system.

MR susceptibility contrast imaging using a 2D simultaneous multi-slice gradient-echo sequence at 7T

Purpose

To develop a 7T simultaneous multi-slice (SMS) 2D gradient-echo sequence for susceptibility contrast imaging, and to compare its quality to 3D imaging.

Methods

A frequency modulated and phase cycled RF pulse was designed to simultaneously excite multiple slices in multi-echo 2D gradient-echo imaging. The imaging parameters were chosen to generate images with susceptibility contrast, including T₂*-weighted magnitude/phase images, susceptibility-weighted images and quantitative susceptibility/R₂* maps. To compare their image quality with 3D gradient-echo imaging, both 2D and 3D imaging were performed on 11 healthy volunteers and 4 patients with multiple sclerosis (MS). The signal to noise ratio (SNR) in gray and white matter and their contrast to noise ratio (CNR) was simulated for the 2D and 3D magnitude images using parameters from the imaging. The experimental SNRs and CNRs were measured in gray/white matter and deep gray matter structures on magnitude, phase, R₂* and QSM images from volunteers and the visibility of MS lesions on these images from patients was visually rated. All SNRs and CNRs were compared between the 2D and 3D imaging using a paired t-test.

Results

Although the 3D magnitude images still had significantly higher SNRs (by 13.0~17.6%), the 2D magnitude and QSM images generated significantly higher gray/white matter or globus pallidus/putamen contrast (by 13.3~87.5%) and significantly higher MS lesion contrast (by 5.9~17.3%).

Conclusion

2D SMS gradient-echo imaging can serve as an alternative to often used 3D imaging to obtain susceptibility-contrast-weighted images, with an advantage of providing better image contrast and MS lesion sensitivity.

Imaging putative foetal cerebral blood oxygenation using susceptibility weighted imaging (SWI)

OBJECTIVE

To evaluate the magnetic susceptibility, ∆χ v , as a surrogate marker of venous blood oxygen saturation, S v O 2, in second- and third-trimester normal human foetuses.

METHODS

Thirty-six pregnant women, having a mean gestational age (GA) of 31 2/7 weeks, underwent magnetic resonance imaging (MRI). Susceptibility-weighted imaging (SWI) data from the foetal brain were acquired. ∆χ v of the superior sagittal sinus (SSS) was quantified using MR susceptometry from the intra-vascular phase measurements. Assuming the magnetic property of foetal blood, ∆χ do , is the same as that of adult blood, S v O 2 was derived from the measured Δχ v . The variation of ∆χ v and S v O 2, as a function of GA, was statistically evaluated.

RESULTS

The mean ∆χ v in the SSS in the second-trimester (n = 8) and third-trimester foetuses (n = 28) was found to be 0.34± 0.06 ppm and 0.49 ±0.05 ppm, respectively. Correspondingly, the derived S v O 2 values were 69.4% ±3.27% and 62.6% ±3.25%. Although not statistically significant, an increasing trend (p = 0.08) in Δχ v and a decreasing trend (p = 0.22) in S v O 2 with respect to advancing gestation was observed.

CONCLUSION

We report cerebral venous blood magnetic susceptibility and putative oxygen saturation in healthy human foetuses. Cerebral oxygen saturation in healthy human foetuses, despite a slight decreasing trend, does not change significantly with advancing gestation.

KEY POINTS

• Cerebral venous magnetic susceptibility and oxygenation in human foetuses can be quantified. • Cerebral venous oxygenation was not different between second- and third-trimester foetuses. • Foetal cerebral venous oxygenation does not change significantly with advancing gestation.

Time efficient whole-brain coverage with MR Fingerprinting using slice-interleaved echo-planar-imaging

Magnetic resonance fingerprinting (MRF) is a promising method for fast simultaneous quantification of multiple tissue parameters. The objective of this study is to improve the coverage of MRF based on echo-planar imaging (MRF-EPI) by using a slice-interleaved acquisition scheme. For this, the MRF-EPI is modified to acquire several slices in a randomized interleaved manner, increasing the effective repetition time of the spoiled gradient echo readout acquisition in each slice. Per-slice matching of the signal-trace to a precomputed dictionary allows the generation of T1 and T2* maps with integrated B1+ correction. Subsequent compensation for the coil sensitivity profile and normalization to the cerebrospinal fluid additionally allows for quantitative proton density (PD) mapping. Numerical simulations are performed to optimize the number of interleaved slices. Quantification accuracy is validated in phantom scans and feasibility is demonstrated in-vivo. Numerical simulations suggest the acquisition of four slices as a trade-off between quantification precision and scan-time. Phantom results indicate good agreement with reference measurements (Difference T1: -2.4 ± 1.1%, T2*: -0.5 ± 2.5%, PD: -0.5 ± 7.2%). In-vivo whole-brain coverage of T1, T2* and PD with 32 slices was acquired within 3:36 minutes, resulting in parameter maps of high visual quality and comparable performance with single-slice MRF-EPI at 4-fold scan-time reduction.

Rapid brain MRI acquisition techniques at ultra-high fields

Ultra-high-field MRI provides large increases in signal-to-noise ratio (SNR) as well as enhancement of several contrast mechanisms in both structural and functional imaging. Combined, these gains result in a substantial boost in contrast-to-noise ratio that can be exploited for higher-spatial-resolution imaging to extract finer-scale information about the brain. With increased spatial resolution, however, there is a concurrent increased image-encoding burden that can cause unacceptably long scan times for structural imaging and slow temporal sampling of the hemodynamic response in functional MRI - particularly when whole-brain imaging is desired. To address this issue, new directions of imaging technology development - such as the move from conventional 2D slice-by-slice imaging to more efficient simultaneous multislice (SMS) or multiband imaging (which can be viewed as "pseudo-3D" encoding) as well as full 3D imaging - have provided dramatic improvements in acquisition speed. Such imaging paradigms provide higher SNR efficiency as well as improved encoding efficiency. Moreover, SMS and 3D imaging can make better use of coil sensitivity information in multichannel receiver arrays used for parallel imaging acquisitions through controlled aliasing in multiple spatial directions. This has enabled unprecedented acceleration factors of an order of magnitude or higher in these imaging acquisition schemes, with low image artifact levels and high SNR. Here we review the latest developments of SMS and 3D imaging methods and related technologies at ultra-high field for rapid high-resolution functional and structural imaging of the brain. Copyright © 2016 John Wiley & Sons, Ltd.

Three-dimensional volumetric MRI with isotropic resolution: improved speed of acquisition, spatial resolution and assessment of lesion conspicuity in patients with recurrent soft tissue sarcoma

BACKGROUND

To assess the acquisition speed, lesion conspicuity, and inter-observer agreement associated with volumetric T(1)-weighted MR sequences with isotropic resolution for detecting recurrent soft-tissue sarcoma (STS).

METHODS

Fifteen subjects with histologically proven recurrent STS underwent MRI, including axial and coronal T(1)-weighted spin echo (T(1)-WSE) (5-mm slice thickness) and coronal 3D volumetric T(1)-weighted (fat-suppressed, volume-interpolated, breath-hold examination; repetition time/echo time, 3.7/1.4 ms; flip angle, 9.5°; 1-mm slice thickness) sequences before and after intravenous contrast administration. Subtraction imaging and multiplanar reformations (MPRs) were performed. Acquisition times for T(1)-WSE in two planes and 3D sequences were reported. Two radiologists reviewed images for quality (>50 % artifacts, 25-50 % artifacts, <25 % artifacts, and no substantial artifacts), lesion conspicuity, contrast-to-noise ratio (CNR(muscle)), recurrence size, and recurrence-to-joint distance. Descriptive and intraclass correlation (ICC) statistics are given.

RESULTS

Mean acquisition times were significantly less for 3D imaging compared with 2-plane T(1)-WSE (183.6 vs 342.6 s; P = 0.012). Image quality was rated as having no substantial artifacts in 13/15 and <25 % artifacts in 2/15. Lesion conspicuity was significantly improved for subtracted versus unsubtracted images (CNR(muscle), 100 ± 138 vs 181 ± 199; P = 0.05). Mean recurrent lesion size was 2.5 cm (range, 0.7-5.7 cm), and measurements on 3D sequences offered excellent interobserver agreement (ICC, 0.98 for lesion size and 0.96 for recurrence-to-joint distance with MPR views).

CONCLUSION

Three-dimensional volumetric sequences offer faster acquisition times, higher spatial resolution, and MPR capability compared with 2D T(1)-WSE for postcontrast imaging. Subtraction imaging provides higher lesion conspicuity for detecting recurrent STS in skeletal muscle, with excellent interobserver agreement between readers.

Rapid and robust variable flip angle T1 mapping using interleaved two-dimensional multislice spoiled gradient echo imaging

PURPOSE

Conventional T₁ mapping using three-dimensional (3D) radiofrequency (RF) spoiled gradient echo (SPGR) imaging with short repetition times (TR) is adversely affected by incomplete spoiling (i.e. residual T₂ dependency). In this work, an optimized interleaved 2D multislice SPGR sequence scheme and an adapted postprocessing procedure are evaluated for highly T₂ -insensitive T₁ quantification of human brain tissues.

METHODS

An efficient 2D multislice SPGR protocol including a relatively long TR of 200 ms is investigated with careful consideration of cross talk and magnetization transfer effects. Based on the derived scan protocol, T₁ is quantified from the signal ratio of two SPGR datasets acquired at different flip angles. The effect of nonideal RF excitation profiles is incorporated into the SPGR signal model by performing Bloch simulations.

RESULTS

Simulations showed that the parameters of the SPGR protocol (such as TR and the spoiler gradient moments) guarantee virtually complete spoiling. This result was confirmed by T₁ measurements both in vitro using a 2% agar probe doped with 0.1 mM Gd (Gadovist) and in vivo in the human brain.

CONCLUSION

The derived 2D multislice SPGR protocol offers efficient, highly reproducible, and in particular T₂ -insensitive T₁ quantification of human brain tissues. Magn Reson Med 77:1606-1611, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Artifact-suppressed optimal three-dimensional T1 - and T2 *-weighted dual-echo imaging

PURPOSE

To develop a new artifact-suppressed optimal three-dimensional (3D) T₁ - and T₂ *-weighted dual-echo imaging.

METHODS

We optimized flip angles for 3D T₁ - and T₂ *-weighted imaging by conventional dual-echo in vivo experiments and computer simulations, and then implemented a dual-echo sequence with an echo-specific k-space reordering scheme to satisfy the optimal flip angles for both T₁ and T₂ * contrast. We also proposed two strategies to suppress ringing artifacts induced by the abrupt flip angle jumps in the proposed dual echo sequence: (i) implementing smooth transition regions and (ii) discarding the k-space regions of the abrupt flip angle jumps as dummy phase-encoding steps.

RESULTS

The optimal flip angles measured from experiments were different between T₁ - and T₂ *-weighted contrast, in agreement with simulations. The echo-specific k-space reordered dual-echo sequence showed optimal T₁ and T₂ * contrast simultaneously, but also showed ringing artifacts because of high flip-angle changes between k-space regions. The two proposed strategies effectively suppressed the ringing artifacts.

CONCLUSION

The proposed 3D dual-echo sequence provided optimal T₁ and T₂ * contrast simultaneously with no artifacts and thus is potentially applicable to routine clinical applications for simultaneous high resolution T₁ - and T₂ *-weighted imaging. Magn Reson Med 76:1504-1511, 2016. © 2015 International Society for Magnetic Resonance in Medicine.

Comparison of three-dimensional isotropic and two-dimensional conventional indirect MR arthrography for the diagnosis of rotator cuff tears

OBJECTIVE

To compare the accuracy between a three-dimensional (3D) indirect isotropic T1-weighted fast spin-echo (FSE) magnetic resonance (MR) arthrography and a conventional two-dimensional (2D) T1-weighted sequences of indirect MR arthrography for diagnosing rotator cuff tears.

MATERIALS AND METHODS

The study was approved by our Institutional Review Board. In total, 205 patients who had undergone indirect shoulder MR arthrography followed by arthroscopic surgery for 206 shoulders were included in this study. Both conventional 2D T1-weighted FSE sequences and 3D isotropic T1-weighted FSE sequence were performed in all patients. Two radiologists evaluated the images for the presence of full- or partial-thickness tears in the supraspinatus-infraspinatus (SSP-ISP) tendons and tears in the subscapularis (SSC) tendons. Using the arthroscopic findings as the reference standard, the diagnostic performances of both methods were analyzed by the area under the receiver operating characteristic curve (AUC).

RESULTS

Arthroscopy confirmed 165 SSP-ISP tendon tears and 103 SSC tendon tears. For diagnosing SSP-ISP tendon tears, the AUC values were 0.964 and 0.989 for the 2D sequences and 3D T1-weighted FSE sequence, respectively, in reader I and 0.947 and 0.963, respectively, in reader II. The AUC values for diagnosing SSC tendon tears were 0.921 and 0.925, respectively, for reader I and 0.856 and 0.860, respectively, for reader II. There was no significant difference between the AUC values of the 2D and 3D sequences in either reader for either type of tear.

CONCLUSION

3D indirect isotropic MR arthrography with FSE sequence and the conventional 2D arthrography are not significantly different in terms of accuracy for diagnosing rotator cuff tears.

Quiet T1-weighted imaging using PETRA: initial clinical evaluation in intracranial tumor patients

PURPOSE

To compare the lesion contrast and signal to noise ratio (SNR) obtained with T1-weighted pointwise encoding time reduction with radial acquisition (PETRA) to those of Magnetization-Prepared RApid Gradient-Echo (MPRAGE) for contrast-enhanced imaging of primary and metastatic intracranial tumors, and to investigate whether PETRA is able to reduce acoustic noise for improved patient comfort.

MATERIALS AND METHODS

Fifteen patients with intracranial tumors underwent 3 Tesla MRI including inversion-prepared PETRA and MPRAGE. The two sequences had comparable scan times, spatial resolution and spatial coverage. "Tumor conspicuity" was rated qualitatively by two radiologists, while enhancing lesion-to-white matter contrast to noise ratio (CNR) and white-matter SNR were analyzed quantitatively using paired t-tests. The acoustic noise generated by each sequence was measured.

RESULTS

Qualitative rating of "tumor conspicuity" by two radiologists resulted in nearly identical average scores for the two sequences. Quantitative analyses revealed that (i) there was no significant difference between the mean CNR values of the two sequences (P = 0.57), (ii) the mean SNR of PETRA was significantly higher than that of MPRAGE (P < 0.01), and (iii) the mean sound level of PETRA was significantly lower than that of MPRAGE (P < 0.01).

CONCLUSION

Inversion-prepared PETRA was found to be viable as a quiet alternative to MPRAGE for contrast-enhanced T1-weighted studies of intracranial tumors.

A historical overview of magnetic resonance imaging, focusing on technological innovations

Magnetic resonance imaging (MRI) has now been used clinically for more than 30 years. Today, MRI serves as the primary diagnostic modality for many clinical problems. In this article, historical developments in the field of MRI will be discussed with a focus on technological innovations. Topics include the initial discoveries in nuclear magnetic resonance that allowed for the advent of MRI as well as the development of whole-body, high field strength, and open MRI systems. Dedicated imaging coils, basic pulse sequences, contrast-enhanced, and functional imaging techniques will also be discussed in a historical context. This article describes important technological innovations in the field of MRI, together with their clinical applicability today, providing critical insights into future developments.

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.

In vivo magnetic resonance imaging of amyloid-β plaques in mice

Transgenic mice are used increasingly to model brain amyloidosis, mimicking the pathogenic processes involved in Alzheimer's disease (AD). In this chapter, an in vivo strategy is described that has been successfully used to map amyloid-β deposits in transgenic mouse models of AD with magnetic resonance imaging (MRI), utilizing both the endogenous contrast induced by the plaques attributed to their iron content and by selectively enhancing the signal from amyloid-β plaques using molecular-targeting vectors labeled with MRI contrast agents. To obtain sufficient spatial resolution for effective and sensitive mouse brain imaging, magnetic fields of 7-Tesla (T) or more are required. These are higher than the 1.5-T field strength routinely used for human brain imaging. The higher magnetic fields affect contrast agent efficiency and dictate the choice of pulse sequence parameters for in vivo MRI, all addressed in this chapter. Two-dimensional (2D) multi-slice and three-dimensional (3D) MRI acquisitions are described and their advantages and limitations are discussed. The experimental setup required for mouse brain imaging is explained in detail, including anesthesia, immobilization of the mouse's head to reduce motion artifacts, and anatomical landmarks to use for the slice alignment procedure to improve image co-registration during longitudinal studies and for subsequent matching of MRI with histology.

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

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

Murine diffusion imaging using snapshot interleaved EPI acquisition at 7T

Diffusion tensor imaging (DTI) is a powerful magnetic resonance imaging tool for quantitative assessment of white matter micro structure. The majority of DTI methods employ Echo Planar Imaging (EPI) because it is insensitive to motion. However, EPI suffers from distortions and signal losses induced by inhomogeneities in magnetic field susceptibility. This is particularly accentuated in murine imaging at very high magnetic fields. The purpose of this study is to demonstrate that a Snapshot Interleaved EPI acquisition block combined with a stimulated echo module for diffusion sensitization can be successfully used to obtain high quality DTI of a mouse brain at 7T. This technique preserves the EPI speed but reduces its susceptibility artifacts and signal losses. Signal to noise ratio is also reduced but remains higher than in the DTI acquisitions based on a fast low angle shot technique. In vivo results using this new approach are presented along with a full description of the methodology.

Cochlear implantation update: contemporary preoperative imaging and future prospects - the dual modality approach as a standard of care

The selection of cochlear implant (CI) candidates requires consideration of a variety of clinical and radiographic factors. The present article reviews the current knowledge regarding the preoperative imaging of CI candidates and explores emerging developments in different imaging modalities. Preoperative radiologic assessment should evaluate the status of the middle/inner ear, auditory nerve and central acoustic pathways. Preoperative computed tomography displays anatomic middle ear variations of surgical importance. MRI can demonstrate fluid/obliteration in the inner ear and depict the retrocochlear auditory pathways. Dual modality imaging with high-resolution computed tomography and MRI of the petrous bone and brain can provide the maximum information regarding surgical landmarks and detect deafness-related abnormalities. Cost-effectiveness issues also justify its use. New systems are now becoming available, offering improved soft-tissue delineation, sophisticated segmentation techniques, volumetric measurements, semitransparent views and superior surface resolution, thus significantly advancing our diagnostic acumen and making the preoperative evaluation of CI candidates more accurate and reliable.

Retrospective correction for T1-weighting bias in T2 values obtained with various spectroscopic spin-echo acquisition schemes

Localized tissue transverse relaxation time (T(2)) is obtained by fitting a decaying exponential to the signals from several spin-echo experiments at different echo times (TE). Unfortunately, time constraints in magnetic resonance spectroscopy (MRS) often mandate in vivo acquisition schemes at short repetition times (TR), that is, comparable with the longitudinal relaxation constant (T(1)). This leads to different T(1)-weighting of the signals at each TE. Unaccounted for, this varying weighting causes systematic underestimation of the T(2)'s, sometimes by as mush as 30%. In this article, we (i) analyze the phenomenon for common MRS spin-echo T(2) acquisition schemes; (ii) propose a general post hoc T(1)-bias correction for any (TR, TE) combination; (iii) show that approximate knowledge of T(1) is sufficient, since a 20% uncertainty in T(1) leads to under 3% bias in T(2); and consequently, (iv) efficient, precision-optimized short TR spin-echo T(2) measurement protocols can be designed and used without risk of accuracy loss. Tables of correction for single-refocusing (conventional) spin-echo and double refocusing, such as, PRESS acquisitions, are provided.

Increased dosage of DYRK1A and brain volumetric alterations in a YAC model of partial trisomy 21

A yeast artificial chromosome (YAC) transgenic murine model of partial trisomy 21 overexpressing five human genes -- including DYRK1A, which encodes a serine threonine kinase involved in cell cycle control -- has been shown to present an increase in brain weight. We analyzed this new phenotype by measuring total and regional brain volumes at different ages, using a 7 Tesla magnetic resonance imaging volumetric approach. Volumetric measurements showed a total volume increase of 13.6% in adult mice. Changes in brain morphogenesis were already visible at a very early postnatal stage (postnatal days 2-7). Region-specific changes were characterized from postnatal day 15 to 5 months. These results, made it possible to define region-specific effects of DYRK1A overexpression, with the strongest increase seen in the thalamus-hypothalamus area (24%).

Optimum pulse flip angles for multi-scan acquisition of hyperpolarized NMR and MRI

The optimum pulse flip angles were calculated for multi-scan acquisition of hyperpolarized NMR and MRI. The derived formulae could be correlated with the best angle for ordinary steady-state acquisition, the so-called Ernst angle. Although single-scan acquisition has been popular in hyperpolarized measurements, signal accumulation by increasing scans may become very effective for improving the total signal gain, especially when the sample's longitudinal spin relaxation time is long. The optimum angles were calculated from theoretical relations between the exponential of the pulse repetition time/relaxation time ratio and the total scan counts. Constant and variable flip angle cases are presented, both of which yield similar cumulative signal amplitudes. For the constant angle case, a numerically calculated semi-universal curve is presented for the rough estimation of the best angle, as the results were not significantly dependent upon the degree of hyperpolarization within the realistic range. Meanwhile, for the variable angle case, the best angles were approximated from a clean trigonometric series relation, in which the initial pulse became near the Ernst angle and the last pulse was always 90 degrees . A modification of the variable angle scheme enables the acquisition of uniform signal amplitude throughout all scans.

Contrast-enhanced MRI of right ventricular abnormalities in Cx43 mutant mouse embryos

Imaging of the mammalian cardiac right ventricle (RV) is particularly challenging, especially when a two-dimensional method such as conventional histology is used to evaluate the morphology of this asymmetric, crescent-shaped chamber. MRI may improve the characterization of mutants with RV phenotypes by allowing analysis of the samples in any plane and by facilitating three-dimensional image reconstruction. MRI was used to examine the conditional knockout Cx43-PCKO mouse line known to have RV malformations. To help delineate the cardiovascular system and facilitate identification of the right ventricular outflow tract (RVOT), embryonic day (E) 17.5 embryos were perfusion fixed through the umbilical vein followed by a gadolinium-based contrast agent mixed in 7% gelatin. Micro-MRI experiments were performed at 7 T and followed by paraffin embedding of specimens, histological sectioning and hematoxylin and eosin (H&E) staining. Imaging of up to four embryos simultaneously allowed for higher throughput than traditional individual imaging techniques, while intravascular contrast afforded excellent signal-to-noise characteristics. All control embryos (n = 4) and heterozygous Cx43 knockout embryos (n = 4) had normal-appearing right ventricular outflow tract contours by MRI. Obvious abnormalities in the RVOT, including abnormal bulging and infiltration of contrast into the wall of the RV, were seen in three out of four Cx43-PCKO mutants with MRI. Furthermore, three-dimensional reconstruction of MR images with orthogonal projections as well as maximum-intensity projection allowed for visualization of the relationship of infundibular bulging segments to the pulmonary trunk in Cx43-PCKO mutant hearts. The addition of MRI to standard histology in the characterization of RV malformations in mutant mouse embryos aids in the assessment and understanding of morphologic abnormalities. Flexibility in the viewing of MR images, which can be retrospectively sectioned in any desired orientation, is particularly useful in the investigation of the RV, an asymmetric chamber that is difficult to analyze with two-dimensional techniques.

Three-dimensional prepolarized magnetic resonance imaging using rapid acquisition with relaxation enhancement

Prepolarized MRI (PMRI) with pulsed electromagnets has the potential to produce diagnostic quality 0.5- to 1.0-T images with significantly reduced cost, susceptibility artifacts, specific absorption rate, and gradient noise. In PMRI, the main magnetic field cycles between a high field (B(p)) to polarize the sample and a homogeneous, low field (B(0)) for data acquisition. This architecture combines the higher SNR of the polarizing field with the imaging benefits of the lower field. However, PMRI can only achieve high SNR efficiency for volumetric imaging with 3D rapid imaging techniques, such as rapid acquisition with relaxation enhancement (RARE) (FSE, TSE), because slice-interleaved acquisition and longitudinal magnetization storage are both inefficient in PMRI. This paper demonstrates the use of three techniques necessary to achieve efficient, artifact-free RARE in PMRI: quadratic nulling of concomitant gradient fields, electromotive force cancelation during field ramping, and phase compensation of CPMG echo trains. This paper also demonstrates the use of 3D RARE in PMRI to achieve standard T(1) and fat-suppressed T(2) contrast in phantoms and in vivo wrists. These images show strong potential for future clinical application of PMRI to extremity musculoskeletal imaging and peripheral angiography.

Optimizing the efficiency of high-field multivoxel spectroscopic imaging by multiplexing in space and time

A new strategy to yield information from the maximum number of voxels, each at the optimum signal-to-noise ratio (SNR) per unit time, in MR spectroscopic imaging (MRSI) is introduced. In the past, maximum acquisition duty-cycle was obtained by multiplexing in time several single slices each repetition time (TR), while optimal SNR was achieved by encoding the entire volume of interest (VOI) each TR. We show that optimal SNR and acquisition efficiency can both be achieved simultaneously by multiplexing in space and time several slabs of several slices, each. Since coverage of common VOIs in 3D proton MRSI in the human brain typically requires eight or more slices, at 3 T or higher magnetic fields, two or more slabs can fit into the optimum TR (approximately 1.6 s). Since typically four or less slices would then fit into each slab, Hadamard encoding is favored in that direction for slice profile reasons. It is demonstrated that per fixed examination length, the new method gives, at 3 T, twice as many voxels, each of the same SNR and size, compared with current 3D chemical shift imaging techniques. It is shown that this gain will increase for more extensive spatial coverage or higher fields.

Interleaved snapshot echo planar imaging of mouse brain at 7.0 T

Single-shot echo planar imaging (EPI) of a mouse brain at high field is very challenging. Large susceptibility-induced gradients affect much of the brain volume, causing severe image deformations and signal loss. Segmented EPI and other conventional multi-shot approaches alleviate these problems but suffer from lower temporal resolution and motion artifacts. We demonstrate that interleaved snapshot EPI represents a simple and robust alternative approach and one that is particularly suitable for high-field T2*-weighted functional imaging of a mouse brain. Similarly to segmented multi-shot techniques, it significantly reduces the susceptibility-related artifacts. At the same time, it preserves the high temporal resolution and the snapshot capability of a conventional EPI by acquiring entire image within a single TR period. We discuss implementation details of the interleaved snapshot EPI sequence and the trade-offs involved between the imaging efficiency, the number of interleaved excitation-acquisition blocks and the artifact reduction. To document the sequence utility, murine brain in vivo imaging with the interleaved snapshot EPI method was compared with a conventional EPI. We found that at least five interleaved blocks were necessary to restore the signal in most cortical areas. We also show that a standard global shimming procedure provides sufficient homogeneity for multi-slice interleaved snapshot EPI acquisition. In contrast, the conventional EPI of comparable image quality would be limited to a single slice with highly optimized local shim. Finally, an in vitro comparison with turbo FLASH acquisition shows the interleaved snapshot EPI to have superior time resolution and signal-to-noise ratio.

REST-PEEP: reduced scan time phase-encoded echo planar imaging

Echo planar methodology can be used for rapid acquisition in three dimensions of k-space. There are two groups of sequences which have thus far been implemented. The first group is characterized by three-dimensional acquisition from a single RF excitation. Echo planar shift mapping and echo volume imaging are single-shot chemical shift imaging and three-dimensional spatial imaging techniques, respectively. Even though these methods are extremely fast, their spatial and spectral resolutions are poor. In the second group of sequences, echo planar imaging acquisition is repeated for every phase-encode gradient step to improve upon the spatial resolution and signal-to-noise ratio at the expense of acquisition time. Here we report a novel combination of these two groups of sequences aimed at providing additional flexibility in trade-offs between the spectral bandwidth, signal-to-noise ratio, spatial resolution and imaging time. Preliminary results for both chemical shift imaging and three-dimensional spatial imaging are presented. The chemical shift imaging was optimized for excitation of the N-acetyl aspartate (NAA). An interesting consequence of our approach is that the Nyquist ghost is transferred from the spectrum to the metabolite image.

Polymer gel dosimetry using a three-dimensional MRI acquisition technique

In this work, three-dimensional (3-D) MRI techniques are employed in N-Vinylpyrrolidone-Argon-(VIPAR-) based polymer gel dosimetry. VIPAR gels were irradiated using a Nucletron microSelection 192Ir HDR brachytherapy remote afterloading system with single source dwell position and intravascular brachytherapy irradiation protocols. A single VIPAR gel and a single irradiation are adequate to obtain the full calibration curve needed. The 3-D dose distributions obtained with the 3-D MRI method were found to be in good agreement with the corresponding Monte Carlo calculations, for brachytherapy and intravascular irradiations. The method allows the reconstruction of isodose contours over any plane, with increased spatial resolution and accuracy following a single MR acquisition. VIPAR gel measurements using a 3-D MRI readout technique can be of particular use in the experimental dosimetry of brachytherapy sources, as well as for dose verification purposes when complex irradiation regimes and three-dimensional dose gradients are investigated.

MOSES: multiple oversampled slabs EPI sequence

A new technique is proposed which combines the advantages of phase encoded and multi-slice echo planar imaging (EPI) methods. Its principle is to interleave multiple phase encoded EPI slabs. This approach can provide a larger spatial coverage than multi-slice EPI for the same signal to noise ratio and total imaging time and a shorter minimum imaging time than 3D EPI for the same coverage and repetition time. Other advantages include availability of the steady state image contrasts and potentially lower acoustic noise and RF specific absorption rate compared to the standard multi-slice EPI. A full discussion of its potential as well as in vivo results at 1.5 and 3 Tesla are presented in this paper.

Sensitivity and performance time in MRI dephasing artifact reduction methods

Although shimming can improve static field inhomogeneity, local field imperfections induced by tissue susceptibility differences cannot be completely corrected and can cause substantial signal loss in gradient echo images through intravoxel dephasing. Dephasing increases with voxel size so that one simple method of reducing the effect is to use thin slices. Signal-to-noise ratio (SNR) can then be increased by averaging over the subslices to form the final, thick slice. We call this method subslice averaging or SSAVE. Alternatively, a range of different amplitude slice select rephase gradients can be used to compensate for different susceptibility induced gradient offsets. The final image can then be formed by combining individual images in a variety of ways: summation, summation of the squares of the images, forming the maximum intensity projection of the image set, and Fourier transformation followed by summation. We show here that, contrary to previous claims, the theoretical sensitivity (i.e., SNR divided by the square root of the imaging time) of all these alternative methods is very similar. However, performance time (i.e., minimum-imaging time) of the simplest method, SSAVE, is much shorter than that of alternatives. This is confirmed experimentally on phantoms and anesthetized mice. Magn Reson Med 45:470-476, 2001.

Comparison of 2-D turbo spin echo and 3-D gradient echo sequences for the detection of the trigeminal nerve and branches anatomy

The aim of this study was to assess the detectability of the trigeminal nerve and its branches using T1 weighted (w.) 3-D magnetization prepared rapid gradient echo (MP-RAGE), T2* w. 3D CISS and T2 w. 2-D turbo spin echo MR sequences. Thirty healthy volunteers were examined for this purpose using a 1.5 Tesla MR unit. The detectability of the trigeminal nerve and Gasser's Ganglion, i.e. structures that are surrounded by liquor was best using 3-D CISS. In the case of the ophthalmic, maxillary and mandibular nerves, the T1 w. 3-D MPRAGE was significantly better than T2* w. CISS and T2 w. 2-D turbo spin echo. The latter yielded the poorest results. We conclude that both high resolution T2* w. and T1 w. 3-D sequences are necessary in order to detect the liquor-surrounded trigeminal nerve and its soft tissue-surrounded branches. We would therefore recommend the inclusion of constructive interference in steady state (CISS) and MP-RAGE in a MR imaging protocol of the trigeminal nerve and its branches.