Removal of olefinic fat chemical shift artifact in diffusion MRI.

Diffusion-weighted (DW) MRI has emerged as a key tool for assessing the microstructure of tissues in healthy and diseased states. Because of its rapid acquisition speed and insensitivity to motion, single-shot echo-planar imaging is the most common DW imaging technique. However, the presence of fat signal can severely affect DW-echo planar imaging acquisitions because of the chemical shift artifact. Fat suppression is usually achieved through some form of chemical shift-based fat saturation. Such methods effectively suppress the signal originating from aliphatic fat protons, but fail to suppress the signal from olefinic protons. Olefinic fat signal may result in significant distortions in the DW images, which bias the subsequently estimated diffusion parameters. This article introduces a method for removing olefinic fat signal from DW images, based on an echo time-shifted acquisition. The method is developed and analyzed specifically in the context of single-shot DW-echo-planar imaging, where image phase is generally unreliable. The proposed method is tested with phantom and in vivo datasets, and compared with a standard acquisition to demonstrate its performance.

Robust water/fat separation in the presence of large field inhomogeneities using a graph cut algorithm.

Water/fat separation is a classical problem for in vivo proton MRI. Although many methods have been proposed to address this problem, robust water/fat separation remains a challenge, especially in the presence of large amplitude of static field inhomogeneities. This problem is challenging because of the nonuniqueness of the solution for an isolated voxel. This paper tackles the problem using a statistically motivated formulation that jointly estimates the complete field map and the entire water/fat images. This formulation results in a difficult optimization problem that is solved effectively using a novel graph cut algorithm, based on an iterative process where all voxels are updated simultaneously. The proposed method has good theoretical properties, as well as an efficient implementation. Simulations and in vivo results are shown to highlight the properties of the proposed method and compare it to previous approaches. Twenty-five cardiac datasets acquired on a short, wide-bore scanner with different slice orientations were used to test the proposed method, which produced robust water/fat separation for these challenging datasets. This paper also shows example applications of the proposed method, such as the characterization of intramyocardial fat.

Joint estimation of water/fat images and field inhomogeneity map.

Water/fat separation in the presence of B 0 field inhomogeneity is a problem of considerable practical importance in MRI. This article describes two complementary methods for estimating the water/fat images and the field inhomogeneity map from Dixon-type acquisitions. One is based on variable projection (VARPRO) and the other on linear prediction (LP). The VARPRO method is very robust and can be used in low signal-to-noise ratio conditions because of its ability to achieve the maximum-likelihood solution. The LP method is computationally more efficient, and is shown to perform well under moderate levels of noise and field inhomogeneity. These methods have been extended to handle multicoil acquisitions by jointly solving the estimation problem for all the coils. Both methods are analyzed and compared and results from several experiments are included to demonstrate their performance.

Accelerating Advanced MRI Reconstructions on GPUs.

Computational acceleration on graphics processing units (GPUs) can make advanced magnetic resonance imaging (MRI) reconstruction algorithms attractive in clinical settings, thereby improving the quality of MR images across a broad spectrum of applications. This paper describes the acceleration of such an algorithm on NVIDIA's Quadro FX 5600. The reconstruction of a 3D image with 128(3) voxels achieves up to 180 GFLOPS and requires just over one minute on the Quadro, while reconstruction on a quad-core CPU is twenty-one times slower. Furthermore, relative to the true image, the error exhibited by the advanced reconstruction is only 12%, while conventional reconstruction techniques incur error of 42%.

A network flow method for improved MR field map estimation in the presence of water and fat.

Field map estimation is an important problem in MRI, with applications such as water/fat separation and correction of fast acquisitions. However, it constitutes a nonlinear and severely ill-posed problem requiring regularization. In this paper, we introduce an improved method for regularized field map estimation, based on a statistically motivated formulation, as well as a novel algorithm for the solution of the corresponding optimization problem using a network flow approach. The proposed method provides theoretical guarantees (local optimality with respect to a large move), as well as an efficient implementation. It has been applied to the water/fat separation problem and tested on a number of challenging datasets, showing high-quality results.

Location and phylogenetic analysis of the region immediately upstream of the granulin gene of the Clostera anachoreta granulovirus.

The region immediately upstream of the granulin gene from Clostera anachoreta granulovirus (ClanGV) was identified from hybridization experiments and sequenced. The sequence of 5122nt EcoRI restriction fragment was presented and compared with the equivalent area in other GVs. Database searches showed that this region contained three open reading frames (ORFs) similar to the baculovirus genes (egt, fgf and me53, respectively) and four ORFs unique to ClanGV genome. Phylogenetic trees of the baculovirus genes egt and me53 were constructed. These analyses indicated that ClanGV genes may be more closely related to CfGV, CpGV, ClGV, PoGV and AoGV than to PxGV and XcGV.

Characterization and partial genome sequence analysis of Clostera anachoreta granulovirus.

The morphological and biological properties as well as partial genomic sequencing of a granulovirus isolated from Clostera anachoreta (Lepidoptera: Notodontidae), C. anachoreta granulovirus (ClanGV), were carried out. The ovoidal occlusion bodies were 337 nm x 170 nm in size, and each granule contained one single rod-shape virion, with a mean size of 250 nm x 46 nm. Granulin had a molecular weight of approximately 30 kDa. ClanGV genome size was estimated as 104.34 kb based on the restriction fragments. The restriction pattern of the ClanGV genome was different from other GVs. A restriction fragment genomic library of ClanGV genome was constructed. The library consisted of nine SalI fragments, seven HindIII fragments and seven EcoRI fragments. One 4.8 kb fragment of the genome, digested by SalI, was sequenced and analyzed. This region was composed of eight unknown ORFs, two baculoviruses homologous gene (vp1054 and lef10) and partial sequence of lef-8. The unknown ORFs included three unique to ClanGV, the other five ORFs were related to baculoviruses. The ORFs, located within this restriction fragment, were compared to homologues in other GVs. The results indicated that ClanGV, CpGV, ClGV, AoGV and PoGV had similar arrangement and orientation of the homologous ORFs. Phylogenetic analysis of VP1054 proteins from 20 baculoviruses indicated that ClanGV was more closely related to CpGV, ClGV, AoGV and PoGV than to other baculoviruses.

A bound on mutual information for image registration.

An upper bound is derived for the mutual information between a fixed image and a deformable template containing a fixed number of gray-levels. The bound can be calculated by maximizing the entropy of the template under the constraint that the conditional entropy of the template, given the fixed image, be zero. This bound provides useful insight into the properties of mutual information as a similarity metric for deformable image registration. Specifically, it indicates that maximizing mutual information may not necessarily produce an optimal solution when the deformable transform is too flexible.

fMri studies of Stroop tasks reveal unique roles of anterior and posterior brain systems in attentional selection.

The brain's attentional system identifies and selects information that is task-relevant while ignoring information that is task-irrelevant. In two experiments using functional magnetic resonance imaging, we examined the effects of varying task-relevant information compared to task-irrelevant information. In the first experiment, we compared patterns of activation as attentional demands were increased for two Stroop tasks that differed in the task-relevant information, but not the task-irrelevant information: a color-word task and a spatial-word task. Distinct subdivisions of dorsolateral prefrontal cortex and the precuneus became activated for each task, indicating differential sensitivity of these regions to task-relevant information (e.g., spatial information vs. color). In the second experiment, we compared patterns of activation with increased attentional demands for two Stroop tasks that differed in task-irrelevant information, but not task-relevant information: a color-word task and color-object task. Little differentiation in activation for dorsolateral prefrontal and precuneus regions was observed, indicating a relative insensitivity of these regions to task-irrelevant information. However, we observed a differentiation in the pattern of activity for posterior regions. There were unique areas of activation in parietal regions for the color-word task and in occipitotemporal regions for the color-object task. No increase in activation was observed in regions responsible for processing the perceptual attribute of color. The results of this second experiment indicate that attentional selection in tasks such as the Stroop task, which contain multiple potential sources of relevant information (e.g., the word vs. its ink color), acts more by modulating the processing of task-irrelevant information than by modulating processing of task-relevant information.

Lactate quantitation in a gerbil brain stroke model by GSLIM of multiple-quantum-filtered signals. Generalized spectral localization by imaging.

Quantitative magnetic resonance imaging of lactate using a zero-quantum/double-quantum filter and generalized spectral localization by imaging (GSLIM) was applied to a model of unilateral stroke in gerbil brain. GSLIM lactate images at 4T clearly reveal elevated concentrations of lactate in the ischemic compared with the normal hemisphere 100-175 minutes after unilateral carotid ligation. These results indicate that the technique is capable of studies of brain infarcts, and that application to human ischemic pathology in brain and other tissues may be possible.

A fast spin echo technique with circular sampling.

This paper presents a fast spin echo (FSE) imaging method that employs circular sampling of k-space. The technique has been implemented on a 2 Tesla imaging system and validated on both phantoms and living animals. Experimental studies have shown that circular sampling can produce artifact-free FSE images without the need of phase correction. Although not fully explored, preliminary results also show that circular sampling may have advantages over the conventional rectilinear FSE in signal-to-noise ratio and imaging efficiency. A major disadvantage is the increased sensitivity to off-resonance effects. The authors expect that the FSE technique with circular sampling will find its applications in magnetic resonance microscopy, neuro-functional imaging, and real-time dynamic studies.

A comparison of RIGR and SVD dynamic imaging methods.

Several constrained imaging methods have recently been proposed for dynamic imaging applications. This paper compares two of these methods: the Reduced-encoding Imaging by Generalized-series Reconstruction (RIGR) and Singular Value Decomposition (SVD) methods. RIGR utilizes a priori data for optimal image reconstruction whereas the SVD method seeks to optimize data acquisition. However, this study shows that the existing SVD encoding method tends to bias the data acquisition scheme toward reproducing the known features in the reference image. This characteristic of the SVD encoding method reduces its capability to capture new image features and makes it less suitable than RIGR for dynamic imaging applications.

Quantitative lactate-specific MR imaging and 1H spectroscopy of skeletal muscle at macroscopic and microscopic resolutions using a zero-quantum/double-quantum coherence filter and SLIM/GSLIM localization.

Quantitative lactate imaging and spectroscopy were performed on phantoms and on electrically stimulated, excised frog skeletal muscle at macroscopic and microscopic resolutions. Lactate selectivity was achieved by use of a zero-quantum/double-quantum coherence (ZQC/DQC) lactate filter, which suppressed all signals besides lactate, including water and lipid, to below noise level. Three-dimensional lactate data sets were acquired in 1-3 h; one of these spatial dimensions was frequency-encoded and the other two were phase-encoded. High-resolution images were reconstructed using the spectral localization by imaging (SLIM) and generalized SLIM (GSLIM) techniques. Lactate quantitation was achieved by employing an external lactate concentration standard and was verified by comparison to quantitative STEAM-localized and nonlocalized spectra that used total creatine as an internal concentration reference. Additionally, quantitatively accurate behavior of the SLIM and GSLIM techniques as applied to data sets of low signal-to-noise ratio and to macroscopically heterogeneous objects was verified using simulations and real muscle lactate data sets with known heterogeneity.

Biochemical heterogeneity in hysterectomized uterus measured by 31P NMR using SLIM localization.

Ultrasound and magnetic resonance imaging show contrast between the inner and outer myometrium, which is useful in the diagnosis of gynecological disorders. To determine whether the image contrast is associated with biochemical differences between these myometrial regions, phosphorus metabolite concentrations in the inner one third of the myometrium (the junctional zone; JZ) were compared with the outermost one third of the myometrium (OM) in hysterectomized uteri using 31P spectral localization by imaging (SLIM). The technique was validated by comparing the results of SLIM with the results of standard Fourier-encoded spectroscopic imaging (FSI) analysis using phantoms, and by nonlocalized spectroscopy on biopsies taken from the same hysterectomy specimens. As expected theoretically, SLIM yielded better localization than FSI, as judged by spectral intensity and leakage measurements on phantom compartments of known composition. SLIM localization revealed that the JZ has a higher intracellular phosphomonoester (PME) concentration than does the OM, which was confirmed by nonlocalized spectroscopy, and that there is very little NMR-visible phosphorus in the cervix.

Partial Radon transforms.

This article formally defines partial Radon transforms for functions of more than two dimensions. It shows that a generalized projection-slice theorem exists which connects planar and hyperplanar projections of a function to its Fourier transform. In addition, a general theoretical framework is provided for carrying out n-dimensional backprojection reconstruction in a multistage fashion through the use of the partial Radon transform.

A software system for interactive MR signal processing.

This paper describes a new software platform called "V" which is designed for interactive processing of magnetic resonance data. The package currently contains a variety of functions for image reconstruction and spectral data analysis. More importantly, it provides a framework to facilitate the exchange and application of processing algorithms among researchers in the field. We discuss the architecture of the package, give an example to demonstrate its operation and provide instructions for obtaining the software.

A simulation study to assess SVD encoding for interventional MRI: effect of object rotation and needle insertion.

Singular value decomposition (SVD) encoding offers great promise to provide high spatial and temporal resolution required for interventional MRI (I-MRI) (1). This study investigates its efficacy when (a) objects are rotated and (b) a small device (ie, a needle) is moved within anatomic structures. It was found that SVD-encoded MRI is biased toward the reference from which encoding vectors are derived, thus providing a potential limitation under conditions in which the object has undergone significant global change. Reference images with partial device insertion may be needed to accurately resolve the device or track the object motion. Theoretically, the differences between the reference and the object being imaged suggest that SVD encoding is suboptimal (in a minimum mean squared error sense). Other encoding/reconstruction algorithms may come closer to achieving the desired advantages in spatial and temporal fidelity.

Application of reduced-encoding imaging with generalized-series reconstruction (RIGR) in dynamic MR imaging.

Dynamic MRI has proven to be an important tool in studies of transient physiologic changes in animals and humans. High sensitivity and temporal resolution in such measurements are critical for accurate estimation of dynamic information. Fast imaging, often involving expensive hardware, has evolved for use in such cases. We demonstrate herein the possibility of accelerated data acquisition schemes on conventional machines using standard pulse sequences for dynamic studies. This is achieved by combining reduced-encoded dynamic data (typically 30 to 40 phase encodings) with a priori high-resolution data via a novel constrained image reconstruction algorithm. Such an approach reduces image acquisition time significantly (by a factor of 3 to 4 in the examples described here) without loss in the accuracy of information.