Mono-planar T-Hex: Speed and flexibility for high-resolution 3D imaging

Purpose

The aim of this work is the reconciliation of high spatial and temporal resolution for MRI. For this purpose, a novel sampling strategy for 3D encoding is proposed, which provides flexible k‐space segmentation along with uniform sampling density and benign filtering effects related to signal decay.

Methods

For time‐critical MRI applications such as functional MRI (fMRI), 3D k‐space is usually sampled by stacking together 2D trajectories such as echo planar imaging (EPI) or spiral readouts, where each shot covers one k‐space plane. For very high temporal and medium to low spatial resolution, tilted hexagonal sampling (T‐Hex) was recently proposed, which allows the acquisition of a larger k‐space volume per excitation than can be covered with a planar readout. Here, T‐Hex is described in a modified version where it instead acquires a smaller k‐space volume per shot for use with medium temporal and high spatial resolution.

Results

Mono‐planar T‐Hex sampling provides flexibility in the choice of speed, signal‐to‐noise ratio (SNR), and contrast for rapid MRI acquisitions. For use with a conventional gradient system, it offers the greatest benefit in a regime of high in‐plane resolution <1 mm. The sampling scheme is combined with spirals for high sampling speed as well as with more conventional EPI trajectories.

Conclusion

Mono‐planar T‐Hex sampling combines fast 3D encoding with SNR efficiency and favorable depiction characteristics regarding noise amplification and filtering effects from T2∗ decay, thereby providing flexibility in the choice of imaging parameters. It is attractive both for high‐resolution time series such as fMRI and for applications that require rapid anatomical imaging.

T-Hex: Tilted hexagonal grids for rapid 3D imaging

PURPOSE

The purpose of this work is to devise and demonstrate an encoding strategy for 3D MRI that reconciles high speed with flexible segmentation, uniform k-space density, and benign T 2 ∗ effects.

METHODS

Fast sampling of a 3D k-space is typically accomplished by 2D readouts per shot using EPI trains or spiral readouts. Tilted hexagonal (T-Hex) sampling is a way of acquiring more k-space volume per excitation while maintaining uniform sampling density and a smooth T 2 ∗ filter. The k-space volume covered per shot is controlled by the tilting angle. Image reconstruction is performed with a 3D extension of the iterative SENSE approach, incorporating actual field dynamics and static off-resonance. T-Hex imaging is compared with established 3D schemes in terms of speed and noise performance.

RESULTS

Tilted hexagonal acquisition is found to achieve greater imaging speed than known alternatives, particularly in combination with spiral trajectories. The interplay of the proposed 3D trajectories, array detection, and off-resonance is successfully addressed by iterative inversion of the full signal model. Enhanced coverage per shot is of greatest utility for high speed in an intermediate resolution regime of 1 to 4 mm. T-Hex EPI combines the benefits of extended coverage per shot with increased robustness against off-resonance effects.

CONCLUSION

Sampling of tilted hexagonal grids is a feasible means of gaining 3D imaging speed with near-optimal SNR efficiency and benign depiction properties. It is a particularly promising technique for time-resolved applications such as fMRI.

Echo-planar imaging of the human head with 100 mT/m gradients and high-order modeling of eddy current fields

PURPOSE

To demonstrate the utility of a high-performance gradient insert for ultrafast MRI of the human head.

METHODS

EPI was used for the first time with a readout gradient amplitude of 100 mT/m, 1200 T/m/s slew rate, and nearly 1 MHz signal bandwidth for human head scanning. To avoid artefacts due to eddy currents, the magnetic field was dynamically monitored with NMR probes at multiple points, modeled by solid harmonics up to fifth order, and included in the image reconstruction. An approximation of a negligible intra-echo effect of the eddy currents was made to accelerate the high-order reconstruction. The field monitoring-based approach was compared with a recently proposed phase error estimation from separate reconstructions of even and odd echoes.

RESULTS

Images obtained with the gradient insert have significantly lower distortions than it is the case with the whole body 30 mT/m, 200 T/m/s gradients of the same system. However, eddy currents of high spatial order must be properly characterized and corrected for in order to avoid a persistent 2D Nyquist ghost. Multi-position monitoring proves to be a robust method to measure the eddy currents and allows higher undersampling rates than the image-based approach. The proposed approximation of the eddy currents effect allows a significant acceleration of the high-order reconstruction by a separate processing of each spatial dimension.

CONCLUSION

Strong gradients with adequate switching rates are highly beneficial for the quality of EPI provided that robust measures are taken to include the contribution of eddy currents to the image encoding.

Neurochemical profile of the human cervical spinal cord determined by MRS

MRS enables insight into the chemical composition of central nervous system tissue. However, technical challenges degrade the data quality when applied to the human spinal cord. Therefore, to date detection of only the most prominent metabolite resonances has been reported in the healthy human spinal cord. The aim of this investigation is to provide an extended metabolic profile including neurotransmitters and antioxidants in addition to metabolites involved in the energy and membrane metabolism of the human cervical spinal cord in vivo. To achieve this, data quality was improved by using a custom-made, cervical detector array together with constructive averaging of a high number of echo signals, which is enabled by the metabolite cycling technique at 3T. In addition, the improved spinal cord spectra were extensively cross-validated, in vivo, post-mortem in situ and ex vivo. Reliable identification of up to nine metabolites was achieved in group analyses for the first time. Distinct features of the spinal cord neurochemical profile, in comparison with the brain neurotransmission system, include decreased concentrations of the sum of glutamate and glutamate and increased concentrations of aspartate, γ-amino-butyric acid, scyllo-inositol and the sum of myo-inositol and glycine.

Pax1 and Pax9 synergistically regulate vertebral column development

The paralogous genes Pax1 and Pax9 constitute one group within the vertebrate Pax gene family. They encode closely related transcription factors and are expressed in similar patterns during mouse embryogenesis, suggesting that Pax1 and Pax9 act in similar developmental pathways. We have recently shown that mice homozygous for a defined Pax1 null allele exhibit morphological abnormalities of the axial skeleton, which is not affected in homozygous Pax9 mutants. To investigate a potential interaction of the two genes, we analysed Pax1/Pax9 double mutant mice. These mutants completely lack the medial derivatives of the sclerotomes, the vertebral bodies, intervertebral discs and the proximal parts of the ribs. This phenotype is much more severe than that of Pax1 single homozygous mutants. In contrast, the neural arches, which are derived from the lateral regions of the sclerotomes, are formed. The analysis of Pax9 expression in compound mutants indicates that both spatial expansion and upregulation of Pax9 expression account for its compensatory function during sclerotome development in the absence of Pax1. In Pax1/Pax9 double homozygous mutants, formation and anteroposterior polarity of sclerotomes, as well as induction of a chondrocyte-specific cell lineage, appear normal. However, instead of a segmental arrangement of vertebrae and intervertebral disc anlagen, a loose mesenchyme surrounding the notochord is formed. The gradual loss of Sox9 and Collagen II expression in this mesenchyme indicates that the sclerotomes are prevented from undergoing chondrogenesis. The first detectable defect is a low rate of cell proliferation in the ventromedial regions of the sclerotomes after sclerotome formation but before mesenchymal condensation normally occurs. At later stages, an increased number of cells undergoing apoptosis further reduces the area normally forming vertebrae and intervertebral discs. Our results reveal functional redundancy between Pax1 and Pax9 during vertebral column development and identify an early role of Pax1 and Pax9 in the control of cell proliferation during early sclerotome development. In addition, our data indicate that the development of medial and lateral elements of vertebrae is regulated by distinct genetic pathways.

Identification of caspases and apoptosis in the simple metazoan Hydra

Apoptosis is a normal process by which cells die and are eliminated from tissue by phagocytosis [1]. It is involved in regulating cell numbers in adult tissues and in eliminating 'excess' cells during embryogenesis and development. Apoptosis is mediated by activation of caspases, which then cleave a variety of cellular substrates and thereby cause the characteristic morphology of apoptotic cells (rounded cells, condensed chromatin, susceptibility to phagocytosis) [2]. Although apoptosis has been well documented in nematodes, insects and mammals, it is not yet clear how early in evolution apoptosis or its component enzymes arose. In the simple metazoan Hydra vulgaris, cell death regulates cell numbers [3] [4] [5]. In starved animals, for example, epithelial cell proliferation continues at a nearly normal rate although the tissue does not increase in size; the excess cells produced are eliminated by phagocytosis. Cell death can also be induced in wild-type hydra by treatment with colchicine [6] or in a mutant strain (sf-1) by temperature shock [7]. Here, we show that cell death in hydra is morphologically indistinguishable from apoptosis in higher animals, that hydra polyps express two genes with strong homology to members of the caspase 3 family, and that caspase-3-specific enzyme activity accompanies apoptosis in hydra. The occurrence of apoptosis and caspases in a member of the ancient metazoan phylum Cnidaria supports the idea that the invention of apoptosis was an essential feature of the evolution of multicellular animals.

Targeted disruption of Pax1 defines its null phenotype and proves haploinsufficiency

The murine paired box-containing gene Pax1 is required for normal development of the vertebral column, the sternum, and the scapula. Previous studies have shown that three natural Pax1 mouse mutants, the undulated alleles, exhibit phenotypes of different severity in these skeletal elements. Nevertheless, these analyses have not clarified whether the semidominant Undulated short-tail (Uns) mutation, in which the complete Pax1 locus is deleted, represents a null allele. Moreover, the analyses of the classical undulated mutants did not allow a conclusion with respect to haploinsufficiency of Pax1. To address both questions we have created a Pax1 null allele in mice by gene targeting. Surprisingly, the phenotype of this defined mutation exhibits clear differences to that of Uns. This result strongly indicates the contribution of additional gene(s) to the Uns mutant phenotype. Furthermore, the phenotype of mice heterozygous for the null allele demonstrates that Pax1 is haploinsufficient in some though not all skeletal elements which express Pax1 during embryonic development.