K-space filter deconvolution and flip angle self-calibration in 2D radial hyperpolarised 3He lung MRI

In hyperpolarised (3)He lung MRI with constant flip angles, the transverse magnetisation decays with each RF excitation imposing a k-space filter on the acquired data. For radial data acquired in an angularly-sequential order, this filter causes streaking, angular shading and loss of spatial resolution in the images. The main aim of this work was to reduce the effects of the RF depletion k-space filter in radial acquisitions. Two approaches are presented; (i) retrospective deconvolution of the k-space filter for sequentially-acquired data and (ii) golden angle acquisition order. Radial trajectories sample the centre of k-space with every projection, thereby self-tracking signal decay. The inverse of the signal decay function was used to retrospectively deconvolve RF depolarisation k-space filter effects and the method was demonstrated in 2D radial imaging in phantoms and human lungs. A golden angle radial acquisition was shown to effectively suppress artefacts caused by the RF depletion k-space filter. In addition, the average flip angle per slice was calculated from the signal decay and the values were found to correspond with conventional flip angle maps, providing a means of flip angle self-calibration.     

Three‐dimensional accurate detection of lung emphysema in rats using ultra‐short and zero echo time MRI

Emphysema is a life‐threatening pathology that causes irreversible destruction of alveolar walls. In vivo imaging techniques play a fundamental role in the early non‐invasive pre‐clinical and clinical detection and longitudinal follow‐up of this pathology. In the present study, we aimed to evaluate the feasibility of using high resolution radial three‐dimensional (3D) zero echo time (ZTE) and 3D ultra‐short echo time (UTE) MRI to accurately detect lung pathomorphological changes in a rodent model of emphysema.Porcine pancreas elastase (PPE) was intratracheally administered to the rats to produce the emphysematous changes. 3D ZTE MRI, low and high definition 3D UTE MRI and micro‐computed tomography images were acquired 4 weeks after the PPE challenge. Signal‐to‐noise ratios (SNRs) were measured in PPE‐treated and control rats. T₂* values were computed from low definition 3D UTE MRI. Histomorphometric measurements were made after euthanizing the animals. Both ZTE and UTE MR images showed a significant decrease in the SNR measured in PPE‐treated lungs compared with controls, due to the pathomorphological changes taking place in the challenged lungs. A significant decrease in T₂* values in PPE‐challenged animals compared with controls was measured using UTE MRI. Histomorphometric measurements showed a significant increase in the mean linear intercept in PPE‐treated lungs. UTE yielded significantly higher SNR compared with ZTE (14% and 30% higher in PPE‐treated and non‐PPE‐treated lungs, respectively).This study showed that optimized 3D radial UTE and ZTE MRI can provide lung images of excellent quality, with high isotropic spatial resolution (400 µm) and SNR in parenchymal tissue (>25) and negligible motion artifacts in freely breathing animals. These techniques were shown to be useful non‐invasive instruments to accurately and reliably detect the pathomorphological alterations taking place in emphysematous lungs, without incurring the risks of cumulative radiation exposure typical of micro‐computed tomography. Copyright © 2015 John Wiley & Sons, Ltd.     

Partitioning k‐space for cylindrical three‐dimensional rapid acquisition with relaxation enhancement imaging in the mouse brain

Three‐dimensional rapid acquisition with relaxation enhancement (RARE) scans require the assignment of each phase encode step in two dimensions to an echo in the echo train. Although this assignment is frequently made across the entire Cartesian grid, collection of only the central cylinder of k‐space by eliminating the corners in each phase encode dimension reduces the scan time by ~22% with negligible impact on image quality. The recipe for the assignment of echoes to grid points for such an acquisition is less straightforward than for the simple full Cartesian acquisition case, and has important implications for image quality. We explored several methods of partitioning k‐space—exploiting angular symmetry in one extreme or emulating a cropped Cartesian acquisition in the other—and acquired three‐dimensional RARE magnetic resonance imaging (MRI) scans of the ex vivo mouse brain. We evaluated each partitioning method for sensitivity to artifacts and then further considered strategies to minimize these through averaging or interleaving of echoes and by empirical phase correction. All scans were collected 16 at a time with multiple‐mouse MRI. Although all schemes considered could be used to generate images, the results indicate that the emulation of a standard Cartesian echo assignment, by partitioning preferentially along one dimension within the cylinder, is more robust to artifacts. Samples at the periphery of the bore showed larger phase deviations and higher sensitivity to artifacts, but images of good quality could still be obtained with an optimized acquisition protocol. A protocol for high‐resolution (40 μm) ex vivo images using this approach is presented, and has been used routinely with a success rate of 99% in over 1000 images.     

Hyperpolarized 129Xe lung MRI in spontaneously breathing mice with respiratory gated fast imaging and its application to pulmonary functional imaging

In the present study, a balanced steady-state free precession pulse sequence combined with compressed sensing was applied to hyperpolarized (129) Xe lung imaging in spontaneously breathing mice. With the aid of fast imaging techniques, the temporal resolution was markedly improved in the resulting images. Using these protocols and respiratory gating, (129) Xe lung images in end-inspiratory and end-expiratory phases were obtained successfully. The application of these techniques for pulmonary functional imaging made it possible to simultaneously evaluate regional ventilation and gas exchange in the same animal. A comparative study between healthy and elastase-induced mouse models of emphysema showed abnormal ventilation as well as gas exchange in elastase-treated mice.     

Volumetric imaging of myelin in vivo using 3D inversion recovery‐prepared ultrashort echo time cones magnetic resonance imaging

Direct myelin imaging is promising for characterization of multiple sclerosis (MS) brains at diagnosis and in response to therapy. In this study, a 3D inversion recovery‐prepared ultrashort echo time cones (IR‐UTE‐Cones) sequence was used for both morphological and quantitative imaging of myelin on a clinical 3 T scanner. Myelin powder phantoms with different myelin concentrations were imaged with the 3D UTE‐Cones sequence and it showed a strong correlation between concentrations and UTE‐Cones signals, demonstrating the ability of the UTE‐Cones sequence to directly image myelin in the brain. Quantitative myelin imaging with multi‐echo IR‐UTE‐Cones sequences show similar T₂* values for a D₂O‐exchanged myelin phantom (T₂* = 0.33 ± 0.04 ms), ex vivo brain specimens (T₂* = 0.20 ± 0.04 ms) and in vivo healthy volunteers (T₂* = 0.254 ± 0.023 ms), further confirming the feasibility of 3D IR‐UTE‐Cones sequences for direct myelin imaging in vivo. In ex vivo MS brain study, signal loss is observed in MS lesions, which was confirmed with histology. For the in vivo study, the lesions in MS patients also show myelin signal loss using the proposed direct myelin imaging method, demonstrating the clinical potential for MS diagnosis. Furthermore, the measured IR‐UTE‐Cones signal intensities show a significant difference between normal‐appearing white matter in MS patients and normal white matter in volunteers, which cannot be found in clinical used T₂‐FLAIR sequences. Thus, the proposed 3D IR‐UTE‐Cones sequence showed clinical potential for MS diagnosis with the capability of direct myelin detection of the whole brain.     

3D variable‐density SPARKLING trajectories for high‐resolution T2*‐weighted magnetic resonance imaging

We have recently proposed a new optimization algorithm called SPARKLING (Spreading Projection Algorithm for Rapid K‐space sampLING) to design efficient compressive sampling patterns for magnetic resonance imaging (MRI). This method has a few advantages over conventional non‐Cartesian trajectories such as radial lines or spirals: i) it allows to sample the k‐space along any arbitrary density while the other two are restricted to radial densities and ii) it optimizes the gradient waveforms for a given readout time. Here, we introduce an extension of the SPARKLING method for 3D imaging by considering both stacks‐of‐SPARKLING and fully 3D SPARKLING trajectories. Our method allowed to achieve an isotropic resolution of 600 μm in just 45 seconds for T2? ‐weighted ex vivo brain imaging at 7 Tesla over a field‐of‐view of 200 × 200 × 140 mm³ . Preliminary in vivo human brain data shows that a stack‐of‐SPARKLING is less subject to off‐resonance artifacts than a stack‐of‐spirals.     

Comparison of basis functions and q‐space sampling schemes for robust compressed sensing reconstruction accelerating diffusion spectrum imaging

Time constraints placed on magnetic resonance imaging often restrict the application of advanced diffusion MRI (dMRI) protocols in clinical practice and in high throughput research studies. Therefore, acquisition strategies for accelerated dMRI have been investigated to allow for the collection of versatile and high quality imaging data, even if stringent scan time limits are imposed. Diffusion spectrum imaging (DSI), an advanced acquisition strategy that allows for a high resolution of intra‐voxel microstructure, can be sufficiently accelerated by means of compressed sensing (CS) theory. CS theory describes a framework for the efficient collection of fewer samples of a data set than conventionally required followed by robust reconstruction to recover the full data set from sparse measurements. For an accurate recovery of DSI data, a suitable acquisition scheme for sparse q‐space sampling and the sensing and sparsifying bases for CS reconstruction need to be selected. In this work we explore three different types of q‐space undersampling schemes and two frameworks for CS reconstruction based on either Fourier or SHORE basis functions. After CS recovery, diffusion and microstructural parameters and orientational information are estimated from the reconstructed data by means of state‐of‐the‐art processing techniques for dMRI analysis. By means of simulation, diffusion phantom and in vivo DSI data, an isotropic distribution of q‐space samples was found to be optimal for sparse DSI. The CS reconstruction results indicate superior performance of Fourier‐based CS‐DSI compared to the SHORE‐based approach. Based on these findings we outline an experimental design for accelerated DSI and robust CS reconstruction of the sparse measurements that is suitable for the application within time‐limited studies.     

Pushing functional MRI spatial and temporal resolution further: High‐density receive arrays combined with shot‐selective 2D CAIPIRINHA for 3D echo‐planar imaging at 7 T

To be able to examine dynamic and detailed brain functions, the spatial and temporal resolution of 7 T MRI needs to improve. In this study, it was investigated whether submillimeter multishot 3D EPI fMRI scans, acquired with high‐density receive arrays, can benefit from a 2D CAIPIRINHA sampling pattern, in terms of noise amplification (g‐factor), temporal SNR and fMRI sensitivity. High‐density receive arrays were combined with a shot‐selective 2D CAIPIRINHA implementation for multishot 3D EPI sequences at 7 T. In this implementation, in contrast to conventional inclusion of extra k_z gradient blips, specific EPI shots are left out to create a CAIPIRINHA shift and reduction of scan time. First, the implementation of the CAIPIRINHA sequence was evaluated with a standard receive setup by acquiring submillimeter whole brain T₂*‐weighted anatomy images. Second, the CAIPIRINHA sequence was combined with high‐density receive arrays to push the temporal resolution of submillimeter 3D EPI fMRI scans of the visual cortex. Results show that the shot‐selective 2D CAIPIRINHA sequence enables a reduction in scan time for 0.5 mm isotropic 3D EPI T₂*‐weighted anatomy scans by a factor of 4 compared with earlier reports. The use of the 2D CAIPIRINHA implementation in combination with high‐density receive arrays, enhances the image quality of submillimeter 3D EPI scans of the visual cortex at high acceleration as compared to conventional SENSE. Both the g‐factor and temporal SNR improved, resulting in a method that is more sensitive to the fMRI signal. Using this method, it is possible to acquire submillimeter single volume 3D EPI scans of the visual cortex in a subsecond timeframe. Overall, high‐density receive arrays in combination with shot‐selective 2D CAIPIRINHA for 3D EPI scans prove to be valuable for reducing the scan time of submillimeter MRI acquisitions.     

3D spatially encoded and accelerated TE‐averaged echo planar spectroscopic imaging in healthy human brain

Several different pathologies, including many neurodegenerative disorders, affect the energy metabolism of the brain. Glutamate, a neurotransmitter in the brain, can be used as a biomarker to monitor these metabolic processes. One method that is capable of quantifying glutamate concentration reliably in several regions of the brain is TE‐averaged ¹H spectroscopic imaging. However, this type of method requires the acquisition of multiple TE lines, resulting in long scan durations. The goal of this experiment was to use non‐uniform sampling, compressed sensing reconstruction and an echo planar readout gradient to reduce the scan time by a factor of eight to acquire TE‐averaged spectra in three spatial dimensions. Simulation of glutamate and glutamine showed that the 2.2–2.4 ppm spectral region contained 95% glutamate signal using the TE‐averaged method. Peak integration of this spectral range and home‐developed, prior‐knowledge‐based fitting were used for quantitation. Gray matter brain phantom measurements were acquired on a Siemens 3 T Trio scanner. Non‐uniform sampling was applied retrospectively to these phantom measurements and quantitative results of glutamate with respect to creatine 3.0 (Glu/Cr) ratios showed a coefficient of variance of 16% for peak integration and 9% for peak fitting using eight‐fold acceleration. In vivo scans of the human brain were acquired as well and five different brain regions were quantified using the prior‐knowledge‐based algorithm. Glu/Cr ratios from these regions agreed with previously reported results in the literature. The method described here, called accelerated TE‐averaged echo planar spectroscopic imaging (TEA‐EPSI), is a significant methodological advancement and may be a useful tool for categorizing glutamate changes in pathologies where affected brain regions are not known a priori. Copyright © 2016 John Wiley & Sons, Ltd.     

Expression of ERCC1 and class IIIβ tubulin for predicting effect of carboplatin/paclitaxel in patients with advanced inoperable non‐small cell lung cancer

It was recently reported that expression of excision repair cross‐complementation group 1 (ERCC1), a DNA repair protein, predicts sensitivity to platinum‐based chemotherapy drugs. Microtubule inhibitors such as paclitaxel demonstrate anticancer effects by inhibiting spindle fibers during mitosis; and class IIIβ tubulin (IIIβ tubulin), a microtubule component, is thought to be resistant to microtubule inhibitors. The purpose of the present study was to examine the correlation between prognosis and expression of these proteins using biopsy tissues obtained from 40 patients with advanced inoperable non‐small cell lung cancer who had been treated with carboplatin plus Taxol. On immunostaining 27 patients (68%) were positive for ERCC1 and 22 (55%) were positive for IIIβ tubulin. The prognosis of the ERCC1‐negative group was significantly better than that for the ERCC1‐positive group (P= 0.014). As for IIIβ tubulin, the prognosis for the negative group was also significantly better than that for the positive group (P= 0.025). Multivariate analysis showed that the expression of ERCC1 was an independent predictor of prognosis (hazard ratio: 3.485; 95% confidence interval: 1.123–10.818, P= 0.031). It was concluded that determination of the expression of these proteins is useful to predict the effects of platinum‐based anticancer drugs.