Project description:Energy metabolism is fundamental for life. It encompasses the utilization of carbohydrates, lipids, and proteins for internal processes, while aberrant energy metabolism is implicated in many diseases. In the present study, using three-dimensional (3D) printing from polycarbonate via fused deposition modeling, we propose a multi-nuclear radiofrequency (RF) coil design with integrated 1H birdcage and interchangeable X-nuclei (2H, 13C, 23Na, and 31P) single-loop coils for magnetic resonance imaging (MRI)/magnetic resonance spectroscopy (MRS). The single-loop coil for each nucleus attaches to an arc bracket that slides unrestrictedly along the birdcage coil inner surface, enabling convenient switching among various nuclei and animal handling. Compared to a commercial 1H birdcage coil, the proposed 1H birdcage coil exhibited superior signal-excitation homogeneity and imaging signal-to-noise ratio (SNR). For X-nuclei study, prominent peaks in spectroscopy for phantom solutions showed excellent SNR, and the static and dynamic peaks of in vivo spectroscopy validated the efficacy of the coil design in structural imaging and energy metabolism detection simultaneously.
Project description:ObjectLower-field MR is reemerging as a viable, potentially cost-effective alternative to high-field MR, thanks to advances in hardware, sequence design, and reconstruction over the past decades. Evaluation of lower field strengths, however, is limited by the availability of lower-field systems on the market and their considerable procurement costs. In this work, we demonstrate a low-cost, temporary alternative to purchasing a dedicated lower-field MR system.Materials and methodsBy ramping down an existing clinical 3 T MRI system to 0.75 T, proton signals can be acquired using repurposed 13C transmit/receive hardware and the multi-nuclei spectrometer interface. We describe the ramp-down procedure and necessary software and hardware changes to the system.ResultsApart from presenting system characterization results, we show in vivo examples of cardiac cine imaging, abdominal two- and three-point Dixon-type water/fat separation, water/fat-separated MR Fingerprinting, and point-resolved spectroscopy. In addition, the ramp-down approach allows unique comparisons of, e.g., gradient fidelity of the same MR system operated at different field strengths using the same receive chain, gradient coils, and amplifiers.DiscussionRamping down an existing MR system may be seen as a viable alternative for lower-field MR research in groups that already own multi-nuclei hardware and can also serve as a testing platform for custom-made multi-nuclei transmit/receive coils.
Project description:Balun or trap circuits are critical components for suppressing common-mode currents flowing on the outer conductors of coaxial cables in RF coil systems for Magnetic Resonance Imaging (MRI) and Magnetic Resonance Spectroscopy (MRS). Common-mode currents affect coils' tuning and matching, induce losses, pick up extra noise from the surrounding environment, lead to undesired cross-talk, and cause safety concerns in animal and human imaging. First proposed for microwave antenna applications, the Lattice balun has been widely used in MRI coils. It has a small footprint and can be easily integrated with coil tuning/matching circuits. However, the Lattice balun is typically a single-tuned circuit and cannot be used for multi-nuclear MRI and MRS with two RF frequencies. This work describes a dual-tuned Lattice balun design that is suitable for multi-nuclear MRI/MRS. It was first analyzed theoretically to derive component values. RF circuit simulations were then performed to validate the theoretical analysis and provide guidance for practical construction. Based on the simulation results, a dual-tuned balun circuit was built for 7T 1H/23Na MRI and bench tested. The fabricated dual-tuned balun exhibits superior performance at the Larmor frequencies of both 1H and 23Na, with less than 0.15 dB insertion loss and better than 17 dB common-mode rejection ratio at both frequencies.
Project description:Proton MRS (1 H MRS) provides noninvasive, quantitative metabolite profiles of tissue and has been shown to aid the clinical management of several brain diseases. Although most modern clinical MR scanners support MRS capabilities, routine use is largely restricted to specialized centers with good access to MR research support. Widespread adoption has been slow for several reasons, and technical challenges toward obtaining reliable good-quality results have been identified as a contributing factor. Considerable progress has been made by the research community to address many of these challenges, and in this paper a consensus is presented on deficiencies in widely available MRS methodology and validated improvements that are currently in routine use at several clinical research institutions. In particular, the localization error for the PRESS localization sequence was found to be unacceptably high at 3 T, and use of the semi-adiabatic localization by adiabatic selective refocusing sequence is a recommended solution. Incorporation of simulated metabolite basis sets into analysis routines is recommended for reliably capturing the full spectral detail available from short TE acquisitions. In addition, the importance of achieving a highly homogenous static magnetic field (B0 ) in the acquisition region is emphasized, and the limitations of current methods and hardware are discussed. Most recommendations require only software improvements, greatly enhancing the capabilities of clinical MRS on existing hardware. Implementation of these recommendations should strengthen current clinical applications and advance progress toward developing and validating new MRS biomarkers for clinical use.
Project description:PurposeTo demonstrate feasibility of developing a noninvasive extracellular pH (pHe ) mapping method on a clinical MRI scanner for molecular imaging of liver cancer.MethodsIn vivo pHe mapping has been demonstrated on preclinical scanners (e.g., 9.4T, 11.7T) with Biosensor Imaging of Redundant Deviation in Shifts (BIRDS), where the pHe readout by 3D chemical shift imaging (CSI) depends on hyperfine shifts emanating from paramagnetic macrocyclic chelates like TmDOTP5- which upon extravasation from blood resides in the extracellular space. We implemented BIRDS-based pHe mapping on a clinical 3T Siemens scanner, where typically diamagnetic 1 H signals are detected using millisecond-long radiofrequency (RF) pulses, and 1 H shifts span over ±10 ppm with long transverse (T2 , 102 ms) and longitudinal (T1 , 103 ms) relaxation times. We modified this 3D-CSI method for ultra-fast acquisition with microsecond-long RF pulses, because even at 3T the paramagnetic 1 H shifts of TmDOTP5- have millisecond-long T2 and T1 and ultra-wide chemical shifts (±200 ppm) as previously observed in ultra-high magnetic fields.ResultsWe validated BIRDS-based pH in vitro with a pH electrode. We measured pHe in a rabbit model for liver cancer using VX2 tumors, which are highly vascularized and hyperglycolytic. Compared to intratumoral pHe (6.8 ± 0.1; P < 10-9 ) and tumor's edge pHe (6.9 ± 0.1; P < 10-7 ), liver parenchyma pHe was significantly higher (7.2 ± 0.1). Tumor localization was confirmed with histopathological markers of necrosis (hematoxylin and eosin), glucose uptake (glucose transporter 1), and tissue acidosis (lysosome-associated membrane protein 2).ConclusionThis work demonstrates feasibility and potential clinical translatability of high-resolution pHe mapping to monitor tumor aggressiveness and therapeutic outcome, all to improve personalized cancer treatment planning.
Project description:IntroductionPatients with MS are MRI scanned continuously throughout their disease course resulting in a large manual workload for radiologists which includes lesion detection and size estimation. Though many models for automatic lesion segmentation have been published, few are used broadly in clinic today, as there is a lack of testing on clinical datasets. By collecting a large, heterogeneous training dataset directly from our MS clinic we aim to present a model which is robust to different scanner protocols and artefacts and which only uses MRI modalities present in routine clinical examinations.MethodsWe retrospectively included 746 patients from routine examinations at our MS clinic. The inclusion criteria included acquisition at one of seven different scanners and an MRI protocol including 2D or 3D T2-w FLAIR, T2-w and T1-w images. Reference lesion masks on the training (n = 571) and validation (n = 70) datasets were generated using a preliminary segmentation model and subsequent manual correction. The test dataset (n = 100) was manually delineated. Our segmentation model https://github.com/CAAI/AIMS/ was based on the popular nnU-Net, which has won several biomedical segmentation challenges. We tested our model against the published segmentation models HD-MS-Lesions, which is also based on nnU-Net, trained with a more homogenous patient cohort. We furthermore tested model robustness to data from unseen scanners by performing a leave-one-scanner-out experiment.ResultsWe found that our model was able to segment MS white matter lesions with a performance comparable to literature: DSC = 0.68, precision = 0.90, recall = 0.70, f1 = 0.78. Furthermore, the model outperformed HD-MS-Lesions in all metrics except precision = 0.96. In the leave-one-scanner-out experiment there was no significant change in performance (p < 0.05) between any of the models which were only trained on part of the dataset and the full segmentation model.ConclusionIn conclusion we have seen, that by including a large, heterogeneous dataset emulating clinical reality, we have trained a segmentation model which maintains a high segmentation performance while being robust to data from unseen scanners. This broadens the applicability of the model in clinic and paves the way for clinical implementation.
Project description: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 × 0.94 mm resolution are presented, and in a single brain at 0.73 × 0.73 × 0.73 mm 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.
Project description:The differentiation grade of cervical cancer is histologically assessed by examining biopsies or surgical specimens. MRS is a highly sensitive technique that images tissue metabolism and can be used to increase the specificity of tissue characterization in a non-invasive manner. We aim to explore the feasibility of using in vivo 1 H-MRS at 7 T in women with cervical cancer to study tissue fatty acid composition. 10 women with histologically proven Stage IB1-IIB cervical cancer were scanned with a whole-body 7 T MR system with a multi-transmit system and an internal receive only monopole antenna. A STEAM sequence was used to obtain 1 H-MRS data. Fatty acid resonances were fitted with Lorentzian curves and the 2.1 ppm/1.3 ppm ratios were calculated. 1 H-MRS data showed fatty acid signals resonating at 2.1 ppm, 1.9 ppm, 1.5 ppm, 1.3 ppm and 0.9 ppm. Mean 2.1/1.3 ppm ratios were 0.019 ± 0.01, 0.021 ± 0.006, 0.12 ± 0.089 and 0.39 ± 0.27 for normal, Grade I, Grade II and Grade III groups respectively. Poorly differentiated tumor tissue (Grade III) showed elevated fatty acid ratios when compared with the well differentiated tumor (Grade I) or normal tissue. 1 H-MRS in cervical cancer at 7 T is feasible and individual fatty acid signals were detected. In addition, poorly differentiated tumors show more fatty acid unsaturation. The 2.1 ppm/1.3 ppm ratio has potential for tumor characterization in a non-invasive manner for uterine cervical cancer.
Project description:BackgroundGreater brain atrophy is associated with disability progression (DP) in patients with multiple sclerosis (PwMS). However, methodological challenges limit its routine clinical use.ObjectiveTo determine the feasibility of atrophy measures as markers of DP in PwMS scanned across different MRI field strengths.MethodsA total of 980 PwMS were scanned on either 1.5 T or 3.0 T MRI scanners. Demographic and clinical data were retrospectively collected, and the presence of DP was determined according to standard clinical trial criteria. Lateral ventricular volume (LVV) change was measured with the NeuroSTREAM technique on clinical routine T2-FLAIR images. Percent brain volume change (PBVC) was measured using SIENA and ventricular cerebrospinal fluid (vCSF) % change was measured using VIENA and SIENAX algorithms on 3D T1-weighted images (WI). Stable vs. DP PwMS were compared using analysis of covariance (ANCOVA). Mixed modeling determined the effect of MRI scanner change on MRI-derived atrophy measures.ResultsLongitudinal LVV analysis was successful in all PwMS. SIENA-based PBVC and VIENA-based changes failed in 37.6% of cases, while SIENAX-based vCSF failed in 12.9% of cases. PwMS with DP (n = 241) had significantly greater absolute (20.9% vs. 8.7%, d = 0.66, p < 0.001) and annualized LVV % change (4.1% vs. 2.3%, d = 0.27, p < 0.001) when compared to stable PwMS (n = 739). In subjects with both analyses available, both 3D-T1 and T2-FLAIR-based analyses differentiated PwMS with DP (n = 149). However, only NeuroSTREAM and VIENA-based LVV/vCSF were able to show greater atrophy in PwMS that were scanned on different scanners. PBVC and SIENAX-based vCSF % changes were significantly affected by scanner change (Beta = -0.16, t-statistics = -2.133, p = 0.033 and Beta = -2.08, t-statistics = -4.084, p < 0.001), whereas no MRI scanner change effects on NeuroSTREAM-based PLVVC and VIENA-based vCSF % change were noted.ConclusionsLVV-based atrophy on T2-FLAIR is a clinically relevant measure in spite of MRI scanner changes and mild disability levels.
Project description:PurposeMultiple data formats in the MRS community currently hinder data sharing and integration. NIfTI-MRS is proposed as a standard spectroscopy data format, implemented as an extension to the Neuroimaging informatics technology initiative (NIfTI) format. This standardized format can facilitate data sharing and algorithm development as well as ease integration of MRS analysis alongside other imaging modalities.MethodsA file format using the NIfTI header extension framework incorporates essential spectroscopic metadata and additional encoding dimensions. A detailed description of the specification is provided. An open-source command-line conversion program is implemented to convert single-voxel and spectroscopic imaging data to NIfTI-MRS. Visualization of data in NIfTI-MRS is provided by development of a dedicated plugin for FSLeyes, the FMRIB Software Library (FSL) image viewer.ResultsOnline documentation and 10 example datasets in the proposed format are provided. Code examples of NIfTI-MRS readers are implemented in common programming languages. Conversion software, spec2nii, currently converts 14 formats where data is stored in image-space to NIfTI-MRS, including Digital Imaging and Communications in Medicine (DICOM) and vendor proprietary formats.ConclusionNIfTI-MRS aims to solve issues arising from multiple data formats being used in the MRS community. Through a single conversion point, processing and analysis of MRS data are simplified, thereby lowering the barrier to use of MRS. Furthermore, it can serve as the basis for open data sharing, collaboration, and interoperability of analysis programs. Greater standardization and harmonization become possible. By aligning with the dominant format in neuroimaging, NIfTI-MRS enables the use of mature tools present in the imaging community, demonstrated in this work by using a dedicated imaging tool, FSLeyes, for visualization.