bluuebunny/crossref_metadata_2025 huggingface dataset:
On the interplay of encoding and readout in turbulent flow imaging
Authors: McGrath Charles , Dirix Pietro , Weine Jonathan , Kozerke Sebastian
Published: August 2024

The accuracy of turbulent flow quantification using phase-contrast MRI depends on both the turbulence energy spectrum to be imaged and the sampling spectrum of the velocity encoding gradients. In the present work their interplay is studied in detail, revealing erroneous quantification of intravoxel standard deviation and turbulent kinetic energy in particular in cases exhibiting low turbulence frequencies. It is concluded that experimental design for turbulent flow quantification needs to consider the joint effect of velocity encoding and imaging gradients. Keywords: Turbulence, TKE, Phase Constrast, Simulation, Flow, Cardiovascular
Prediction of Eddy Current-Induced Background Phase Offsets in 2D Phase Contrast-MRI
Authors: Oscanoa Julio , Middione Matthew , Loecher Michael , Solana Ana Beatriz , Vasanawala Shreyas , Ennis Daniel
Published: August 2024

We propose a physics-driven approach for prediction of eddy current-induced background phase offsets in 2D PC-MRI. The method leverages the applied gradient waveforms and a circuit model to estimate the system-dependent parameters that govern the background phase. The aim is to use these parameters and the model to predict the background phase of clinical acquisitions from pulse sequence information only. Our method achieved an RMSE of 1.05 cm/s and adequate visual quality.
Reconstructing 3D Velocity and Pressure Fields From 2D Flow Measurements Using Physics Informed Neural Networks
Authors: Buoso Stefano , Dirix Pietro , Kozerke Sebastian
Published: August 2024

We propose physics-informed neural networks to augment 2D phase-contrast flow measurements in order to reconstruct full 3D velocity and pressure fields. In this conceptual work, 2D flow measurements are assimilated using the incompressible Navier-Stokes equations defined on the vessel anatomy reconstructed from anatomical scans. The network leverages a low-rank representation of velocity and pressure fields as physical prior and it is demonstrated to reconstruct 3D velocity and pressure gradient fields with good accuracy.
View-Sharing and KWIC Filtering Deblur 64-fold Accelerated Real-Time Phase-Contrast MRI Obtained with Radial k-space Sampling
Authors: Yang Huili , Larsen Andrine , Robinson Joshua , Hong KyungPyo , Rigsby Cynthia , Kim Daniel
Published: August 2024

Highly-accelerated real-time phase-contrast (rt-PC) using compressed sensing may underestimate (~17%) velocity measurements due to over regularization. We sought to address this underestimation by incorporating view-sharing (VS) and k-space weighted image contrast (KWIC) filtering. This is particularly important for pediatric patients who have faster heart rates and smaller hearts than adults, it is particularly important to achieve high temporal resolution. The proposed reconstruction achieves 25 ms temporal resolution without significant temporal blurring artifacts.
Digital Twinning of Aortae from 2D+time MRI
Authors: Wolkerstorfer Gloria , Buoso Stefano , Kozerke Sebastian
Published: August 2024

We propose an automatic pipeline to generate digital twin aortae from 2D+time MRI slices. First, a statistical shape model is fitted to the segmentation of 2D slices over time and then local refinements are applied to closely match dynamics over time. The approach is exemplified on a dataset of 10 aortic stenosis patients on which we quantify the impact of the number of available slices on the reconstructed anatomy.
Validation of real-time phase contrast MRI with online compressed sensing reconstruction in phantom and patients
Authors: Lala Tania , Christierson Lea , Frieberg Petter , Giese Daniel , Hakacova Nina , Sjöberg Pia , Ostenfeld Ellen , Töger Johannes
Published: August 2024

Real-time Phase Contrast MRI with Compressed Sensing reconstruction is a promising method to image cardiac flow in patients with arrhythmia, where cardiac-gated sequences fail. In this study, we compared it against the gated standard clinical flow MRI using a phantom model and in patients. The phantom underwent pulsatile periodic and non-periodic flow. For in vivo validation, non-arrhythmic patient data (N=10) and data from patient with atrial fibrillation (N=1) were collected from the ascending aorta. Non-periodic flow was captured both in the phantom and in vivo. Real-time MRI showed good accuracy in net flow quantification and underestimated peak flow.
Ocular Dominance Columns Examined using BOLD fMRI with Phase Regression at 7 T
Authors: Liem Brett , Akbari Atena , Gati Joseph , Zeman Peter , Menon Ravi
Published: August 2024

We investigated the signal spatial specificity of the GRE-BOLD contrast with and without phase regression in ocular dominance columns and layers of human V1. Phase regression is a post-processing technique that uses phase data to suppress the large vein signal, thus improving the GRE signal spatial specificity. Our results showed that the phase regressed laminar BOLD signal profile peaks towards the middle cortical depth, while that of GRE-BOLD was biased towards the cortical surface. Phase regression did not improve the contrast between columns, suggesting that the phase is not sensitive to intracortical veins running parallel to the cortical surface.
Pushing limits of spatial resolution in 3D EPI for fMRI on the NexGen 7T scanner
Authors: Beckett Alexander , Ma Samantha , Vu An , Feinberg David
Published: August 2024

Resolution in functional imaging can be increased by limiting the Field of View (FOV) for the image, increased acceleration and faster imaging using specialized gradient systems. Here we combine the high performance gradients of the NexGen 7T scanner with limited FOV imaging to collect ultra-high resolution fMRI in the occipital pole. Isotropic resolutions of 0.35mm are demonstrated using 3D EPI.
3D High-Resolution T1 Mapping of Brain Metabolites
Authors: Zhao Yibo , Guo Rong , Li Yudu , Jin Wen , Li Yao , Luo Jie , Liang Zhi-Pei
Published: August 2024

In MRSI studies, T1 values of metabolites are desirable for correcting relaxation and B1 inhomogeneity effects, and for evaluating microenvironmental changes in pathological conditions. Current metabolite T1 mapping has been limited to single-voxel or single-slice experiments due to SNR and imaging time constraints. In this work, we demonstrated the feasibility of 3D high-resolution T1 mapping of brain metabolites using a novel data acquisition and processing method featuring physics-based low-rank tensor modelling and FID acquisitions. The proposed method has been validated using phantom and in vivo data, producing encouraging results.
Reproducibility of non-localized 13C-MRS using a quadrature surface coil for assessing hepatic carbohydrate metabolism in humans
Authors: Jonuscheit Marc , Korzekwa Benedict , Kupriyanova Yuliya , Mevenkamp Julian , Roden Michael , Schrauwen-Hinderling Vera
Published: August 2024

We determined day-to-day variation and intra-session reproducibility of 13C-MRS based hepatic glycogen quantification by phantom replacement, using a custom-created rigid quadrature surface coil and determining the C1-glycogen signal in eight healthy volunteers. The quadrature coil allows measurements at high distances, which can be important for applications in overweight and obese people. Coefficients of variation were less than 22% for day-to-day variation and less than 9% for intra-session reproducibility (with repositioning of volunteer). In conclusion, our 13C-MRS protocol yields robust absolute concentrations of the hepatic glycogen and the day-to-day variation assessed here can be the basis for sample size calculations.
Diffusion-weighted MR spectroscopy of the prostate
Authors: Stamatelatou Angeliki , Rizzo Rudy , Simsek Kadir , van Asten Jack , Heerschap Arend , Scheenen Tom , Kreis Roland
Published: August 2024

Diffusion-weighted Magnetic Resonance Spectroscopy (DW-MRS) is ideally suited to explore complex microstructure with metabolites selectively distributed in different subspaces. So far this technique was applied in brain and muscle only. In this work, we explored DW-MRS for the first time in the prostate, an organ, with potentially more motion problems. Thus, dedicated acquisition and post-processing techniques were used including the measurement of water next to that of metabolites for corrections. ADC values of citrate, total choline, total creatine and spermine were estimated and evaluated according to the compartmental structure of the prostate indicating hindered metabolite diffusion in the luminal space.
Deep Learning Augmented PROPELLER Reconstruction for Improved MRI Motion Correction
Authors: Liu Sixing , Mei Lifeng , Huang Shoujin , Lyu Mengye
Published: August 2024

Applying the Periodically Rotated Overlapping Parallel Lines with Enhanced Reconstruction (PROPELLER) technique is one of the strategies to mitigate motion artifacts in MR images. However, due to technical limitations, existing method estimates motion parameters with unsatisfactory results, motion artifacts will still be presented in the final image. Deep learning algorithms are expected to optimize the motion parameter estimation part of PROPELLER technique. We develop a PROPELLER imaging technique incorporating a deep learning model that can provide accurate results and greatly shorten the elapsed time.
A Rotatable Twisted Solenoid TRASE Phase Gradient Head Coil
Authors: Sedlock Christopher , Purchase Aaron , Tomanek Boguslaw , Sharp Jonathan
Published: August 2024

TRASE is an MR encoding sequence that utilizes phase gradients of the RF transmit field for k-space encoding. A promising RF coil for TRASE imaging is the twisted solenoid due to its compact design and efficient B1 field. In this work we present the first TRASE head coil, consisting of a geometrically decoupled parallel-transmit (pTx) rotatable twisted solenoid pair. No RF switching hardware is required. The encoding direction of this coil pair is set by rotation angle, allowing for 2D radial k-space acquisitions. This method is compatible with the addition of a static B0 slice selection gradient for multi-slice.
Miniature and flexible Bazooka balun for MRI RF coils
Authors: Chai Shuyang , Yan Xinqiang
Published: August 2024

Flexible receive coil design has been researched on for a long time. However, several challenges is still presenting. One of them is the still bulky and rigid balun. Here we exhibit a novel flexible bazooka balun. It can be built on any coaxial cable and is formed by heat shrinks and braided wires. The flexible balun is smaller than conventional balun in length and size.
Metabolic similarity of prostate cancer patient-derived xenografts propagated in the bone versus liver
Authors: Upadhyay Deepti , Agarwal Shubhangi , Sun Jinny , Bok Robert , Aggarwal Rahul , Peehl Donna , Kurhanewicz John , Sriram Renuka
Published: August 2024

Metabolic plasticity due to cell intrinsic properties, its inherent dependence on organ of origin as well as its interaction with microenvironmental factors are considered key to establishment of metastases and is believed to be heterogenous. This in turn has a significant impact and differential response to the treatment of choice making this a lethal disease. Here, we investigate using magnetic resonance imaging and spectroscopy the biochemical profile of the same patient derived xenografts of small cell neuroendocrine prostate cancer, an aggressive phenotype, implanted in two different sites, liver and bone that are associated with reduced survival.
Distinct contrast patterns in patient-derived tumor xenografts (PDX) mouse model revealed by pH-sensitive MR contrast agent
Authors: Sumiyoshi Akira , Nomoto Takahiro , Iiyama Megumi , Osada Kensuke , Bakalova Rumiana , Nishiyama Nobuhiro , Aoki Ichio
Published: August 2024

Here we performed a molecular MR imaging study on patient-derived tumor xenografts (PDX) mouse model. In vivo molecular MR imaging demonstrated that proliferative vs. non-proliferative regions exist in PDX model and highly specific contrast agent such as PEGMnCap (pH-responsive nanoparticle based on Mn) can delineate active and hypoxic regions while small-molecular size contrast agent such as Gd-DOTA (gadoterate meglumine) can delineate non-active tumor regions. These MR image separations were not clearly obtained with a cancer cell line, suggesting more complex microenvironment of PDX model and may provide valid translational feedbacks for clinical practice.
Voxel-based analysis of renal fibrosis with diffusion MRI in mouse models
Authors: Virgincar Rohan , Avraham Shimrit , Barck Kai , Webster Joshua , Hung Jeffrey , Wong Aaron , Brightbill Hans , Caplazi Patrick , Forrest Bill , Bell Laura , Choy Man Kin , Shaw Andrey , de Crespigny Alex , Xie Luke
Published: August 2024

Voxel-based analysis (VBA) can enable voxel-wise statistical analysis of control and disease images without the need for user-defined regions-of-interest (ROI), but has not been widely used beyond neuroimaging. We demonstrate that VBA can be successfully applied to mouse models of renal fibrosis. Diffusion MRI parametric maps of control and disease groups were registered non-linearly to a common coordinate space and VBA successfully identified distinct regions of fibrosis in two different models, which strongly corresponded to whole-kidney histology. VBA therefore has potential in the clinic to identify regions of fibrosis, where whole-kidney histology cannot be obtained.
Optimized metabolic imaging of rat’s kidney on clinical MRI scanners. Comparison to small-animal high-field imaging
Authors: Ibrahim El-Sayed , Parchur Abdul , Kidambi Srividya , Liang Mingyu , Cowley Allen
Published: August 2024

T2*-based blood oxygenation level-dependent (BOLD) MRI has been used to investigate renal metabolism in the rat’s kidney, which is typically conducted on high-field small-animal MRI scanners. However, T2* is very small at high-field strength, e.g., 9.4T, which results in borderline signal-to-noise ratio and questions the measurements accuracy. In this study, we investigated the capability of BOLD imaging of the rat’s kidney on a clinical 3T MRI scanner, where T2* is much higher, and compared the results to those acquired on 9.4T small-animal scanner. The results showed the capability for distinguishing different oxygenation levels in the kidney on clinical 3T scanners.
Cardiac MR Image Segmentation in the Presence of Respiratory Motion Artifacts
Authors: Khalil Yasmina Al , Amirrajab Sina , Pluim Josien , Breeuwer Marcel , Scannell Cian
Published: August 2024

Object motion during the acquisition of magnetic resonance images can negatively impact image quality by introducing inconsistencies in the k-space data and in turn, blurring and ghosting artifacts on the acquired images. Such artifacts represent significant challenges in the clinical deployment of automated segmentation algorithms. In this work, we present an ensemble of approaches aimed at developing a robust and generalizable segmentation model, particularly tailored to handle the appearance of respiratory motion artifacts. We achieve this by introducing k-space based simulation for augmentation, as well as by reducing common errors across basal and apical slices with a region-focused segmentation approach.
Automatic segmentation of myocardial 3D whole-heart T1 and T2 maps using a nnU-Net.
Authors: Velasco Carlos , Jakubicek Roman , Hua Alina , Fotaki Anastasia , Botnar René , Prieto Claudia
Published: August 2024

The high amount of data obtained from a single 3D whole heart multiparametric scan (up to ~40 slices per parametric map) increases considerably the time required to segment and analyse the quantitative maps. Thus, an automated segmentation tool for these maps is desirable to perform this otherwise prohibitively laborious task. In this work, we leverage the potential of nnU-Net to perform fast, automated segmentation of 3D whole-heart simultaneous T1 and T2 maps and show its feasibility to predict segmentation masks with comparable quality while shortening the segmentation and analysis time by ~100x.
Breast Segmentation of MRI Based on U-Net and Multi-Headed Self-Attention Mechanism
Authors: Yu Hang , Guo Yuru , Xie Lizhi , Liu Zhiheng , Xie Zichuan , Li Chenyang , Zhou Suiping
Published: August 2024

In breast MRI, overall breast segmentation is a key step in performing breast cancer risk assessment. To achieve automatic and accurate breast segmentation in breast MR images, we propose a breast segmentation model based on U-Net and multi-head self-attention mechanism, which adds global information through multi-head self-attention module and changes the cascade structure in U-Net network to pixel-by-pixel summation. On the breast MRI dataset, the proposed model can achieve accurate, effective and fast breast segmentation with an average DSC and an average MIOU of 97.28 % and 92.01 %, respectively, which are 4.7 % and 5.56 % higher compared to U-Net, respectively.
Full spine 3D T2-weighted MRI with improved stitching for segmentation of the intrathecal space
Authors: Rua Catarina , Lambrechts Mari , Tanner Mark , Davies James , Ghayoor Ali , Dobson Howard , Becerra Lino
Published: August 2024

Computational fluid dynamics (CFD) has been used to model the behavior of cerebral-spinal-fluid (CSF) flow along the spine in research of intrathecal drug delivery. However, the model geometry highly impacts the CFD-based prediction of CSF flow. Enhanced images of the spinal CSF can be obtained with T2-weighted MRI, typically collected in 3-4 stations. Here we present a method to stitch spine images for CSF segmentation and compare it to the scanner’s stitching technique. Our offline approach appears more robust to movement and field-of-view adjustments while scanning and presents acceptable CSF signal intensity homogeneity across the spine for tissue segmentation.
HYBRID MULTI-LEVEL GRAPH NEURAL NETWORK FOR CARDIAC MAGNETIC RESONANCE SEGMENTATION
Authors: Li Xiaodi , Li Peng , Hu Yue
Published: August 2024

Due to the inherent locality of convolutional operations, convolution neural network (CNN) often exhibits limitations in explicitly modeling long-distance dependencies. In this paper, we propose a novel hybrid multi-level graph neural (HMGN) network that combines the CNN and graph neural network to capture both local and non-local image features at multiple scales. With the proposed patch graph attention module, the HMGN network can capture image features over a large receptive field, resulting in more accurate segmentation of cardiac structures. Experiments on two public datasets show the proposed method obtains improved segmentation performance over the state-of-the-art methods.
Lifelong collaborative learning improves the performance of complex muscle MR image segmentation tasks
Authors: Santini Francesco , Wasserthal Jakob , Agosti Abramo , Deligianni Xeni , Keene Kevin , Kan Hermien , Sommer Stefan , Stuprich Christoph , Wang Fengdan , Weidensteiner Claudia , Manco Giulia , Mazzoli Valentina , Desai Arjun , Pichiecchio Anna
Published: August 2024

An open-source, federated-learning-based segmentation software termed Dafne (Deep Anatomical Federated Network) is presented. This software continuously adapts the deep learning models used for the segmentation (currently for the muscles of the leg and thigh) based on the input of the users, who are in multiple institutions. This software was validated through data usage statistics of more than 50 users and through a retrospective study on 38 datasets of patients with suspected myositis, showing that the continuous learning approach is able to improve and generalize the performance of the original models.
Automatic enhancing objects detection and segmentation in breast DCE-MRI
Authors: DESCARPENTRIES Adam , FERET Florence , ROUYER Julien
Published: August 2024

The aim of our work is to detect any enhancing object of interest for reporting purposes. A deep learning approach combined with a multi-constructor and multi-centric database enabled to initiate the development of a versatile tool in line with clinical real life. The detection problem was addressed using a two-stage three-dimensional cascaded U-Net architecture. A total of 610 single-breast images were used for the model development. Results present interesting score in term of Dice similarity index (0.83) which agree well with the recent literature. Discussion section focuses on the potential benefit in the use of a recently reported loss function.
Simultaneous Multi-slice Single-shot Spiral Acquisitions for Accelerated Diffusion-weighted Imaging
Authors: Li Guangqi , Jiang Yuancheng , Guo Hua
Published: August 2024

Single-shot acquisition techniques are commonly used to acquire diffusion-weighted images due to their high sampling efficiency. Single-shot uniform-density spiral sampling combined with in-plane under-sampling has been used to achieve diffusion imaging. In this study, we investigated simultaneous multi-slice (SMS) -accelerated single-shot spiral imaging (SMS-SSH-Spiral) to further improve the scan efficiency of DWI. The in vivo results demonstrate the feasibility of SMS-SSH-Spiral acquisitions for diffusion tensor imaging with 2-fold slice acceleration and 3-fold in-plane acceleration. Diffusion data with 1.5mm isotropic resolution is acquired using our multi-band single-shot acquisition strategy.
Spatiotemporal signal drift in diffusion MRI of the brain and ways to correct for it: effects on estimates of ADC and IVIM f
Authors: Jalnefjord Oscar , Warsame Amina , Rosenqvist Louise
Published: August 2024

Signal drift has been identified as a confounding factor in diffusion MRI (dMRI), causing increases variance and potential bias in derived parameter maps. In this work, we show that temporal signal drift is spatially dependent in human brain images for dMRI, thus calling for spatiotemporal corrections. We also show that signal drift can have a substantial effect on short-term repeatability of ADC and IVIM f obtained from data acquired with a protocol ordered by b-value as is commonly done in clinical practice.
Higher-order diffusion MRI data acquired in clinical settings: what are the pitfalls, and how to correct them?
Authors: Chen Jenny , Ades-Aron Benjamin , Maithani Saurabh , Lui Yvonne , Novikov Dmitry , Veraart Jelle , Fieremans Els
Published: August 2024

Multi-shell diffusion MRI (dMRI) opens up the opportunity for microstructure mapping, but is not routinely acquired in clinics. This study retrospectively analyzed a large diffusion kurtosis imaging (DKI) dataset (N=7984) acquired as multi-series in the clinic and proposes a workflow to inspect the data before preprocessing. Automated analysis of dicom headers shows about 36% with incomplete acquisition, likely due to time constraints and patient discomfort, and 32% with image discrepancies. Finally, we show that signal variations between series occur and need to be corrected for in preprocessing. Our results indicate higher-order dMRI in the clinical setting is feasible.
Noise and distortion reduction for Reduced FOV diffusion utilizing Compressed SENSE framework for single shot EPI (EPICS)
Authors: Wu Zhigang , Zhang Yajing , Su Wengu , Yoneyama Masami , Sun Peng , Zhang Jing , Zhao Yan , Wang Jiazheng
Published: August 2024

DWI is very important for MRI examination, but it has limited resolution due to distortion, blurring, and signal loss caused by B0 inhomogeneity. Reduced FOV imaging could decrease these impacts. However, due to the coil geometry penalty, it’s hard to combine it with parallel imaging to further improve the image quality, it will suffer from noise breakthrough issues and unfolding artifacts. We propose a framework that combines reduced FOV imaging, Compressed SENSE framework simultaneously to overcome these issues. This framework allows a new solution for reduced FOV based diffusion imaging with high resolution, low distortion, and without noise breakthrough issue.
The value of 3D APTw Combined Intravoxel Incoherent Motion in Evaluation of the Renal Function in Chronic Kidney Disease
Authors: Wang Yue , Ju Ye , Zheng Dandan , Liu Ailian
Published: August 2024

Early diagnosis of chronic kidney disease (CKD) is difficult because of its hidden condition, mild symptoms and imperceptible symptoms. Amide proton transfer weighted (APTw) is a new contrast-free MR imaging technique, which can non-invasively detect the changes of amide proton concentration in endogenous mobile proteins and polypeptides in tissues. Intravoxel income motion (IVIM) can simultaneously obtain the microcirculation perfusion and water molecule diffusion of patients. The results showed that APTw and IVIM parameters APT, D* and D had good diagnostic efficiency in evaluating CKD renal function, especially the cortex APT value.
The feasibility of amide proton transfer imaging at 3T for renal masses: a preliminary study
Authors: Xu Yun , Wan Qingxuan , Ren Xihui , Wang Fang , Shen Aijun , WU Peng , Wang Peijun
Published: August 2024

This study aims to assess the feasibility of amide proton transfer-weighted (APTw) imaging in depicting renal lesions and its ability to differentiate malignant from benign tumors. The results show that APTw can be used to discriminate renal tumors from normal kidney tissues, as well as to identify benign and malignant renal tumors. However, the technique still needs to be improved to reduce artifacts.
Preliminary exploration of the influence of demographic characteristics on 3D-APTw imaging of right normal kidney
Authors: Tian Gang , Wang Xia , Ma Ruirui , Zhang Wei , Zhao Na , Jia Min , Yu Chanjuan , Yue Xiuzheng , Chan Queenie , Han Yuedong
Published: August 2024

APTw imaging is able to detect free protein and peptide molecules in cells non-invasively. The aim of this study was to investigate the influence of age, gender and BMI on the APT values of right normal kidney. The results showed that there was a low correlation of APT values and age or BMI; and the male mean APT values was lower than that in female. The influence of age, gender and BMI factors should be taken into account in scientific research and clinical application of renal APTw imaging.
Evaluation of pulmonary artery hemodynamic changes in COPD patients with different emphysema volume by using 4D-Flow MRI
Authors: Sun Jiwei , Zhang Hong , Yu Anhong , Lian Jianxiu , Gao Yufan , Yuan Wei , Yang Yapeng
Published: August 2024

Few studies quantitatively evaluate pulmonary artery hemodynamic changes caused by emphysema. 34 COPD patients were divided into two groups according to emphysema volume and 12 healthy volunteers were matched. Hemodynamic parameters were calculated by 4D-Flow MRI and right ventricular function indicators were evaluated for three groups. The right systolic pressure drop and RVEF were lower in moderate and severe emphysema group but the right EL was higher. The whole-lung emphysema score correlated negatively with RVEF and the right systolic pressure drop. 4D-Flow combined with cine image can comprehensively evaluate the pulmonary artery hemodynamics and right ventricular function of COPD patients.
3D phase contrast blood flow measurements in the coronary arteries
Authors: Lichthardt Denise , Wetzl Jens , Schmidt Michaela , Speier Peter , Nagel Armin , Giese Daniel
Published: August 2024

Phase contrast MRI enables flow measurement in the coronary arteries. Herewith we propose a 3D Flow sequence and present a novel 3D visualization and quantification tool. Whole heart 3D PC measurements were performed in more than 20 healthy volunteers. An isotropic resolution of 1.2x1.2x1.2mm3 was used, as well as an undersampling factor of 14 in combination with a compressed sensing reconstruction. Our postprocessing tool was used for the 3D visualization of blood flow information as well as quantification of flow velocities per slice perpendicular to the vessel centerline.
Patients with liver cirrhosis have more stagnant portal venous blood flow compared to non-cirrhotic subjects: analysis using 4D flow MRI
Authors: Hyodo Ryota , Takehara Yasuo , Mizuno Takashi , Ichikawa Kazushige , Ishizu Yoji , Ogura Yasuhiro , Naganawa Shinji
Published: August 2024

Although liver cirrhosis is an independent risk factor for portal vein thrombosis (PVT), the individual thrombotic risk assessment is complex. Recently, 4D flow MRI has begun to assess portal blood flow; however, there have been no reports of the use of RRT, an indicator of blood flow stagnation, in the portal system. RRT may be used to measure the risk of PVT in liver cirrhosis. In this study, we evaluated the mean RRT value of the main PV calculated with 4D flow MRI and found that the value was significantly higher in cirrhotic patients than in non-cirrhotic subjects.
Using PINS pulses to saturate inflow effects from slice gaps in functional MRI
Authors: Hodono Shota , Wu Chia-yin , Dixon Carl , Maillet Donald , Jin Jin , Polimeni Jonathan , Cloos Martijn
Published: August 2024

In this work, we demonstrate the use of PINS pulses to mitigate unwanted inflow effects in 2D multi-slice sequences. A PINS pulse was played prior to slice-selective excitation to saturate the magnetization within all slice gaps. Bloch simulation and flow-phantom experiments show inflow effects can be removed completely. Functional scans using twice-refocused spin echo suggest that inflow effects may have noticeable contributions to SE-BOLD fMRI response. This PINS implementation allows us to further understand fMRI signal dynamics by modulating the inflow effect.
Neurochemical profile of major depressive disorder in adolescents: 7 T MRS study
Authors: Genovese Guglielmo , Croarkin Paul , Ozger Can , Marjańska Małgorzata
Published: August 2024

Major depressive disorder in adolescents (MDD) is a substantial public health problem. Existing treatments are often ineffective and do not target relevant neurobiological markers. It has been hypothesized that neurobiological mechanism underlying depression involves a dysfunction of the excitatory/inhibitory neurotransmitters. Here, the neurochemical profile from the occipital lobe of twenty adolescents with MDD and twenty-four age-matched healthy volunteers (HV) were acquired at 7 T. Larger SDs were observed for some metabolites in MDD versus HV and suggest heterogeneity of depression severity in the MDD cohort. Positive correlation in MDD between aspartate and GABA could be indicative of a neurotransmitter imbalance.
Novel urease inhibitor as potential treatment of hepatic encephalopathy led to brain glutamine decrease
Authors: Simicic Dunja , Evstafeva Diana , Ilievski Filip , Bao Yinyin , Kang Sunghyun , Sessa Dario , Mitrea Stefanita-Octavian , Pierzchala Katarzyna , Leroux Jean-Christophe , Cudalbu Cristina
Published: August 2024

Type C hepatic encephalopathy (HE) is a severe neuropsychiatric disorder associated with chronic liver disease. Ammonia (partially produced in the gut by bacterial urease activity) has been pinpointed to explain the observed neurological alterations in HE and connected with the increase in brain Gln measured using 1H-MRS. As such current treatment strategies focus on either reducing ammonia production and absorption or on promoting its elimination. We showed that targeting urease activity using the urease inhibitor 2-octynoHA has a beneficial effect in reducing blood ammonia levels and reducing brain Gln measured using 1H-MRS at 9.4T in the cerebellum.
Fast Uncertainty Estimation of IVIM parameters using Bayesian Neural Networks
Authors: Zhang Zehuan , Genči Matej , Fan Hongxiang , Luk Wayne , Wetscherek Andreas
Published: August 2024

We transformed the state-of-the art IVIM-NET for IVIM parameter fitting into a Bayesian Neural Network (BNN). BNNs can estimate uncertainty for quantitative MRI parameters, which is relevant for clinical decision making. We found that training on data with the highest SNR outperformed IVIM-BNNET models trained on matching SNR regarding parameter errors and uncertainties. A region with artificially increased noise could be identified from IVIM-BNNET's uncertainty output. Compared with traditional fitting, IVIM-BNNET achieved comparable accuracy, while being 21 times faster and providing less correlated parameter estimates. Monte-Carlo dropout rate 0.4 provided the best trade-off between low errors and low uncertainty.
Accelerating Phase and Quantitative susceptibility mapping with Scan-Specific Complex Convolutional Neural Networks
Authors: Nimje Swetali , de Rochefort Ludovic , Artières Thierry
Published: August 2024

MRI data is inherently complex-valued, the vast majority of deep learning frameworks do not yet support complex-valued data. Most reconstruction networks separate real and imaginary components into two separate real-valued channels, which may not be the most efficient way to represent complex numbers. Phase is essential for many MRI applications, including phase contrast velocity mapping and Quantitative Susceptibility Mapping (QSM) etc. We propose a new crRAKI, a scan-specific complex-valued residual convolutional neural network for 2D/3D MRI data for accelerating phase mapping and QSM. A comparison is made with GRAPPA and rRAKI for the accelerated reconstruction of MRI images.
A Wrap-on Decoupled Coaxial Transmission Line (CTL) Transceive Array for Head MR Imaging at 10.5T
Authors: Zhang Xiaoliang , DelaBarre Lance , Payne Komlan , Waks Matt , Adriany Gregor , Ugurbil Kamil
Published: August 2024

In this work, a wrap-on 447MHz transceiver array using the 2nd mode of coaxial transmission line resonator is designed, constructed and tested for human head imaging at the ultrahigh field of 10.5T. Results demonstrate the unique decoupling performance among the resonant elements achievable even for non-overlapped array layouts. The 10.5T images of a human head phantom acquired from the proposed array along with numerical simulations are shown.
Multi-channel, Stretchable, Self-Tuning Coil Array Based on Liquid Metal Technology
Authors: Motovilova Elizaveta , Ching Terry , Vincent Jana , Tan Ek Tsoon , Taracila Victor , Hashimoto Michinao , Robb Fraser , Sneag Darryl , Winkler Simone
Published: August 2024

Stretchable receive coils can provide conformal fitting, improved SNR, and dynamic imaging capabilities. However, conductor stretching alters the resonance frequency, reducing potential SNR advantages. Previously, we proposed and demonstrated in a single element prototype a smart self-tuning coil design which allows to maintain the desired Larmor frequency with stretching. This work investigates the applicability of self-tuning techniques in a multi-channel stretchable coil array and demonstrates its performance in silico and in vitro. Simulation results show stable resonance frequency (<1%) and sensitivity (±5%) for varied load/stretching conditions. In vitro imaging demonstrates consistent performance of individual coil elements and the array (SNR=146).
Feasibility of simultaneous fMRI and optical imaging for head-fixed freely-behaving mice
Authors: Pan Wen-Ju , Watters Harrison , Meyer-Baese Lisa , Singer Annabelle , Keilholz Shella
Published: August 2024

For simultaneous optical imaging and fMRI with freely-behaving mice, head-fixed without body restriction in minimal stress awake state, optimizations were conducted on multiple aspects, including multi-wavelength optical imaging system for both optical intrinsic signals and extrinsic fluorescence studies of genetically encoded calcium indicators (GECI) and voltage indicators (GEVI) mice with tube lens design instead of imaging fiber bundle, transparent cranial window development, integrated quadrature coil in head holder, and the designed belt treadmill/ virtual reality (VR) system to fit a customized rodent cradle in the commonly used 12cm ID gradient for the small animal MRI system.
Mapping the effect of oxytocin on the mouse brain using Q2TIPS arterial spin labelling and BOLD fMRI at 9.4T
Authors: Kim Eugene , di Censo Davide , Li Zhuoni , MacNicol Eilidh , Hertz Alexandra , Craig Michael , Cash Diana , Petrinovic Marija
Published: August 2024

Currently, standard Bruker protocols for arterial spin labelling (ASL) in mice are limited to single-slice methods. Here, we implemented multi-slice Q2TIPS ASL on a Bruker 9.4T scanner for whole-brain mapping of cerebral blood flow (CBF) in mice. There was good agreement between Q2TIPS and the standard Bruker FAIR ASL. Pharmacological MRI using Q2TIPS ASL and BOLD fMRI revealed that systemic administration of a behaviorally relevant dose of oxytocin caused a global decrease in CBF and increase in functional connectivity in healthy, wildtype mice. These opposing effects corroborate a recent concept of mutual exclusivity between neuronal activity and functional connectivity.
31P MRSI coil combination using 23Na sensitivity information acquired with the same loop array at 7T: preliminary verification
Authors: Dai Jiying , Gosselink Mark , Raaijmakers Alexander , Klomp Dennis
Published: August 2024

We utilized a quintuple-tuned RF head coil array by using the high-SNR 23Na signals from the brain to optimize the weighting for combining signals from the same coil array elements for the low-concentrated 31P metabolites. 23Na-weighted Roemer combination of 31P MRSI signals is verified on EM simulations and MR experiments. Comparing to 31P self-weighted combination, 23Na-weighted combination shows higher SNR and better-combined spectra in regions with low intrinsic SNR. It also shows potential of mitigating the signal contaminations when using 31P-self-weights for 31P data acquired with large voxels.
Apparent diffusion coefficients of 31P metabolites in the human calf muscle at 7T
Authors: Huang Zhiwei , Gambarota Giulio , Xiao Ying , Wenz Daniel , Xin Lijing
Published: August 2024

31P diffusion magnetic resonance spectroscopy could assess the diffusion properties of high energy metabolites. In this study, a diffusion weighted (DW) STEAM sequence was implemented, and spectra were acquired in the human calf muscle of six healthy volunteers. Frequency and phase alignments were applied prior to spectral averaging. The ADC of phosphocreatine (PCr), adenosine triphosphate (ATP), inorganic phosphate (Pi) and glycerol phosphorylcholine (GPC) were (0.24±0.02, 0.15±0.04, 0.43±0.14, 0.40±0.09)×10-3 mm2/s. To the best of our knowledge, this is the first study reporting the ADCs of ATP, Pi, and GPC, and the second study reporting the ADC of PCr in human.
Deep Learning Based Self-Navigated Diffusion Weighted Multi-Shot EPI with Supervised Denoising
Authors: Dong Yiming , Koolstra Kirsten , Beljaards Laurens , Staring Marius , van Osch Matthias J.P. , Börnert Peter
Published: August 2024

Advanced diffusion weighted self-navigated multi-shot MRI can run at high scan efficiencies resulting in good image quality. However, the model-based image reconstruction is rather time consuming. Deep learning-based reconstruction approaches could function as a faster alternative. Tailored network architectures with appropriately set physical model constraints can help to shorten reconstruction times, resulting in good image quality with reduced noise propagation.
BUAN 2.0, streamlines as functions, nonlinear registration, and subdivision of bundles for advanced tractometry
Authors: Chandio Bramsh , Thomopoulos Sophia , Thompson Paul , Harezlak Jaroslaw , Garyfallidis Eleftherios
Published: August 2024

We propose BUAN 2.0, which adds new advancements to its predecessor BUAN. It sub-segments bundles with varying substructures in them. It uses nonlinear registration of bundles to find accurate correspondences among bundle segments across subjects. The number of horizontal segments is decided based on the bundle and data specifications. More importantly, in BUAN 2.0, instead of treating each point on the streamline as an independent observation, we treat each streamline as a complete entity, as a function. Streamlines are analyzed by deploying functional data analysis (FDA) methods for studying group differences in populations along the length of the tracts.
Multiparametric quantitative MRI of Healthy Adult Pancreas: Correlations with Gender and Age
Authors: Wang Lixia , Liang Lu , Zhang Jiyang , Zhou Yang , Yu Yang , Zhang Chen , Jiang Tao , Yang Qi , Jeon Christie , Gaddam Srinivas , Pandol Stephen , Xie Yibin , Li Debiao
Published: August 2024

The pancreas plays an important role in nutrition and metabolism of the whole body. Changes of pancreatic morphology and function are related to many diseases. Multiparametric MR provides quantitative information about pancreatic morphology and function. In this work, we measured the normal range of T1, T2, and ADC values for different gender and age groups, and found significant differences between age groups. Gender difference was only found in T2. There are negative correlations between T2/ADC and age, and positive correlation between T1 and age.
The value of DWI and T2 mapping in evaluating lymphatic vascular invasion of rectal cancer
Authors: Li Xiwei , Chen Anliang , Wang Nan , Wang Jiazheng , Lin Liangjie , Liu Ailian
Published: August 2024

Lymphatic vascular invasion(LVI)can help clinicians choose the best treatment strategy for patients. Pathological examination is the gold standard for the diagnosis of LVI in rectal cancer, but it is an invasive method. Multiparametric magnetic resonance imaging is valuable for the prediction of LVI in rectal cancer. In this study, we quantitatively evaluated the value of LVI in rectal cancer using T2 mapping and DWI sequences.
Synthetic magnetic resonance quantitative relaxation maps for preoperative staging of rectal cancer
Authors: Liu Wenguang , Pei Yigang , Liu Weiyin , Wang Xiao , Bai Yu , Luo Yijing , Zhou Gaofeng , Li Wenzheng
Published: August 2024

To preoperative assessment of tumor and node staging for rectal cancer patients is very important. This study aimed to investigate the feasibility of predicting pathological TN staging with synthetic MRI quantitative relaxation maps for rectal cancer patients. A total of 123 patients were identified in this study. Our results showed that the T1 and T2 values from synthetic MRI can distinguish effectively between pT1-2 and pT3-4 group, pN- and pN+ group, which is vital to selection of therapy strategy for rectal cancer patients.
T2*BOLD for evaluating coronary arteries with hemodynamic changes in stable multivessel coronary artery disease
Authors: Zhao Lei , Chen Weibo , Wang Yongyi , Xue Song , Wu Lianming
Published: August 2024

This study used T2*BOLD and QFR to evaluate coronary arteries with hemodynamic changes in coronary artery disease. Fifty patients with at least 1 significant coronary artery stenosis (diameter stenosis >50%) and 21 healthy control subjects underwent coronary angiography combined with QFR measurements and CMR. The CMR protocol consisted of T2* mapping and resting perfusion, contrasted with QFR. QFR≤0.80 was considered to indicate the presence of hemodynamic obstruction. Our study revealed that T2* BOLD and QFR have good agreement in detecting hemodynamic changes of stenotic coronary arteries. T2* BOLD is superior to semiquantitative perfusion imaging in analyzing myocardial perfusion without stress.
Navigator acceptance window width does not affect accuracy and precision in free-breathing 2D cardiac MR fingerprinting of the myocardium at 3T.
Authors: Calarnou Pauline , Ogier Augustin , Hullin Roger , Meyer Philippe , Yerly Jérôme , Van Heeswijk Ruud
Published: August 2024

We implemented and characterized a free-breathing 2D cardiac joint T1-T2 MR fingerprinting technique at 3T named PARMA that includes a lung-liver navigator to minimize through-plane motion. We assessed the effect of rejected navigators on the relaxation times. Joint T1-T2 maps with four different navigator acceptance window widths (NAWWs from ±4mm to ±32mm) were acquired in 6 healthy volunteers and compared to clinical routine techniques. The accuracy and precision of the maps resulting from the different NAWWs did not significantly differ, suggesting that the NAWW can be chosen as a balance between navigator inefficiency and through-plane motion.
Deuterated trityl spin probe for in vivo pO2 imaging with improved precision using Time-Domain EPR
Authors: KISHIMOTO SHUN , Devasahayam Nallathamby , Yamashita Kota , Horie Kazumasa , Yamamoto Kazutoshi , Brender Jeffrey , Krishna Murali
Published: August 2024

Due to the narrow linewidth and slower signal decay, it was expected that Ox071 is suitable for wide range pO2 estimation. In this work, we present our first 3D in vivo EPR oximetry using Ox071 in comparison with Ox063. EPR imaging of MIA Paca-2 tumor and healthy kidneys were performed on successive days by using either Ox071 or Ox063, resulting in similar spin density, pO2 maps, and pO2 histograms in the tumor regions and more homogeneous pO2 profile with Ox071 in kidney compared with Ox063. The result suggested that Ox071 is applicable for oximetry in tissue at higher pO2.
Behavioural Relevance modulates BOLD-fMRI responses in the rat Visual Cortex
Authors: Valente Ana Mafalda , Gil Rita , Shemesh Noam
Published: August 2024

Neuronal responses are shaped by experiences. Plasticity can occur at single neuron level or at the full population level. Here, we established a novel behavioural task requiring rats to distinguish between continuous and flickering lights. We then performed fMRI in trained vs naive animals and investigated BOLD-fMRI responses along the visual pathway. When light flashes become meaningful in trained animals, the BOLD activation patterns are significantly modulated compared to naive counterparts, in particular in higher visual cortex and associative areas. BOLD-fMRI signals are thus capable of deciphering plasticity arising from strong associations with actions and rewards.
Computing hemodynamic point-spread functions with biophysical simulations of microvascular networks: effects of trans-laminar capillaries
Authors: Hartung Grant , Berman Avery , Varadarajan Divya , Chen Jingyuan , Polimeni Jonathan
Published: August 2024

Here we attempted to estimate a “point-spread function” of blood flow and oxygenation in the cerebral cortex through biophysical simulations based on a reconstructed vascular anatomical network. We stimulated individual pre-capillary arterioles and computed the downstream capillary flow and oxygenation based on fluid dynamics and oxygen transport through blood and tissue. We quantified this spread in the directions radial and tangential to the cortex. While several biases in spread were observed, we found a roughly 400 μm spread in the radial direction and generally narrower spread in the tangential direction, although both varied with cortical depth.
Development of a quantitative BOLD phantom for validation of acquisition strategies.
Authors: Alzaidi Ahlam , Panek Rafal , Blockley Nicholas
Published: August 2024

A phantom to produce R2' (reversible transverse relaxation rate) contrast was developed by inducing subvoxel magnetic susceptibility variations that mimic the quantitative Blood Oxygenation Level Dependant (qBOLD) MRI signal. Microscopic glass bubbles were used for this purpose and offer a cheaper option for making large volume phantoms than existing phantoms that use precision polystyrene microspheres. A linear relationship between R2' and the glass bubble volume fraction was found. Comparisons of multiparametric qBOLD acquisitions between two MR vendors were also made. In the future, phantoms such as this could facilitate quality assurance for qBOLD acquisition strategies and assist with multicentre harmonization.
Simulating BOLD fMRI transverse relaxation at 3 T: How accurate is the infinite cylinder model of blood vessels?
Authors: Berman Avery , Chausse Jacob , Hartung Grant , Polimeni Jonathan , Chen J. Jean
Published: August 2024

Simulations of the BOLD signal have provided invaluable insights into the biophysical underpinnings of BOLD contrast. Typically, infinite cylinders are used to represent the vasculature, although, in reality the vasculature is much more complex. In this study, we compared several biophysical modelling techniques for simulating the BOLD effect, including using Vascular Anatomical Networks (VANs) to model the capillary bed with realistic geometry. We found the majority of the different simulation approaches produced relatively consistent results with each other. The VAN simulations were consistent with the infinite cylinders, suggesting that infinite cylinders are a reasonable approximation to more realistic vascular models.