bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a Benchtop 7T cryogen-free animal MRI system
Authors: Wang Yaohui , Wang Qiuliang , Zhao Jigang , Liu Yang , Zheng Yijie , Chen Zhifeng , Liu Feng
Published: August 2023

A small-size, light-weight, cryogen-free 7T animal MRI system is being developed in IEE CAS. The magnet system has been completed and acceptable magnetic field strength and homogeneity indices have been achieved. The gradient assembly with passive shimming is going into the final assembly stage and the RF coil is ready for tunning. The integration of the whole system will be very soon and a mouse experiment will be conducted then. It is expected the ultimate product will largely boost the scientific research activities that are unapproachable to advanced MRI scanners.
Eddy-Currents Computations Using A Single-Layer Stream-Function Method
Authors: Alsharafi Sadeq , Kassahun Haile , Badawi Ahmed , El-Sharkawy AbdEl-Monem
Published: August 2023

Eddy-currents induced by MRI gradient coils due to rapid switching result in undesirable thermal effects, field distortions and acoustic-noise. Efficient numerical computations are needed to analyze eddy-currents for complex configurations. The skin-depth adds an extra computational burden for numerical eddy-current computations since meshing in the skin-depth direction may be needed to achieve reliable computations during harmonic analysis. Here, we use a single-layer stream-function method (SSM) applying resistance compensation and compare our results to a multi-layer integral method (MIM) approach. We show that SSM method achieves accurate comparable results relative to both MIM and Ansys albeit at higher computational effeciency.
Observing Clearance Pathway in Alzheimer Patients Using T2 Component Analysis
Authors: Oshio Koichi , Yui Masao , Shimizu Seiko , Yamada Shinya , Nakajima Madoka , Akiba Chihiro , Bandai Hideki , Miyajima Masakazu
Published: August 2023

A method to visualize possible waste clearance pathway in the brain was proposed earlier. The method is based on an assumption that there exist water containing macromolecules along the clearance pathway, and this water can be visualized using T2 component analysis. Preliminary results of this method applied for Alzheimer patients, as well as healthy volunteers, are presented. Distinct differences between the patients and healthy volunteers were observed. It is expected that this method can be a powerful tool for understanding the patho-physiology of the Alzheimer disease.
Tau accumulation is associated with fiber-specific white matter degeneration in Alzheimer's disease
Authors: Ahmadi Khazar , Pereira Joana , van Westen Danielle , Nilsson Markus , Spotorno Nicola , Hansson Oskar
Published: August 2023

Fixel-based analysis (FBA) enables investigation of micro- and macrostructural damage in white matter (WM) fiber bundles. However, the link between microscopic changes in fiber density (FD) and macroscopic morphological alterations in fiber cross-section (FC) with the pathological hallmarks of Alzheimer’s disease (AD) including regional tau and amyloid-β (Aβ) accumulation has not been explored yet. Here, we show that reduction in FC in the AD continuum is closely connected with tau tangles in contrast to Aβ pathology.
What to do for an accurate cross-sectional and longitudinal processing of diffusion tensor imaging: application to frontotemporal dementia
Authors: Huang Fan , Rohrer Jonathan , Zhang Hui , Bocchetta Martina
Published: August 2023

We considered the steps needed to analyse Diffusion Tensor Imaging (DTI) cross-sectionally and longitudinally, following a state-of-the-art approach which takes into account image quality, acquisition consistency, artifact correction, spatial correspondence. We applied this method to a small cohort of frontotemporal dementia (FTD) patients and controls to replicate the findings in the existing literature.
A Radial Flow Cell Perfusion System for Hyperpolarized 13C NMR Metabolic Studies at Low Oxygen Levels
Authors: Mancuso Anthony , Pourfathi Mehrdad , Kiefer Ryan , Noji Michael , Siddiqui Sarmad , Profka Enri , Kadlecek Stephen , Rizi Rahim , Gade Terence
Published: August 2023

We have developed new methods for studying cultured cancer cell metabolism with hyperpolarized 13C magnetic resonance spectroscopy (HP 13C MRS) at low oxygen concentrations. Cells grown on the surfaces of microcarriers inside the spectrometer were perfused radially (rather than axially) in a modified NMR tube at controlled oxygen levels. Computational and experimental results demonstrated that cell mass oxygen profiles with radial flow were much more uniform than with conventional axial flow. The metabolism of HP [1-13C]pyruvate was markedly different between the two flow configurations, demonstrating the importance of avoiding large oxygen gradients in cell perfusion experiments.
Early sex dependent changes in the default mode network of the TgF344-AD rat model of Alzheimer’s disease
Authors: Tudela Raúl , Muñoz-Moreno Emma , López-Gil Xavier , Varriano Federico , Soria Guadalupe
Published: August 2023

TgF344-AD rat model has been revealed as an interesting animal model for investigating Alzheimer's disease. About two thirds of persons diagnosed with AD dementia are women, suggesting important sex and gender differences in risk factors for the development of AD. Therefore, it is of high interest to also investigate this issue in the AD animal models. In this study we present preliminary results regarding the effect of sex difference in the functional default mode network between young TgF344-AD rats and Wild-type.
VEGF overexpression in breast cancer xenograft significantly increases nanoparticle-mediated siRNA delivery and target gene downregulation
Authors: Tan Shanshan , Chen Zhihang , Mironchik Yelena , Mori Noriko , Penet Marie-France , Krishnamachary Balaji , Bhujwalla Zaver
Published: August 2023

Effective tumor delivery is a major challenge in achieving small interfering RNA (siRNA) mediated gene silencing. Poor tumor vascularization can limit the delivery of therapeutic siRNA. Here, we used a VEGF overexpression breast cancer murine model and its wildtype counterpart to investigate the influence of increasing tumor vasculature on choline kinase-alpha siRNA nanoparticle delivery.
Apolipoprotein-E (APOE) Deficiency Leads to Neuronal Network Remodeling Characterized by Diffusion MRI and Graph Theory
Authors: Stapleton Margaret , Boehm-Sturm Philipp , Koch Stefan , Mueller Susanne , Cortes Devin , Wu Yijen
Published: August 2023

Allelic difference in Apolipoprotein-E (APOE) is a well-known risk factor for the late-onset Alzheimer’s disease (AD) but how APOE affects brain functions and the subsequent cognitive declination remains unclear. Diffusion MRI followed by network topology analysis found that APOE deficiency in knockout mice resulted in altered neuronal network in the brain regions known to be affected by Alzheimer’s Disease. This study suggests the possible role of APOE in neuronal network organization, which might predispose brains to differential AD vulnerability.
An Evaluation of High-Resolution EPI sequences and Enhanced Image Reconstruction for fMRI at 7T: Siemens-EPI, CMRR-EPI and INM4-EPI
Authors: Yun Seong Dae , Shah N. Jon
Published: August 2023

EPI is of great importance in the MR community due to its wide applicability in various dynamic MR applications. Recent advances in EPI techniques extend its use for the depiction of neuronal activation with a cortical depth-dependence. Therefore, enhanced performance with reliable image quality is highly desirable in EPI. This work presents an in-house designed EPI sequence and its corresponding image reconstruction software at 7T. Results show that our EPI sequence outperforms two widely used sequences: Siemens-EPI and CMRR-EPI. In addition, our image reconstruction routine significantly improves the reconstructed image quality of Siemens and CMRR data.
Phenotypic associations of magnetic susceptibility in the brain
Authors: Wang Chaoyue , Smith Stephen , Alfaro-Almagro Fidel , Douaud Gwenaëlle , Klein Johannes , Llera Alberto , Martins-Bach Aurea , Fiscone Cristiana , Bowtell Richard , Elliott Lloyd , Tendler Benjamin , Miller Karla
Published: August 2023

In this abstract, we describe our findings from the phenotypic association analyses (univariate Pearson correlations) between 17,485 non-imaging phenotypes and QSM (and T2*) measures using data from 35,885 subjects in UK Biobank. In total, we identify statistically-significant associations of 251 phenotypes with QSM IDPs. Here we describe example associations in blood assays, health outcomes, food and drink, and alcohol consumption categories in detail. Our results demonstrate that QSM and T2* contribute complementary information. This new QSM resource provides an opportunity to investigate susceptibility contrast in previously unexplored territory, which might lead to advances in application of QSM in neuroscience.
Daily Measurement of Prostate ADC in Patients Undergoing SABR and Conventional Treatment for Prostate Cancer on an MR-Linac
Authors: Moore Chris , Stickley Joe , Clough Abigael , Nelder Claire , Chuter Robert , Choudhury Ananya , McHugh Damien , Dubec Michael
Published: August 2023

MR-Linacs enable daily functional imaging to be performed in patients being treated with radiotherapy. In this work, the diffusion sequence developed by the MRL Consortium biomarkers working group underwent technical validation, showing accurate and repeatable phantom ADC measurements. Daily, whole-prostate ADC mapping was also performed in patients undergoing treatment for prostate cancer on an MRL. No significant differences were observed in whole-prostate ADC during the course of treatment for conventional and stereotactic ablative body radiotherapy (SABR) treatments. Absence of significant change in ADC could be related to the fact that patients were treated with neo-adjuvant hormone therapy prior to radiotherapy.
Mr CSD – Motion-robust Constrained Spherical Deconvolution for multi-shell multi-tissue brain modelling of infants and other restless patients
Authors: Sairanen Viljami
Published: August 2023

Investigation of brain structure of infants or other uncooperative patients using diffusion-weighted MRI is challenging due to subject motion artefacts. This work proposes a novel robust augmentation to current state-of-the-art multi-shell multi-tissue (MSMT) constrained spherical deconvolution (CSD) pipeline that accounts for these artefacts in both response function estimation and in deconvolution. A proof-of-concept is shown using multi-shell infant dataset and it is compared against the normal MSMT-CSD. The results indicate that motion artefacts can result in incorrect tissue type segmentations and fiber orientation distribution (FOD) estimates which could affect negatively any following analysis such as tractography or microstructural brain modelling.
Validation of the Multicomponent Diffusion Analysis using L1-norm regularized NNLS for Ultra-high b-value Diffusion-weighted MRI protocols
Authors: Gao Jin , Li Weiguo , Magin Richard , Erricolo Danilo
Published: August 2023

Multiple components analysis as a convenient tool to model multiexponential relaxations has been well developed in the applications of T2-weighted MRI. Nevertheless, this analysis is rarely used in diffusion-weighted MRI data and the lack of systematic studies makes the situation worse. Building on our previous studies, to validate the performance of the analysis becomes critical to carry out the ultra-high b-value DWI technique in vivo or translate to the clinical applications. We, therefore, proposed this phantom study to validate the stability and robustness of the multiple components analysis applied in the ultra-high b-value DWI technique.
A comparison of double-matching networks in a double-tuned coil for multinuclear MRI
Authors: Choi Chang-Hoon , Hong Suk-Min , Felder Jörg , Shah N. Jon
Published: August 2023

X-nuclei MR offers unique information relating to cellular and metabolic processes in tissues. Multi-tuned coils are frequently utilised for X-nuclei measurements, and a number of novel approaches for double tuning coils exist. However, designing a well-performing multi-tuned coil is challenging, and making any improvement in SNR is particularly desirable on the X-nucleus coil due to the intrinsically lower MR sensitivity of X-nuclei. This study focuses on the insertion of double-matching networks in a single-structure, double-tuned 1H/23Na coil and compares their effect on the coil performance. The double-matching networks were built using either split or blocking traps.
Adjustable parabolic shape 8Tx/16Rx array for longitudinal cardiac MRI in large animals at 7T: proof of concept
Authors: Terekhov Maxim , Elabyad Ibrahim , Schreiber Laura
Published: August 2023

Cardiovascular MRI at the ultra-high-field is an emerging modality promising a significant increase of the spatial resolution and physical sensitivity of routine cardiac imaging. Pig models play an important role in the establishment and translation of 7T cMRI to humans. The prerequisite for high-quality 7T cMRI data in pigs is dedicated transceiver arrays adapted to the shape of the pig’s thorax. We validated the proof-of-concept of the transceiver pTX cardiac array with adjustable parabolic shape housing for longitudinal studies with pigs. The stability of the transmit and receive characteristics by shape adjustments are tested in-silico and in phantom measurements.
A Flexible 16-Element Transceiver 8Tx/16Rx Coil Array for Parallel Transmit Cardiac MRI in Pigs at 7T
Authors: Elabyad Ibrahim , Terekhov Maxim , Lohr David , Bille Maya , Schreiber Laura
Published: August 2023

A dedicated flexible 16-element transceiver coil array was developed, simulated, and tested for cardiac MRI (cMRI) in pigs at 7T. The 16-elements of the array are printed on a flexible (Kapton polyimide) substrate to conform to the pig thorax. The performance of the elastic array is evaluated by EM-simulations and MR-measurements in a pig phantom and a 45-kg pig in-vivo. The flexible array supports parallel imaging with acceleration factors up to R=4 with reasonable g-factors (g=1.2) in an ROI at the position heart. The array enables geometrical conformity to pig body weights within a large range of sizes and shapes.
Target specific optimization of the transmit k-space trajectory stack-of-spirals and SPINS for pTx pulse design
Authors: Geldschläger Ole , Bosch Dario , Henning Anke
Published: August 2023

Four basis transmit k-space trajectories (a single variable density spiral-in, a two stack of variable density spiral-in, a three stack of variable density spiral-in and a SPINS trajectory) were optimized for pTx radiofrequency pulse design in order to match the excitation target pattern. The parameter to be optimized where the parameter of the analytical equations of the basis trajectories. The procedure was tested on local excitation and whole brain-like excitation target patterns. Optimized trajectories enabled considerably improved radiofrequency pulse performance, compared to radiofrequency pulses based on unsuited trajectories. The optimization code is available online as open source (https://github.com/ole1965/workflow_OTUP.git).
Evaluating a Volumetric High-Permittivity (HPM) Helmet for Brain Imaging at 3.0 T
Authors: Lakshmanan Karthik , Walczyk Jezry , Rupprecht Sebastian , Lanagan Michael , Yang Qing , Brown Ryan , Collins Christopher
Published: August 2023

A thin (8mm) helmet-shaped shell of high-permittivity material (HPM) is seen to double transmit efficiency and increase SNR by 40% at the center of tissue equivalent head phantom when compared to the body coil alone, with little effect on B1 homogeneity within the brain region. While evaluation of effects on receive arrays is ongoing, from the results shown here it seems an HPM helmet could be used at 3T in place of more electronically cumbersome head transmit coils.
The missing third dimension – functional correlations of BOLD signals incorporating white matter
Authors: Zu Zhongliang , Zhao Yu , Gao Yurui , Li Muwei , Ding Zhaohua , Gore John
Published: August 2023

We describe a novel graph analysis that includes a multigraph with multiple edges between a pair of nodes to model brain functional networks, and introduce a three-way correlation between BOLD signals from a pair of gray matter volumes (nodes) and one white matter bundle to define functional connectivity. Characteristics of inter-nodal communication may be derived from this analysis. By examining selected databases, we show inter-nodal communications vary with ages. By integrating fMRI signals from white matter as a third component in network analysis, more comprehensive descriptions of brain function may be obtained.
Improved Fidelity for Resting-State Connectivity Measurements in High-Spatial-Resolution ME-fMRI on a Compact 3T Scanner
Authors: Kang Daehun , In Myung-Ho , Halverson Maria , Meyer Nolan , Gray Erin , Foo Thomas , Madhavan Radhika , Ahmed Zaki , Jo Hang Joon , Fernandez Brice , Black David , Welker Kirk , Trzasko Joshua , Huston John , Bernstein Matt , Shu Yunhong
Published: August 2023

Through echo-combination, multi-echo echo-planar-imaging (ME-EPI) has shown improved performance for fMRI over single-echo (SE)-EPI. The high-performance gradients on a compact 3T scanner enable whole-brain high-spatial-resolution ME-EPI with reasonable echo times and comparable TR to SE-EPI. To evaluate the fidelity of the ME-EPI sequence in resting state fMRI and compare with that of SE-EPI sequence, seed-based and ICA-based functional connectivity (FC) analyses were applied to evaluate scan-time-dependency and accuracy improvement. ME-EPI extracted more and stronger FCs in seed-based connectivity analysis and produced higher sensitivity and accuracy in ICA-based method, compared to SE-EPI.
Benefits of echo combination for high-spatial-resolution ME resting state FMRI on a compact 3T scanner
Authors: Kang Daehun , In Myung-Ho , Halverson Maria , Meyer Nolan , Gray Erin , Foo Thomas , Madhavan Radhika , Ahmed Zaki , Jo Hang Joon , Fernandez Brice , Black David , Welker Kirk , Trzasko Joshua , Huston John , Bernstein Matt , Shu Yunhong
Published: August 2023

For multi-echo EPI, the T2*-weighted echo combination (T2EC) is a commonly used pre-processing step to boost the data quality. We assessed the benefit of T2EC in high-spatial-resolution multi-echo fMRI with explained variances and functional connectivity detectability. The performance was evaluated and compared with single-echo EPI for resting state fMRI on a compact 3T scanner with high-performance gradients. It was shown that a large portion of unwanted signal variance was globally suppressed through T2EC. Multi-echo acquisition shows improved image intensity and enhanced functional sensitivity in brain regions affected by signal-dropout.
Fast 3D fMRI Acquisition over a Small Field-of-View with (k, t)-Space Undersampling
Authors: Luo Qingfei , Sun Kaibao , Scotti Alessandro , Dan Guangyu , Karaman Muge , Zhou Xiaohong
Published: August 2023

The simultaneous multi-slice EPI (SMS-EPI) technique is widely used in fast fMRI studies to achieve a short TR (e.g., < 1 s), but its image quality can be degraded when the slices span only a small brain area. In this study we develop a fast fMRI acquisition technique for imaging a small area by employing (k, t)-space undersampling and three-dimension reduced field-of-view imaging (k-t 3D-rFOVI). Our human fMRI experiments covering the visual cortex demonstrate that k-t 3D-rFOVI can provide higher detection sensitivity of brain activations than SMS-EPI.
Maternal Obesity Alters Neuro-Connectivity in Baboon Offspring
Authors: Zhang Wei , Fox Peter , Huber Hillary , Nathanielsz Peter , Clarke Geoffrey
Published: August 2023

Maternal obesity status was found to affect neural functional connectivity of adult offspring in in a baboon model. Significant differences in connectivity between offspring of obese mothers and age/sex matched controls were found in regions of the left temporal lobe and frontal lobe using rs-fMRI.
Comparing the efficiency of data-driven noise regression in removing cardiac and respiratory signals from rs-fMRI: Difference across age groups
Authors: Golestani Ali , Chen Jean
Published: August 2023

Data-driven methods have been suggested to remove heartbeat and respiration noises from fMRI signals. We compared the effectiveness of these methods (global-signal regression (GS), white matter and CSF (cerebrospinal fluid) regression, anatomical and temporal CompCor, ICA AROMA) in removing the noise. GS, AROMA, and aCompCor removed the most physiological fluctuation, but GS and AROMA also removed most signals under 0.1 Hz. We also observed that all methods removed less noise power and more low-frequency power from young adult data compared to older adults.
Brain Functional Segregation Predicts Symptom Severity and Treatment Response in Psychotic Disorders
Authors: Song Xiaopeng , Song Tao , Zhu Chenyanwen , Ongur Dost , Du Fei
Published: August 2023

Functional segregation, i.e., anticorrelated neural activities, has not been well-explored in fMRI studies. We introduced the Negative Degree Centrality (NDC) method to quantify functional segregation. We found decreased NDC in psychotic disorder patients compared to controls. Positive, negative, and general psychotic symptoms were associated with impaired NDC in three different brain networks respectively. Using NDC and a machine learning approach, we identified two subgroups of patients with distinct recovery trajectories after one-year treatment. Our findings suggested impaired functional segregation in different brain circuits might be the neurobiological mechanisms associated with various psychotic symptoms and outcome heterogeneity in psychotic disorders.
Abnormal glutamate metabolism in prefrontal cortex of post-traumatic stress disorder linked to comorbidity with major depression
Authors: Swanberg Kelley , Prinsen Hetty , Averill Christopher , Campos Leonardo , Kurada Abhinav , Krystal John , Petrakis Ismene , Averill Lynnette , Abdallah Chadi , Juchem Christoph
Published: August 2023

Post-traumatic stress disorder (PTSD) is an anxiety condition evidenced by wide-ranging emotional and cognitive dysfunction. While prefrontal glutamatergic excitotoxicity is thought to contribute to its presentation, no 1H-MRS studies of PTSD have yet been conducted at 7-Tesla field strength facilitating separation of glutamate from metabolic partner glutamine. Here we apply 7-T 1H MRS to investigate medial prefrontal (mPFC) concentrations of glutamate and glutamine with GABA, glutathione, and other metabolites in both PTSD and comorbid major depressive disorder (MDD). We show several PTSD-associated abnormalities in mPFC glutamate metabolism that appear to be driven by MDD status when this comorbidity is considered.
Voxel-wise Comparison of Clinical 2D pCASL and DSC Perfusion of Intra-axial Brain Tumors
Authors: Devos Johannes , Peeters Ronald , Demaerel Philippe
Published: August 2023

Dynamical susceptibility contrast (DSC) and arterial spin labeling (ASL) are MRI techniques to quantify brain tissue perfusion. A voxel-wise analysis in 23 patients showed a moderate to strong linear relationship between tumoral cerebral blood flow measured by 2D echo planar imaging, pseudo-continuous ASL (pCASL) and leakage corrected, cerebral blood volume measurements by DSC. Additionally, mean and 90th percentile of tumor perfusion of all patients showed a strong linear relationship. In conclusion, 2D EPI pCASL is a viable alternative to DSC for perfusion measurements of brain tumors.
Role of PET and ASL simultaneously acquired imaging biomarkers in differentiating progression from radionecrosis in glial brain tumors
Authors: Pyatigorskaya Nadya , Pellerin Arnaud , Kalife Maya , Rozenblum-Beddok Laura , Bertaux Marc , Soret Marine , Yahia-cherif Lydia , Kas Aurélie
Published: August 2023

We aimed at investigating the methods based on coupling of of amino-acid metabolism (18F-DOPA-PET) measurements and cerebral blood flow (CBF) maps to evaluate the diagnostic performance of PET/MRI in glioma imaging. Tumor isocontour maps and T-maps were created using SPM and metabolic/perfusion abnormalities were evaluated with the asymmetry index z-score. SPM map analysis of significant-size clusters and semi-quantitative evaluation were performed and compared to gold standard diagnosis. Both the tumor isocontour maps and T-maps showed the highest specificity for ASL and sensitivity for 18F-DOPA analysis, allowing high diagnostic performance in differentiating between progression and radionecrosis particularly in high-grade treated gliomas.
Quantitative magnetic resonance imaging combined with three-dimensional image analysis in glioblastoma
Authors: Bertalan Gergely , Onken Julia , Schwedler Simone , Hamm Bernd , Bohner Georg , Wiener Edzard
Published: August 2023

Conventional MRI such as T2 and FLAIR do not show sub-regional intensity changes in peritumoral infiltration zone of glioblastoma and cannot visualize tumor margins. Here, we implemented a new method for sub-volumetric analysis of glioblastoma and investigated T1 and T2 relaxation properties in the peritumoral infiltration zone. The results show a decrease in T1 and T2 relaxation times as a function of distance from the contrast-enhanced T1 solid tumor region to the periphery. Our method may help to better select regions for biopsy, to determine the surgical resection margin and improve radiation therapy planning and post-therapeutic progress controls.
Patient-specific hyperdirect pathway activation in DBS for Parkinson's disease
Authors: Amil Alba Segura , Nguyen T.A. Khoa , Nowacki Andreas , Pollo Claudio
Published: August 2023

Deep brain stimulation is an effective treatment in advanced Parkinson’s disease. The aim of the study was to determine activation thresholds for the hyperdirect pathway and corticospinal tract to control motor symptoms and avoid the appearance of side effects. Patient-specific whole brain tractograpy, DBS leads reconstruction, and generation of volumes of tissue activated were performed in 20 Parkinson patients. The activation threshold for the hyperdirect pathway was 60%, and for the corticospinal was 4%. For newly generated volumes of tissue activated, the average prediction error for the hyperdirect pathway was 1 mA and for the corticospinal tract was 1.5 mA.
Initial Clinical Experience with MAGNUS Ultra-High-Performance Gradient Coil for Diffusion Microstructure Imaging of Intracranial Pathology
Authors: Shih Robert , Zhu Ante , DeMarco J , Morris H , Hood Maureen , Abad Nastaren , Madhavan Radhika , Marinelli Luca , Foo Thomas , Ho Vincent
Published: August 2023

The MAGNUS ultra-high-performance gradient coil delivers simultaneous 200 mT/m and 500 T/m/s performance on each axis, with higher PNS thresholds than whole-body gradient coils, which is particularly useful for diffusion microstructure imaging. Our initial clinical experience with the MAGNUS research scanner has successfully identified white matter abnormalities (? intra-axonal edema) using multi-shell DTI (bmax = 4000 s/mm2) and OGSE (fmax = 100 Hz) in an acute symptomatic mTBI subject. It has also successfully identified differences in intracellular volume fraction using multi-shell multi-frequency OGSE (bmax = 2000 s/mm2, fmax = 100 Hz) between a low-grade diffuse astrocytoma and a high-grade glioblastoma.
Radiomics for noninvasive prediction of HCC immunophenotyping
Authors: Bhuiyan Enamul , Bane Octavia , Kennedy Paul , Yildiz Sema , Shareef Muhammed , Fiel M. Isabel , Ward Stephen , Schwartz Myron , Marron Thomas , Merad Miriam , Taouli Bachir
Published: August 2023

The reported rate of intrahepatic recurrence of hepatocellular carcinoma (HCC) after resection is high (up to 50%), even with negative surgical margins, which is postulated to be due to micrometastases. Immunotherapy present new possibilities in cancer treatment with encouraging results in HCC. Selection of patients for immunotherapy may be based on background immune features, thus imaging features associated with immunophenotype may aid in patient selection. Specifically, radiomics features exhibited a fair to excellent diagnostic performance for differentiating tumors with high vs. low/moderate tumor infiltrating lymphocytes (TILs) and presence vs absence of tertiary lymphoid structure (TLS) with AUC range of 0.70-0.95.
Estimation of Lung Parenchyma Transverse Relaxation Rates at 0.55 Tesla
Authors: Li Bochao , Lee Nam , Nayak Krishna
Published: August 2023

Lung MRI with excellent image quality has been demonstrated at 0.55T, largely due to reduced susceptibility effects. Here, we present joint estimation of lung parenchyma transverse relaxation rates $$$R_{2}$$$, $$$R_{2}^{\prime}$$$, and off-resonance $$$\Delta f$$$. A custom echo-shifted turbo spin echo (TSE) pulse sequence with ECG triggering and breath hold was performed in 4 healthy volunteers, resulting in the mean $$$R_{2}$$$ of 23.4s-1, $$$R_{2}^{\prime}$$$ of 53.9s-1, and $$$\Delta f$$$ of 45.7Hz. This work demonstrates the feasibility of echo-shifted TSE for the estimation of three parameters of interest in lung MRI, and confirms prior measurements made with separate pulse sequences.
Motion-Compensated Low-Rank Reconstruction with Iterative Registration for Ventilation Analysis on Ultrashort Echo Time (UTE) Lung MRI
Authors: Tan Fei , Zhu Xucheng , Larson Peder
Published: August 2023

In this abstract, we introduce motion-compensated low-rank constrained reconstruction with iterative registration. This method jointly improves the motion field estimation and the reconstruction, providing both functional and structural images. In addition, we test the effect of the regularization parameter on structural images and ventilation maps. We conclude that the motion-compensated low-rank constrained with iterative registration method is suitable for regional ventilation quantification.
Feasibility of Biliary Imaging at 0.55T: A Comparison to 1.5T
Authors: Ramachandran Anupama , Ropella-Panagis Kathleen , Dudek Nancy , Morehouse Joel , Gulani Vikas , Mendiratta-Lala Mishal , Seiberlich Nicole
Published: August 2023

MRCP exams were performed in three volunteers on 0.55T and 1.5T MRI systems. Images were rated on overall image quality and visualization of ducts by two board certified abdominal radiologists. All images on both systems were rated as excellent diagnostic quality. A paired sample t-test did not show significant differences in acquisition time between the two field strengths. The advantages of performing an MRCP exam on a 0.55T MRI system may include reduced susceptibility artifacts, reduced artifacts from cholecystectomy clips, improved patient comfort due to larger bore sizes, and potentially lower overhead costs.
MRI lung lobe segmentation of pediatric cystic fibrosis patients using a neural network trained with publicly accessible CT datasets
Authors: Pusterla Orso , Heule Rahel , Santini Francesco , Weikert Thomas , Willers Corin , Andermatt Simon , Sandkühler Robin , Nyilas Sylvia , Latzin Philipp , Bieri Oliver , Bauman Grzegorz
Published: August 2023

Pulmonary biomarkers quantifications on a lobar level provide improved specificity against whole-lung analyses. However, lobar quantifications of pulmonary MR data are hardly accessible due to the complex work required for the manual segmentations. Supervised neural networks have shown the premise for automatic segmentation, but it is challenging to gather labelled data for the training. To overcome these limitations, in this work, we “translate” publicly accessible chest CT datasets and lobe segmentations to pseudo-MR data, and we then train a network able to segment consistently lung lobes of acquired MRI data. The cross-modality approach has excellent prospects to automatize MRI analyses.
MR-based Liver Iron Quantification using Gradient Echo: Co-Factors influencing the Calibration of R2* with Reference Liver Iron Content Values
Authors: Wunderlich Arthur , Cario Holger , Kannengießer Stephan , Hering Lena , Götz Michael , Beer Meinrad , Schmidt Stefan
Published: August 2023

Purpose: To analyze the Liver-Iron-Content-(LIC)-R2*-calibration with respect to co-factors.

Methods: 116 patients were scanned with spin-echo (Ferriscan® protocol) and gradient-echo sequences. R2* was correlated to LIC reference values for all patients together and in subgroups divided by e.g. age, gender and underlying diseases. Linear correlations were analyzed with R2* only and including MR-PDFF as suspected co-factor.

Results: Deviating slopes of regression lines were found e.g. in patients after splenectomy vs. patients with spleen, influence of MR-PDFF amongst others in females below 17 years.

Conclusion: Co-factors like disease patterns should be considered in gradient echo based LIC quantification.
3D multi-echo GRE MRI of the whole liver: First experiences of a volumetric segment-by-segment R2* analysis
Authors: Wunderlich Arthur , Cario Holger , Kannengießer Stephan , Grunau Veronika , Götz Michael , Beer Meinrad , Schmidt Stefan
Published: August 2023

Purpose: To test liver segmentation of 3D-multi-gradient-echo MRI data and segmental R2* evaluation.

Methods: 44 patients examined by multi-gradient-echo MRI underwent semiautomatic liver segmentation and subdivision into nine segments. Segmental R2* values were analyzed in all patients together and in patient subgroups.

Results: R2* was lowest in segment 1 (S1), differences to S1 were significant for S3, S5 and S6, highly significant to S2 and S7. Patients with high average R2* showed also significant differences to S1 in some segments.

Conclusions: Inhomogeneity of hepatic iron distribution was found. Low R2* in S1 may be explained by its special vascular supply.
Effect of Acquisition and Analysis Conditions on Accuracy of DTI-Based Muscle Architecture Estimates: Predictions Using Numerical Simulations
Authors: Zhou Xingyu , Lockard Carly , Hooijmans Melissa , Damon Bruce
Published: August 2023

Diffusion-tensor imaging (DTI) based fiber tractography is a useful tool to study the architecture of human skeletal muscle. However, effects of image acquisition and analysis conditions on the outcome of architectural estimates are challenging to examine in vivo. In this work, we describe a numerical simulation framework where the ground truth of muscle architecture is known and the outcome can be tested under different conditions. Results show that the estimate of fiber curvature is most affected by image noise. While second-order polynomial fitting of fiber tracts is more robust to image noise, third-order fitting performs better on highly curved fibers.
Deep Learning Based Automatic Pipeline for Quantitative Assessment of Thigh Muscle Fatty Infiltration in Post-traumatic Osteoarthritis
Authors: Gaj Sibaji , Eck Brendan , Xie Dongxing , Lartey Richard , Lo Charlotte , Yang Mingrui , Nakamura Kunio , Winalski Carl , Spindler Kurt , Li Xiaojuan
Published: August 2023

Quantitative assessment of thigh muscle morphology and fatty infiltration (FF%) in post-traumatic osteoarthritis is limited. In this work, we developed a deep learning based accurate segmentation method for muscles, bone and adipose tissue from thigh MRI and used these segmentation for automated quantification of FF and cross sectional area(CSA) of these tissues. 16 patients at 10 years after ACL reconstruction were studied. The proposed method showed significant improvement in segmentation metrics (Dice, Average surface distance (ASD)) and CSA compared with popular U-Net based deep learning models. For CSA and FF% quantification, automated methods had similar measurements compared with manual segmentation.
Bilateral characterization of fractional anisotropy within the anterior cruciate ligament: A step toward clinical use of DTI in the knee
Authors: Champagne Allen , McGuire Andrew , Shearer Kaden , Brien Don , Martineau Paul , Bardana Davide
Published: August 2023

Diffusion tensor imaging (DTI) has emerged as biomarker to characterize the ligamentization process of the anterior cruciate ligament (ACL), following surgical reconstruction. One major limitation to this approach is the necessity for pre-injury baseline measurements to be used as a frame of reference, in order to inform clinical decision making with respect to recovery of the graft, and return-to-activity (RTA). Here, we explore the linear relationship for anisotropy between knees bilaterally, in healthy participants, to provide a methodological framework that allows for the clinical integration of DTI to monitor recovery of the tendon autograft, following surgical reconstruction, and inform RTA.
Test-retest Repeatability of High-resolution Whole-brain DCE-MRI in High-grade Glioma Patients
Authors: Zhu Zhibo , Bliesener Yannick , Chow Frances , Acharya Jay , Nayak Krishna
Published: August 2023

We perform a prospective test-retest repeatability study of one such approach, in patients with high-grade glioma. Two separate scans were performed within 3-7 days apart. Tumor, scalp, normal white matter, pons, cerebellum and muscle regions were segmented manually. The coefficients of variation of median Kt were 50.4% to 66.6% and of median vp were 23.2% to 80.0%, based on our first 5 subjects.
Quantitative Susceptibility Mapping for Gold Fiducial Marker Localization in Prostate for MRI-Only Radiation Therapy Treatment Planning
Authors: Deng Jie , Shen Chenyang , Wu Junjie , Jiang Steve
Published: August 2023

MRI-only simulation permits superior soft tissue contrast for tumor tissue characterization and target margin delineation. One bottleneck preventing MRI-only simulation to be widely applied in prostate cancer EBRT is the tedious marker localization process on MR images as compared to that on a CT. The fiducial and calcification on MRI also appear to be similar, which reduces the confidence level of the clinician in fiducial localization, and further increases the time needed. In this study, we developed a framework using quantitative susceptibility mapping to automatically identify the fiducial markers based on phase information of gradient-echo MRI.
MRI assessment of abscopal effect induced by radiation/immune checkpoint blockade combination therapy
Authors: Yamashita Kota , Otowa Yasunori , Yamamoto Kazutoshi , Brender Jeffery R. , Devasahayam Nallathamby , Krishna Murali C. , Kishimoto Shun
Published: August 2023

Radiation therapy (RT) occasionally induces regression of non-irradiated metastatic lesions, which is called abscopal effect. Immune checkpoint inhibitors enhance abscopal effects. In this study we examined the physiological changes induced by abscopal effect and identify using MRI-based imaging biomarkers which predict the successful abscopal effect. Hypoxic fraction < 10 mmHg (HF10), permeability, perfusion, and CD8+ T cell infiltration in unirradiated tumor increased after the combination of RT and PD-1 blockade therapy. Interestingly, higher permeability/perfusion and lower HF10 in irradiated tumor before treatment is associated with slower growth of the unirradiated tumor after treatment of the tumor on the contralateral side.
DWI Metrics Differentiating Intraductal Papillary Mucinous Neoplasms from Pancreatic Cancer: A study in GEM Models
Authors: Joaquim Miguel Romanello Giroud , Furth Emma , Fan Yong , Song Hee Kwon , Pickup Stephen , Cao Jianbo , Choi Hoon , Gupta Mamta , Clendenin Cynthia , Karasic Thomas , Duda Jeffrey , Gee James , O'Dwyer Peter , Rosen Mark , Zhou Rong
Published: August 2023

Intraductal Papillary Mucinous Neoplasms (IPMN) are recognized as important precursors to invasive pancreatic ductal adenocarcinoma (PDAC). While IPMN requires surveillance without treatment, a clinical marker is lacking which can identify those undergoing malignant transformation. In two genetic engineered mouse models (KPC and CKS), which resemble human PDAC and IPMN, respectively, we tested the hypothesis that differences in cellular architecture and stromal features between PDAC and IPMN present themselves in DW-MRI and /or DCE-MRI metrics. Our data revealed an almost complete separation of ADC values between CKS (benign) vs. KPC (malignant) tumors and identified histopathological features corroborating the imaging metrics.
Fluorine-19 MRI of Stem Cell-Derived Alveolar-Like Macrophages Tagged with Perfluoropolyether
Authors: Kim Janny , Litvack Michael , Li Daniel , Zanette Brandon , Post Martin , Santyr Giles
Published: August 2023

When stem cell-derived alveolar-like macrophages (ALMs) are labeled with perfluoropolyether (PFPE), they can potentially be monitored and tracked longitudinally in vivo using 19F MRI. In this work, different concentrations of PFPE and 5 million PFPE-labeled ALMs were imaged in vitro using 19F MRI at 3T. The results demonstrated the feasibility of detecting a small number of PFPE-labeled ALMs. This work will provide guidance for the upcoming in vivo instillation experiments in rat lungs. Longitudinal in vivo studies will further aid ALMs to be clinically translated as a stem cell therapy to treat chronic lung diseases.
Brain Connectomics in a Mouse Model of Early and Late Stage Pruritus
Authors: Venkatraman Talaignair , Chen Ouyang , Song Allen , Ji Ru-Rong , Lascola Chris
Published: August 2023

We performed high-resolution ex-vivo DTI in mice with cutaneous T-Cell lymphoma (CTCL) in a mouse model of pruritus. Our results show significant network changes within and between specific brain regions, namely thalamus and hippocampus, by the later stage of disease. At the chronic stage (55 days), micro-structural changes and enhanced connectivity are established between the hippocampus and thalamus.
Automated Brain Extraction from T1-weighted MRI of Rhesus Macaques using a U-Net Deep Learning Framework
Authors: Zhang Anqi , Kim Donghoon , Kim Jeong-chul , Hobson Brad , Elizaldi Sonny , Morrison John , Iyer Smita , Chaudhari Abhijit , Jung Youngkyoo
Published: August 2023

Transfer learning of an advanced deep learning framework, utilizing 3D U-Net pre-trained model, and trained on human brain MRI scans is proposed for brain extraction from MRI of other species. The proposed network architecture successfully performed whole brain extraction from rhesus macaque brain MRIs automatically with high accuracy, reduced errors, and lower computational cost. Options for data augmentation and different learning rates were also tested. Successful implementation of automated brain extraction would offer the potential to apply the same strategy on other animal models.
Investigating time-restricted feeding and metabolic sexual dimorphism in Nile grass rats by time-domain NMR lipid profiling
Authors: Johnson Hayden , Yates Thomas , Ramanathan Chidambaram , Puppa Melissa , van der Merwe Marie , Tipirneni-Sajja Aaryani
Published: August 2023

NMR-based metabolomics is a powerful technique for elucidating the metabolic effects of diet through the identification and quantification of molecules present in tissues. This study utilizes time-domain processing of NMR data for robust, reproducible resonance characterization in the profiling of lipid species in heart and liver tissues of male and female animals subject to high fat diets with and without time-restriction. Results show triglyceride and fatty acid accumulation was associated with eating a high fat diet, but these effects were attenuated by time-restricted feeding. Hepatic lipids expressed a sexually dimorphic response, with higher concentrations of many lipids in female subjects.
Integrating a Unilateral MRI Scanner with a Small Animal Irradiator for Preclinical MR-Guided Radiation Experiments
Authors: Grandinetti Jace , Zhong Yuncheng , Peng Yuting , Shen Chenyang , Zhang Shu , Jia Xun
Published: August 2023

Magnetic Resonance-guided Radiation Therapy (MRgRT) has recently become available in human RT, however, this technology does not currently exist for preclinical systems. We propose a novel approach to develop and integrate an MR system with an existing small animal irradiator and report our ongoing progress constructing such a system. The MR system is comprised of a unilateral Halbach cylinder with permanent magnets and split gradient coils to prevent obstruction of the radiation beam while targeting a 4cm region of interest. Further development is ongoing for a split broadband RF coil and custom pulse sequences to maximize signal-to-noise.
Integrated T1rho Dispersion Imaging and Quantification
Authors: Peng Qi , Peng Gregory , Wu Can
Published: August 2023

T1ρ dispersion imaging is an emerging MRI technique for tissue characterization. Multiple independent repetitions of T1ρ experiments at different spin-lock frequencies have to be performed to generate tissue T1ρ dispersion curve. In this work, we demonstrate the feasibility of an integrated imaging and quantification approach for T1ρ dispersion imaging, which allows simultaneous generation of T1ρ maps at multiple spinlock frequencies in one coherent workflow. This opens door for further data undersampling to exploit redundancy at higher dimension data space, further reducing total scan time needed for the time-consuming T1ρ dispersion imaging.
Denoising MR Fingerprinting by matching against General Noise Model at 0.55 T
Authors: Zhu Ruogu , Seiberlich Nicole , Jiang Yun
Published: August 2023

Low SNR is a challenge for magnetic resonance fingerprinting (MRF) at low-field (0.55 T). In this work, we apply a locally low rank denoising method based on elimination of noise-only principal components according to the Marchenko-Pastur distribution to MRF data. We show that this method is effective at denoising both phantom and in vivo MRF images.
Synergistic Combination of Golden-angle Radial Sampling and Dual-Subspace Modeling for Rapid and Robust High Spatiotemporal Resolution MRA
Authors: Chen Zhifeng , Yan Lirong
Published: August 2023

This study proposes a rapid and robust ASL-based time-resolved MRA technique with high spatiotemporal resolution termed Dual-Subspace MRA (DS-MRA), which employs subspace modeling from both temporal and control/label dimensions as sparsity constraints to improve the robustness of image reconstruction with under-sampled golden-angle radial dynamic MRA. The performance of DS-MRA was compared with conventional iGRASP and 5-dimensional GRASP. Our preliminary data suggests that DS-MRA outperforms conventional GRASP reconstructions with less residual streaking artifacts and noise, especially at higher acceleration rates.
Improved Multi-band Multi-shot Diffusion MRI Reconstruction with Joint Usage of Structured Low-rank Constraints and Explicit Phase Mapping
Authors: Dai Erpeng , Mani Merry , McNab Jennifer
Published: August 2023

Inter-shot phase correction is a critical step in multi-band multi-shot diffusion MRI. The phase correction can be accomplished by first estimating the explicit phase map and then inputting it into the diffusion signal formulation model to recover the diffusion images. Alternatively, the phase information can be used in an indirect manner to determine structured low rank constraints in k-space. The two methods differ in terms of reconstruction accuracy and efficiency. In this study, we propose a new way to combine the two approaches for improved image quality, termed “Joint Usage of structured Low-rank constraints and Explicit Phase mapping” (JULEP).
Learning Deep Linear Convolutional Transforms For Accelerated MRI
Authors: Gu Hongyi , Yaman Burhaneddin , Moeller Steen , Chun Il Yong , Akçakaya Mehmet
Published: August 2023

Research shows that deep learning (DL) based MRI reconstruction outperform conventional methods, such as parallel imaging and compressed sensing (CS). Unlike CS with pre-determined linear representations for regularization, DL uses nonlinear representations learned from a large database. Transform learning (TL) is another line of work bridging the gap between these two approaches. In this work, we combine ideas from CS, TL and DL to learn deep linear convolutional transforms, which has comparable performance to DL and supports uniform under-sampling unlike CS, while enabling sparse convex optimization at inference time.