bluuebunny/crossref_metadata_2025 huggingface dataset:
Rigorous Uncertainty Estimation for MRI Reconstruction
Authors: Wang Ke , Angelopoulos Anastasios , De Goyeneche Alfredo , Kohli Amit , Shimron Efrat , Yu Stella , Malik Jitendra , Lustig Michael
Published: August 2023

Deep-learning (DL)-based MRI reconstructions have shown great potential to reduce scan time while maintaining diagnostic image quality. However, their adoption has been plagued with fears that the models will hallucinate or eliminate important anatomical features. To address this issue, we develop a framework to identify when and where a reconstruction model is producing potentially misleading results. Specifically, our framework produces confidence intervals at each pixel of a reconstruction image such that 95% of these intervals contain the true pixel value with high probability. In-vivo 2D knee and brain reconstruction results demonstrate the effectiveness of our proposed uncertainty estimation framework.
Real-time MRI of speech production at 0.55 Tesla
Authors: Lim Yongwan , Nayak Krishna S.
Published: August 2023

We demonstrate 2D mid-sagittal real-time MRI of speech production at 0.55T by employing a custom designed upper airway coil, spiral-based bSSFP and GRE sequences, and constrained image reconstruction. We found that bSSFP offered superior SNR and tissue contrast compared to GRE, and the quality of images at 0.55T was superior to that commonly reported at 1.5T and 3T field strengths. We attribute this improvement to the significantly reduced off-resonance from air-tissue boundaries at 0.55T, making it possible to leverage bSSFP without suffering from banding artifacts.
Variable Flip, Blip-Up and -Down Undersampling (VUDU) Enables Motion-Robust, Distortion-Free Multi-Shot EPI
Authors: Cho Jaejin , Kim Tae Hyung , Gagoski Borjan , Zhang Zijing , Berman Avery , Liao Congyu , Bilgic Berkin
Published: August 2023

We demonstrate the motion-robustness of multi-shot diffusion imaging using VUDU (Variable flip, blip-Up, and -Down Undersampling) in the brain. VUDU employs FLEET-ordering to acquire all EPI shots of a given slice successively before proceeding to the next slice and maximizes the signal using variable flip angle (vfa) excitation. It also utilizes BUDA (Blip-Up and -Down Acquisition) to eliminate B0 distortion and employs the Hankel low-rank regularization to address shot-to-shot phase variations. VUDU was able to provide high-fidelity diffusion-weighted images from in vivo data acquired during intentional head motion.
Motion insensitive T2-weighted dual-echo steady-state (DESS) imaging of the liver using alternating readout gradients
Authors: Tamada Daiki , Reeder Scott
Published: August 2023

In this work, we present a novel method to reduce motion sensitivity for T2-weighted dual-echo steady-state (DESS) imaging, through the use of a readout alternation (ROA) approach. ROA can be achieved by inverting polarity of gradient pulses in the readout axis, alternating every TR. Bloch equation simulations that included small physiological motion in the liver, and volunteer liver imaging was performed using the proposed method. Simulation and volunteer studies demonstrated that ROA effectively suppresses signal loss and motion-related artifacts.
Circular Echo-Planar Time-resolved Imaging (cEPTI) for Rapid Time-Resolved and Quantitative Imaging
Authors: Wang Nan , Liao Congyu , Srinivasan Siddharth , Cao Xiaozhi , Haldar Justin , Setsompop Kawin
Published: August 2023

EPTI is a highly accelerated time-resolved imaging method for rapid quantitative imaging. To improve the spatiotemporal encoding efficiency of EPTI, we developed a “circular” EPTI sampling trajectory (cEPTI), designed to efficiently traverse a tight circular k-space coverage with full ramp-sampling. A systematic approach was also developed to characterize the noise and effective resolution of the EPTI acquisition and used to guide the optimization of cEPTI’s k-t sampling trajectory. The optimized cEPTI was demonstrated to be capable of producing a 50ms time-resolved series of distortion-free sharp brain images with varying T2* weightings at 1 mm in-plane resolution from a 195ms scan.
DECOMPOSE-STI: decompose sub-voxel diamagnetic and paramagnetic susceptibility tensors
Authors: Chen Jingjia , Gkotsoulias Dimitrios , Jaffe Jennifer , Crockford Catherine , Wittig Roman , Möller Harald E. , Liu Chunlei
Published: August 2023

We investigate susceptibility tensor imaging (STI) reconstruction by separating the diamagnetic from paramagnetic susceptibility tensors using the recently introduced DECOMPOSE method. The resulting para-/diamagnetic susceptibility tensors produce spatially more coherent eigenvectors than conventional STI and it shows the potential to reduce the number of orientations needed for STI.
In vivo quantitative laminar R2* and susceptibility imaging at 0.3 mm in-plane resolution
Authors: Liu Jiaen , van Gelderen Peter , Li Xu , de Zwart Jacco , Lai Kuo-Wei , Sulam Jeremias , Beck Erin , Okar Serhat , van Zijl Peter , Reich Daniel , Duyn Jeff
Published: August 2023

High resolution submillimeter MRI of myelin and iron may enhance our capability to define neural diseases more accurately and at an earlier stage. Susceptibility-weighted MRI methods are intrinsically sensitive to myelin and iron and benefit from the increased contrast-to-noise ratio at 7 T. In this study, we systematically investigated R2* and susceptibility distributions in cortical layers of healthy subjects with 0.3 mm in-plane resolution and 0.4 mm slice thickness. This effort was facilitated by a robust navigator-based motion- and B0-corrected GRE sequence.
In vivo myelin thickness estimates from DIffusion-Prepared Phase Imaging (DIPPI)
Authors: Cottaar Michiel , Wu Wenchuan , Miller Karla , Jbabdi Saad
Published: August 2023

DIPPI is a novel sequence that allows the measurement of the off-resonance field experienced by intra-axonal water, which in myelinated axons is modulated by the surrounding myealin sheath allowing for estimation of the g-ratio. Unlike other g-ratio imaging methods, DIPPI does not rely on combining multiple modalities and can provide g-ratio estimates for individual crossing fibre populations rather than averaged over voxels. We present the first in-vivo DIPPI measurements and correct it for confounds such as subject movement and eddy currents. We then estimate the g-ratio in multiple white matter tracts from the processed off-resonance field maps.
Improved Detection, Description and Efficiency of Multiple Sclerosis Lesions’ Assessment using a Dedicated Software
Authors: Federau Christian , Zhu Guangming , Hainc Nicolin , Paganucci Silvio , Kipp Lukas , Wintermark Max
Published: August 2023

Yearly multiple sclerosis MRI follow-ups require the tedious and time-consuming manual comparing and counting of multiple demyelinating lesions, which can reach hundreds in some cases. We evaluated a semi-automatic software for the efficient assessment of such images, and found that a significant increase in the number of reported new multiple sclerosis lesions can be achieved in two-and-a-half minutes reading on average per case. In contrast, current standard reports missed 80% of the new lesions. In addition, The Jazz software permits the efficient reporting of slowly evolving lesions, an entity growing in clinical relevance and typically overlooked in current reporting.
MTsat is more sensitive to cerebellar myelin abnormality in multiple sclerosis compared to MTR
Authors: Lee Lisa Eunyoung , Vavasour Irene , Hernandez-Torres Enedino , Traboulsee Anthony , Tam Roger , Kolind Shannon , Schweizer Tom , Oh Jiwon
Published: August 2023

Magnetization transfer saturation (MTsat) is suggested to be superior to conventional MT ratio (MTR) in quantifying myelin as it reduces bias from T1 effect and B1 inhomogeneity and is more sensitive to tissue damage. This study aimed to compare the ability of MTsat and MTR to detect cerebellar myelin differences across multiple sclerosis (MS) subtypes and to evaluate whether MTsat or MTR demonstrates stronger correlations with clinical disability. We found that MTsat demonstrated greater group differences and more strongly correlated with clinical disability in cerebellum than MTR suggesting that MTsat may be more sensitive to cerebellar myelin abnormalities than MTR.
Deep-Learning based Wall Shear Stress Assessments from 3D Aortic Shape
Authors: Venkatesh Bharath Ambale , Kachenoura Nadjia , Bouaou Kevin , Dietenbeck Thomas , Swamynathan Rithvik Rithvik , Redheuil Alban , Mousseaux Elie , Lima Joao
Published: August 2023

We develop deep learning for full aortic wall shear stress assessment using 3D aortic shapes and ascending aortic waveforms as input flow. Technically, this would reduce the acquisition time to less than a minute and the post-processing time to a few seconds.
Effect of Temporal Resolution on Flow-Area Aortic Pulse Wave Velocity Measures Using Phase Contrast and Balanced SSFP MRI: A Preliminary Study
Authors: Naren Tarun , Roberts Grant , Wieben Oliver
Published: August 2023

The flow-area (QA) method is a promising phase contrast (PC) technique to assess local aortic pulse wave velocity (PWV). However, validation for reduced temporal resolutions is lacking. Data analysis and automated post-processing are compromised because of varying PC image quality throughout the cardiac cycle. In this study, we acquire PC and bSSFP data at three temporal resolutions and measure QAPWV using PC data alone and by combining PC flow measures with bSSFP areas. We found that the highest temporal resolution datasets (10ms) provide the most accurate PWV measures and the method combining bSSFP and PC was less accurate.
4D Flow MRI Analysis of Flow, Velocity, and Cardiac Flow Compartments in a Swine Model of Pulmonary Hypertension
Authors: Seiter Daniel , Allen Betty , Tabima Diana , Hacker Timothy , Corrado Phil , Oechtering Thekla , Reeder Scott , Chesler Naomi , Wieben Oliver
Published: August 2023

Pulmonary hypertension is a known consequence of left heart failure. However, little is known about the pulmonary vascular and right ventricular changes caused by increased pulmonary venous pressure independent of left heart failure. By surgically banding the inferior pulmonary vein confluence in swine, we created pulmonary venous hypertension without damage to the left heart. Here, we report results from 4D flow MRI analysis of vessel flow, vessel velocity, cardiac flow compartments, and pressures measured via right heart catheterization in this novel model.
High-resolution Spiral First-pass Myocardial Perfusion Imaging at 1.5 T with DEep learning-based rapid Spiral Image REconstruction (DESIRE)
Authors: Wang Junyu , Lozano Patricia Rodriguez , Salerno Michael
Published: August 2023

First-pass contrast-enhanced myocardial perfusion imaging is useful for evaluating coronary artery disease (CAD). Spiral perfusion imaging techniques, using a motion-compensated (SMS-Slice-) L1-SPIRiT reconstruction, are capable of whole-heart high-resolution perfusion imaging. However, this reconstruction is performed off-line and takes ~30 minutes per slice. To address this, we developed a DEep learning-based rapid Spiral Image REconstruction technique (DESIRE) for spiral perfusion imaging at 1.5 T, for both single-slice (SS) and simultaneous multi-slice (SMS) MB=3 and MB=4 acquisitions, to provide rapid and high-quality reconstruction and make rapid online reconstruction feasible. High image quality was demonstrated using the proposed technique.
Rapid Motion Correction with Deep Learning for First-Pass Cardiac Perfusion MRI
Authors: Fan Lexiaozi , Yang Huili , Hsu Li-Yueh , Katsaggelos Aggelos , Allen Bradley , Lee Daniel , Kim Daniel
Published: August 2023

Motion correction (MoCo) is an important pre-processing step for pixel-by-pixel myocardial blood flow (MBF) quantification from cardiac perfusion MRI. It may also improve throughput of visual evaluation of perfusion images. One commonly used method for MoCo is optical flow (OF), which requires a moderate level of computational demand. In this study, we sought to perform rapid MoCo of respiratory motion on cardiac perfusion images using deep learning (DL). Our results show that the proposed DL MoCo performs 418-times faster than the reference OF approach without loss in accuracy.
Investigating Cerebral Perfusion with High Resolution Hyperpolarized [1-13C]Pyruvate MRI
Authors: Hu Jasmine , Vaziri Sana , Bogh Nikolaj , Kim Yaewon , Autry Adam , Bok Robert , Li Yan , Laustsen Christoffer , Larson Peder , Xu Duan , Vigneron Daniel , Gordon Jeremy
Published: August 2023

Acquiring high resolution 7.5 mm2 hyperpolarized [1-13C]pyruvate brain MRI allows for finer spatial delineation of brain structures and can be used to obtain cerebral perfusion parameters. In the healthy volunteers studied, pyruvate rCBV and rCBF were positively correlated to ASL perfusion values. Hyperpolarized pyruvate MRI can be used to assess cerebral metabolism and perfusion within the same study.
Inline Implementation of Motion-Compensated, High-Resolution Myocardial Perfusion Imaging: Initial Experience
Authors: Kunze Karl , Mellor Nina , Moon Tracy , Pushparajah Kuberan , Neji Radhouene , Chiribiri Amedeo
Published: August 2023

This abstract describes a feasibility study for a high-resolution perfusion imaging framework, including a dedicated sampling pattern and a motion compensation framework integrated into temporal regularization and implemented in-line on the scanner with GPU support. The approach was employed successfully in patients with suspected myocarditis at rest, showing superior ability to handle both respiratory and cardiac motion at an image resolution of 1.3 mm2, as compared to a clinical reference perfusion sequence and supported by Late Gadolinium Enhancement imaging findings.
Model-based deconvolution for DSC-MRI: A comparison of accuracy, precision, and computational complexity of transit time distributions
Authors: Sobhan Rashed , Johnson Glyn , Cameron Donnie
Published: August 2023

To identify the optimal model-based deconvolution process for DSC-MRI, four models of transit time distribution (TTD) were compared in terms of goodness and stability of fit, consistency of perfusion estimates, computational complexity, and robustness against noise. Although all models gave similar fits, the gamma function converged faster and more consistently to the global minimum, regardless of the initial guess. Moreover, it gave more accurate and precise perfusion estimates in the presence of noise. We conclude that the gamma function is the most suitable TTD model for perfusion analysis, and may prove useful in urgent clinical situations and multi-centre studies.
Comparison of local SAR and temperature increase between 1.5T and 3T in fetal MRI across five numerical pregnant body models
Authors: Yetisir Filiz , Turk Esra , Estroff Judy , Barnewolt Carol , Adalsteinsson Elfar , Grant Patricia , Wald Lawrence
Published: August 2023

3T can improve fetal MRI compared to 1.5T, but concerns over increased RF safety risk for the fetus exist due to higher field nonuniformity. Previous studies comparing fetal SAR between two field strengths used either a single pregnant body model or artificial pregnant body models. In this study, we compare SAR and temperature increase in the fetus and mother at 1.5T and 3T using 5 anatomically realistic and diverse pregnant body models. Across these models, we find similar or lower levels of fetal SAR and temperature increase at 3T compared to 1.5T.
Structural-functional interplay of the human placenta: in-vivo study using Pseudocontinuous Arterial Spin Labeling
Authors: Link Daphna , Avisdris Netanell , Shao Xingfeng , Ben Sira Liat , Hiersch Liran , Gull Ilan , Wang Danny , Ben Bashat Dafna
Published: August 2023

Adequate placental structure and function are crucial for fetal and maternal health. Here we assessed late-gestation placental perfusion (N=50, GA=31-38 weeks) using pseudocontinuous arterial-spin-labeling and radiomics feature-extraction, and their association with umbilical-cord insertion-site and the risk of fetal-growth-restriction (FGR). Increased blood-flow and arterial-transit-time were detected in our normal cases compared to earlier gestation as reported previously. Perfusion features differences were detected in placentas with marginal compared to central cord-insertion, indicating higher intensity heterogeneity. No differences were found between normal and FGR placentas. This study provides normal late-gestation placental perfusion values based on a large cohort, and implies on structural-functional associations.
Ferumoxytol-Enhanced T2* Mapping of Human Placenta with Fetal Growth Restriction
Authors: Chen Ruiming , Zhu Ante , Johnson Kevin , Bird Ian , Antony Kathleen , Iruretagoyena J. Igor , Reeder Scott , Hernando Diego , Shah Dinesh , Wieben Oliver
Published: August 2023

Fetal growth restriction (FGR) is associated with placental hypoxia, which can be identified by measuring placental T2* value in-vivo. In this pilot study, we acquired T2* maps in 2 subjects in late pregnancy diagnosed with FGR. Mean and histogram of T2* and R2* values in the placenta were analyzed for two timepoints after administration of ferumoxytol reflecting T2* maps dominated by the presence of the iron nanoparticles and a baseline. We observed lower baseline T2* values than previously reported in healthy controls at similar gestation as well as lower baseline T2* values as reported in FGR patients earlier in gestation.
Feasibility of Quantifying Myelin Water Fraction in the Fetal Guinea Pig Brain
Authors: Sethi Simran , Friesen-Waldner Lanette , Wade Trevor , Sarr Ousseynou , Sutherland Brian , Regnault Timothy , McKenzie Charles
Published: August 2023

Myelin water fraction (MWF), a validated marker for myelin lipid, can be used to assess fetal myelination in vivo. Thus, this study aims to demonstrate the feasibility of quantifying fetal MWF. 11 pregnant guinea pigs with 38 fetuses were imaged in a 3T MRI. mcDESPOT was used to quantify MWF in the corpus callosum (CC) of the maternal brain and the CC and fornix (FOR) of the fetal brain. MWF maps were successfully generated in all fetal brains, confirming its feasibility. Maternal MWF results and comparison of fetal CC and FOR MWF results are consistent with published results.
Assessment of pessary position using upright MR imaging of patients with pelvic organ prolapse
Authors: Morsinkhof Lisan , Grob Anique , Straetemans Lianne , Simonis Frank
Published: August 2023

Pessary treatment for pelvic organ prolapse (POP) has a success rate of only 63% and its working mechanism remains unclear. This study applies upright MRI to gain insight into pessary. Patients were scanned in supine and upright position. The pessary was located under the inferior pubic bone in 7 out of 9 patients in upright position, opposed to 1 out of 9 in supine position. This indicates that the pubic bone does not (solely) contribute to the supporting mechanism. The use of upright MRI contributes to knowledge about the working mechanism of the pessary.
CycleSeg-v2: Improving unpaired MR-to-CT Synthesis and Segmentation with pseudo label and LPIPS loss
Authors: Luu Huan Minh , Yoo Gyu-sang , Park Won , Park Sung-Hong
Published: August 2023

Radiotherapy treatment typically requires both CT and MRI as well as labor intensive contouring for effective planning and treatment. Deep learning can enable an MR-only workflow by generating synthetic CT (sCT) and performing automatic segmentation on the MR data. However, MR and CT data are usually unpaired and limited contours are available for MR data. In this study, we proposed CycleSeg-v2 that extends the previously proposed CycleSeg to work with unpaired data. To ensure robust training, we employed LPIPS loss in addition to pseudo label. Experiments with data from prostate cancer patients showed that CycleSeg-v2 improved upon previous approaches.
Hyperpolarized dehydroascorbate reveals ascorbate-mediated oxidative stress increases flux through the pentose phosphate pathway in cancer
Authors: Kim Nathaniel , Berishaj Marjan , de Stanchina Elisa , Shah Manish , Cantley Lewis , Keshari Kayvan
Published: August 2023

HP DHA was demonstrated as an imaging agent for probing the biochemical response to ascorbate therapy in patient derived xenograft (PDX) models of cancer. Changes in DHA/ascorbate metabolism were observed in PDX tumors after prolonged treatment, mirroring the observed treatment response to high dose ascorbate. Metabolomic studies showed that high dose ascorbate therapy induced oxidative stress, leading to increased flux through the pentose phosphate pathway (PPP). DNA damage repair mutants exhibit lower baseline flux through the PPP and are more sensitized to ascorbate induced ROS. These results demonstrate a new method for assessing oxidative stress in vivo using HP DHA.
Comparison of MR spectroscopy cut-off parameters in differential diagnosis between glioma recurrence and radionecrosis
Authors: Pajuelo Dita , Malucelli Alberto , Dezortová Monika , Škoch Antonín , Bartoš Robert , Sameš Martin , Hájek Milan
Published: August 2023

Differential diagnosis between brain tumor recurrence and radionecrosis is still problematic. MR Spectroscopy Imaging (MRSI) is useful in differentiating between these two histologically and radiologically distinct entities. Six methods with different combination of metabolic parameters were used to compare 37 lesions examined by 2D/3D MRSI. The lesional and contralateral comparison of choline-containing compounds and lactate using long echo time achieved the highest sensitivity and specificity. Choline to creatine ratio showed low specificity. The distinction of regressive recurrence as a separate entity is helpful in the effort to discern the complexity of events leading to new enhancing lesions in neurooncologic patients.
The lipid signal in cervical cancer: a 1H MRS pilot study
Authors: Canese Rossella , Dolciami Miriam , Testa Claudia , Manganaro Lucia
Published: August 2023

Cervical cancer (CC) is the fourth most common malignancy and cancer-related mortality cause in women worldwide. A significant portion of these patients are diagnosed as locally advanced cervical cancer (LACC), thus requiring combined therapies. We investigate the role of the lipid signal derived from 1H magnetic resonance (MR)-spectroscopy in assessing response to neoadjuvant chemotherapy of LACC.
MR Molecular Imaging of EDB-Fibronectin for Non-Invasive Monitoring of miR-200c Therapy in Pancreatic Cancer
Authors: Laney Victoria , Hall Ryan , Yeung Grace , Laney Victoria , Apte Suneel , Lu Zheng-Rong
Published: August 2023

PDAC is a highly aggressive malignant cancer and the 3rd leading cause of cancer related deaths in the US. Currently, treatment options for patients are limited due to late detection of the tumors and lack of effective therapies. The aggressive nature of PDAC is in part due to the desmoplastic tumor microenvironment. MiR-200c regulates epithelial-to-mesenchymal transition and extracellular remodeling for effective treatment of aggressive tumors. In this study, we investigate the effectiveness of MR molecular imaging of extradomain-B fibronectin, an extracellular matrix oncoprotein associated with EMT, for non-invasive monitoring of PDAC tumor response to miR-200c therapy in a mouse model.
An untrained deep learning method with model-based regularization for reconstructing dynamic MR images from retrospectively accelerated data
Authors: Slavkova Kalina , DiCarlo Julie , Wadhwa Viraj , Yankeelov Thomas , Tamir Jonathan
Published: August 2023

Acquiring high-resolution MRI data for tissue parameter mapping for quantitative imaging requires additional scan time. As a proof-of-principle, we evaluated the ability of the ConvDecoder architecture regularized with a physical model to reconstruct accelerated variable-flip angle MRI data of the brain for T1-mapping. The performance of our method was compared to non-regularized ConvDecoder, low rank reconstruction, and compressed sensing. Our results suggest that ConvDecoder with physics-based regularization may provide a stopping condition for training that is not dependent on the ground truth data while improving parameter mapping at higher accelerations.
Evaluation of Neural Network Reconstruction of Undersampled Data using a Human Observer Model of Signal Detection
Authors: Herman Joshua , Wong Marcus , Lingala Sajan , Pineda Angel
Published: August 2023

We evaluated images from undersampled data using a U-Net with common metrics (SSIM and NRMSE) and with a model for human observer detection, the sparse difference-of-Gaussians (S-DOG). We also studied how the results vary when changing the loss function and training set size. We saw that the S-DOG model would choose an undersampling of 2X while SSIM and NRMSE would choose 3X. In previous work, human observers also chose a 2X acceleration. The S-DOG model led to the same conclusion as the human observers. This result was consistent with changes in training set size and loss function.
Properties of 2D MR image reconstructions with deep neural networks at high acceleration rates
Authors: Muckley Matthew , Murrell Tullie , Radmanesh Alireza , Knoll Florian , Huang Zhengnan , Sriram Anuroop , Sodickson Daniel , Lui Yvonne
Published: August 2023

We assess the properties of deep neural network-reconstructed brain MR images in the high acceleration regime at factors up to 100. We have three contributions: 1) metrics on model performance from 2- to 100-fold accelerations, 2) a Monte Carlo procedure for scoring the quality of model reconstructions using only subsampled data, and 3) assessment of the acceleration effects on pathology in six cases. Our Monte Carlo procedure can estimate ground truth PSNR with coefficients of determination greater than 0.5 using only subsampled data. Our pathology results were stable in DNN reconstructions up to 8-fold acceleration.
Distortion Free Image Reconstruction using a Deep Neural Network for an MRI-Linac
Authors: Shan Shanshan , Gao Yang , Liu Paul , Whelan Brendan , Sun Hongfu , Liu Feng , Keall Paul , Waddington David
Published: August 2023

The advent of MRI-guided radiotherapy has elevated demand for high geometric fidelity imaging. However, gradient nonlinearity can cause image distortion, which limits the accuracy of radiotherapy. In this work, we develop a deep neural network, namely DFReconNet, to reconstruct distortion free images directly from raw k-space in real time. Experiments on simulated brain datasets and phantom images acquired from an MRI-Linac demonstrated the utility of the proposed method.
Brain Tumor Segmentation Using 3D CMM-Net with Limited and Accessible MR Images
Authors: Choi Yoonseok , Al-masni Mohammed , Kim Dong-Hyun
Published: August 2023

In this work, we investigate the possibility of using a limited number of medical MR images for brain tumor segmentation. This can assist to perform the segmentation task using limited and accessible data in clinical practice. We observed that the FLAIR and T1CE are the most suitable images that maintain comparable segmentation performances similar to the case of using more data (i.e., T1, T2, FLAIR, and T1CE). To further improve the segmentation results, we augment the selected image pair and generate an additional fusion map using the Singular Value Decomposition (SVD).
Magnetic Resonance Spectroscopic Imaging Data Denoising by Manifold Learning: An Unsupervised Deep Learning Approach
Authors: Shamaei Amirmohammad , Starčuková Jana , Kořínek Radim , Starčuk Zenon
Published: August 2023

This work demonstrates an unsupervised deep-learning approach to MRS(I) data denoising, incorporating a non-linear model without relying on MR-theoretical physical prior knowledge. The implemented autoencoder learns the underlying low-dimensional manifold in high-dimensional data vectors representing MRS(I) voxels. The method, developed for denoising water-fat spectroscopic images, was tested against both numerical and acquired phantoms containing milk cream. The proposed method shows results comparable with other techniques in boosting SNR and has been found more robust in low concentration component denoising. Deep learning data denoising for MRSI might result in faster acquisition, vital for MRSI clinical application.
Prospective Motion Correction in Kidney MRI Using Free Induction Decay Navigators
Authors: Ariyurek Cemre , Wallace Tess , Kober Tobias , Koçanaoğulları Aziz , Warfield Simon , Kurugol Sila , Afacan Onur
Published: August 2023

Abdominal MRI scans may require breath-holding to prevent image quality degradation, which can be challenging for patients. In this study, we used free induction decay navigators (FIDnavs) to correct motion prospectively. A short calibration scan was acquired prior to the prospectively corrected scan to create a linear motion model to translate the FIDnav signal into kidney displacement. Shallow, deep and continuous deep breathing scans were acquired with the proposed technique and reconstructed images were compared to those without motion correction. The proposed technique reduces blurriness and motion artifacts in the kidneys by correcting their position prospectively during the MRI acquisition.
Motion-corrected supine breast MRI with online reconstruction
Authors: Isaieva Karyna , Vuissoz Pierre-André , Nohava Lena , Obermann Michael , Laistler Elmar , Fauvel Marc , Dessale Claire , Weber Nicolas , Felblinger Jacques , Odille Freddy
Published: August 2023

A standard breast MRI protocol implies prone position. Supine position has multiple advantages; however, it requires motion correction. In this work we present our results on retrospective nonrigid motion correction of supine breast MRI on 7 healthy volunteers. A respiratory belt was used to capture the chest movements. Images were reconstructed online and fully automatically, including physiological data recording and its transfer to the reconstruction server. It was shown that application of the selected motion correction method improves image sharpness on 32-47% which was cofirmed by visual observations.
Comparison of image and extracorporeal derived arterial input functions for DCE-MRI in mice using an multimodal cross-validation approach
Authors: Gierse Florian , Cufe Juela , Maus Bastian , Kronenberg Katharina , Claesener Michael , Dorten Paulina , Schäfers Klaus , Hermann Sven , Karst Uwe , Faber Cornelius , Schäfers Michael , Büther Florian , Backhaus Philipp
Published: August 2023

Quantitative precise measurements of the dynamic arterial blood concentration (AIF) are challenging in perfusion MRI. As solution an extracorporeal circulation approach for the AIF determination with two different vascular access ways is presented and cross validated with injection of radioactive contrast agent derivatives. Independent of the vascular access way, extracorporeal derived AIFs point towards a high quantitative precision, although dispersion must be considered. However, deconvolution methods based on single gamma variate functions end up in plausible AIFs. The use of novel rapid imaging techniques in connection with extracorporeal AIFs indicates high potential for precise quantitative dual PET/MRI Pharmacokinetic-Modeling in mice.
Mapping Rodent Brain Mechanical Properties In Vivo with Magnetic Resonance Elastography and Nonlinear Inversion
Authors: Williams L. , Milbocker Katrina , Sullivan Seth , Smith Ian , Brengel Eric , LeBlanc Gillian , Klintsova Anna , McGarry Matthew , Johnson Curtis
Published: August 2023

Developing preclinical MRE techniques that are comparable to human MRE is important for translational studies. This pilot study investigates the efficacy of the nonlinear inversion algorithm on rat brain MRE data. Whole-brain MRE scans were performed on female, Long-Evans rats using a custom MRE-EPI sequence and piezoelectric actuator with a resolution of 0.25 mm isotropic and with 600 Hz vibration. NLI parameters were adjusted for brain size and frequency. The resulting shear stiffness and damping ratio maps exhibited strong contrast between different anatomical regions. These results validate the use of NLI in preclinical MRE settings.
Quasi-Diffusion Imaging: A model-based alternative to Diffusional Kurtosis Imaging
Authors: Barrick Thomas , Spilling Catherine , Storey Ian , Hall Matt , Howe Franklyn
Published: August 2023

Quasi-Diffusion Imaging (QDI) is based on a model of diffusion dynamics that assumes diffusion is locally Gaussian within a heterogeneous tissue microstructural environment. We show here that QDI provides a compelling model-based alternative to Diffusional Kurtosis Imaging (DKI). Tensor measures determined by QDI are highly correlated with DKI, but exhibit greater parameter independence, indicating that DKI study results showing sensitivity and specificity to disease could be improved using QDI. As QDI also overcomes the limitations of DKI and can be acquired reproducibly in clinically feasible time it is a non-Gaussian diffusion imaging technique that overcomes barriers to clinical translation.
Does One Size Fit All? Reconstructing Crossing Fibers in Diffusion MRI using Spherical Deconvolution with Local Response Functions
Authors: Eichner Cornelius , Paquette Michael , Gerbeth Hannah , Jäger Carsten , Bock Christian , Gallardo Guillermo , Möller Torsten , Crockford Catherine , Wittig Roman , Weiskopf Nikolaus , Friederici Angela , Anwander Alfred
Published: August 2023

We present Local Spherical Deconvolution (LSD), a diffusion MRI deconvolution method to reconstruct crossing fiber directions in the brain. In contrast to previous approaches which assumed a single deconvolution kernel for the entire brain, LSD utilizes information theory to identify an optimal kernel in each image voxel. Using a high-resolution post-mortem chimpanzee brain, we show that fibers are reconstructed with LSD with increased precision and a reduced number of false peaks compared to conventional methods. A test-retest analysis supports the stability and accuracy of LSD.
Network analysis of multiple sclerosis using pair-wise matched controls and cohesive parcellation of rsfMRI
Authors: Nemani Ajay , Koenig Katherine , Huang Xuemei , Lowe Mark
Published: August 2023

Multiple sclerosis (MS) is characterized by degenerative changes in white matter, resulting in motor and cognitive deficits. The corresponding damage to functional brain networks is not well understood. We studied several graph theoretic network features of multiple sclerosis patients imaged with rsfMRI. Using a data-driven parcellation designed for optimal node-based representation as well as sex and age-matched controls, we find no significant differences. This result was robust to individual and group parcellations, as well as paired and group comparisons. This differs from previous studies based on standard parcellations and pooled group comparisons. Methodologic reasons for the different observations are discussed.
Effect of limited segmentation performance on regional qMRI parameter estimations using FSL FIRST in anatomical regions with poor T1 contrast
Authors: Salman Fahad , Bergsland Niels , Dwyer Michael , Weinstock-Guttman Bianca , Zivadinov Robert , Schweser Ferdinand
Published: August 2023

Most T1w imaging sequences produce only weak deep gray matter (DGM) contrast compared to iron-sensitive techniques such as QSM. In particular, using multi-modal information in both template generation and brain normalization steps has the potential to result in improved segmentation performance. In this study, we compared FIRST to a custom multi-contrast T1w-QSM atlas segmentation approach for estimating thalamic volumes and susceptibility. Our study suggested that an advanced atlas-based approach may result in better regional segmentations of regions with weak T1w contrast and result in more accurate parameter estimates.
Gray Matter Correlates of Patient-Reported Indices of Disability in Multiple Sclerosis
Authors: Sweidan Wafaa , Chen Jenny , Ades-Aron Benjamin , Bacon Tamar , Lee Matthew , Coelho Santiago , Novikov Dmitry , Shepherd Timothy , Kister Ilya , Fieremans Els
Published: August 2023

In a cohort of 172 MS subjects, we identified thalamic atrophy as a significant gray matter correlate of patient-reported indices of motor disability.
Comparing myelin-sensitive markers MWF, ihMTR, and MTsat in healthy and normal-appearing brain tissue and multiple sclerosis lesions
Authors: Berg Ronja , Pongratz Viola , Lauerer Markus , Amthor Thomas , Gilbert Guillaume , Menegaux Aurore , Zimmer Claus , Sorg Christian , Doneva Mariya , Vavasour Irene , Mühlau Mark , Preibisch Christine
Published: August 2023

Measurement of myelin concentration could provide valuable information on the integrity of brain tissue. Several myelin-sensitive magnetic resonance imaging methods have been developed. Here, we compared myelin water fraction (MWF), inhomogeneous magnetization transfer ratio (ihMTR) and magnetization transfer saturation (MTsat) in healthy volunteers and patients with multiple sclerosis (MS). We found highest correlation between MWF and ihMTR but all three measures showed clearly reduced values in MS lesions compared to healthy or normal-appearing white matter. However, the measures varied in differentiating between various WM regions and between peri-lesional tissue and more distant normal-appearing WM.
Differences in myelin measures between slowly evolving and non-slowly evolving lesions
Authors: Vavasour Irene , Elliott Colm , Arnold Doug , Gaetano Laura , Clayton David , Magon Stefano , Bonati Ulrike , Wei Wei , Traboulsee Anthony , Kolind Shannon
Published: August 2023

Multiple sclerosis (MS) slowly evolving lesions (SELs) are defined on MRI as contiguous regions of pre-existing lesions with constant and concentric local expansion on conventional T1-weighted and T2-weighted images. Myelin-related changes using myelin water fraction (MWF) and magnetization transfer ratio (MTR) in SELs and non-SELs were measured over 192 weeks in patients with relapsing MS. SELs showed reduced myelin measures at baseline compared to non-SELs. Furthermore, over the 4 years, only SELs, and not non-SELs, showed a significant mean decrease in MWF and increase in T1. Both results are indicative of progressive demyelination in this subgroup of chronic lesions.
Analysis of Fluid-Structure Stability from 4D Flow MRI to Predict Aortic Dilation
Authors: Zhao Tom , Elisha Guy , Johnson Ethan , Halder Sourav , Smith Ben , Allen Bradley , Markl Michael , Patankar Neelesh
Published: August 2023

We present a novel analysis of 4D flow MRI in the thoracic aorta that identifies fluid structure instabilities, which are elevated in a cohort of 117 suspected-aortopathy patients as compared to 100 healthy subjects, and which are predictive of later complications shown in a follow-up analysis for 72 patients in the cohort.
Free-Running 5D Flow MRI: Impact of Cardiac Temporal Resolution on Flow Quantification
Authors: Weiss Elizabeth , Rigsby Cynthia , Robinson Joshua , Baraboo Justin , Ma Liliana , Falcão Mariana , Roy Christopher , Stuber Matthias , Markl Michael
Published: August 2023

The flexible reconstruction of 5D flow MRI data may be particularly beneficial in pediatric cases where cardiac cycle length varies greatly. We compared flow measurements from 5D flow and 2D phase contrast. 5D flow data was reconstructed using either a cardiac bin width of 40ms or that matching the 2D phase contrast reconstruction. We find excellent correlation of both 5D flow reconstructions with 2D phase contrast. There is overestimation of arterial flow measures by 5D flow, with most overestimation by the short temporal resolution reconstruction. Further study should additionally compare with 4D flow MRI.
Automatic analysis of cardiovascular magnetic resonance 2D phase contrast CMR imaging
Authors: Mariscal-Harana Jorge , O'Hanlon Ciaran , Marquez Carlota Asegurado , Petalcorin Marwenie , Razavi Reza , King Andrew , Ruijsink Bram , Puyol-Antón Esther
Published: August 2023

Cardiovascular magnetic resonance (CMR) based flow volume quantification in the great thoracic vessels is used in the assessment of several cardiovascular diseases such as valvular regurgitation, cardiac shunts and vascular health. Clinically, flow volume quantification is often performed based on semi-automatic segmentation of a vessel throughout the cardiac cycle in a manually positioned 2D phase-contrast (PC) CMR plane. In this work, we proposed a quality-controlled AI-based framework for automatic flow quantification from a full CMR scan that includes automated view selection. Results show high accuracy in view selection and excellent agreement between manual and automated flow quantification analysis.
Multi-delay ASL perfusion imaging: impact of modeling dispersion and interaction with denoising strategies
Authors: Monteiro Sara , Pinto Joana , Chappell Michael , Fouto Ana , Viana-Baptista Miguel , Vilela Pedro , Figueiredo Patrícia
Published: August 2023

Arterial spin labeling (ASL) acquisitions at multiple post-labeling delays allow for appropriate kinetic models to be fitted to the data, potentially providing more accurate perfusion quantification. We investigated the influence of denoising strategies based on repetition averaging and ICA, together with the choice of an extended kinetic model with or without dispersion, on multi-delay ASL measurements from a group of small vessel disease patients and their age-matched controls. While ICA denoising generally improved model fitting, repetition averaging interacted with modeling dispersion and subject group, significantly impacting the estimation of perfusion and macrovascular contributions, mostly in arterial locations and with pathology.
The minimal processing pipeline for arterial spin labeling data from the Human Connectome Project Lifespan studies of Aging and Development
Authors: McConnell Flora Kennedy , Toner Jack , Kirk Thomas , Suzuki Yuriko , Craig Martin , Coalson Timothy , Harms Michael , Glasser Matthew , Chappell Michael
Published: August 2023

The arterial spin labelling (ASL) data from the Human Connectome Project (HCP) Lifespan studies can provide a source of unusually high-resolution hemodynamic measures from >2500 individuals with ages 5-21 and 37-100+. This work presents a summary of the minimal ASL processing pipeline used to provide pre-processed calibrated perfusion and arterial arrival time measurements for the cortical surface and subcortical volumes, from these individuals. The pipeline accounts for slice-wise image intensity variations resulting from the simultaneous multi-slice acquisition used to achieve high spatial resolution. These measures and this pipeline will be made available to the global neuroscience and neuroimaging communities.
F0 determination at the labeling plane: the neglected factor for successful pCASL perfusion MRI
Authors: Vaclavu Lena , van de Ven Kim , van Osch Matthias
Published: August 2023

In perfusion imaging with arterial spin labeling (ASL), the labeling plane is located further away from the isocenter of the scanner, than the imaging volume. This can result in offsets in resonance frequencies which can lead to imperfect inversion and hence lower labeling efficiency. In this study, a perfusion phantom is used to study the influence of off-resonance on two arterial spin labeling schemes, in order to determine whether an additional F0 determination at the labelling plane is the redeeming factor for successful ASL MRI independent of the labeling scheme used.
Feasibility of high-quality uterus DWI with segmented phase-encoding and reduced FOV
Authors: Zhang Yajing , Wu Zhigang , Hu Xiuquan , Jiang Guangyu , Zhang Jing , Wang Jiazheng , Zhao Yan
Published: August 2023

Diffusion-weighted imaging (DWI) of uterus has been crucial for providing useful information in differentiating pathologies such as uterine fibroids and adenomyosis. In this study, we aim to investigate the feasibility of high quality uterus DWI through a segmented phase-encoding acquisition with reduced FOV.
Performance Evaluation of high resolution T2-TSE sequence based on simultaneous multi-slice (SMS) in Female Pelvis MRI
Authors: Wang Hongchao , Jiang Yueluan , Wang Zhuo , Zhang Lei , Shao Zhiqing , Sun Yang , Wang Xiaoye
Published: August 2023

Simultaneous multi-slice (SMS) acquisition is a different option for accelerating 2D TSE MRI through the excitation of multiple slices simultaneously and is associated with much smaller SNR loss than parallel acceleration. In this study, we applied both parallel imaging and multiple slices simultaneous imaging technique to accelerate T2WI TSE of female pelvis MRI. Comparing to conventional TSE sequence, 25% of time could be reduced with more slices with thinner thickness using SMS acceleration with similar performances at 3T. SMS-PI-TSE is a feasible acceleration technique in Pelvis MRI.
A Pilot Evaluation of DKI in Characteristics and Diagnosis of Ovarian Cancer of p53 Status
Authors: Chen Shiqi , Chen Yulin , Li Ye , Liu Ailian
Published: August 2023

The identification and treatment of ovarian cancer(OC) has always been a problem that plagues us[1]. Mutations in the p53 gene showed significantly up-regulation in human OC tissues and was closely associated with the development of human OC. This work aimed at exploring the value of Diffusion kurtosis imaging (DKI) for characteristics and diagnosis of ovarian cancer of p53 status. The results showed that FA provided a promising performance (AUC =0.742 , sensitivity = 100%， specificity = 43.7%) in evaluating p53 status and OC.
Application value of radiomics methods based on DTI sequence FA map for differentiating squamous cell carcinoma from cervix adenocarcinoma
Authors: Ma Changjun , Tian Shifeng , Liu Ailian
Published: August 2023

Through high-throughput quantitative feature extraction, the imaging omics method achieves non-invasive analysis of tumor heterogeneity and improves the accuracy of imaging examination in assisting clinical decision making in tumor screening, diagnosis and prognosis prediction. This study intends to explore the value of imaging omics method based on DTI sequence FA map in differentiating CSCC and CA, and provide imaging basis for the formulation of individualized precision treatment plan for CC patients.
Comparison of single-shot EPI DWI and multi-shot EPI DWI in prostate MRI
Authors: Kido Ayumu , Yamamoto Akira , Takeuchi Mitsuru , Ueda Yu , Neelavalli Jaladhar , Tamada Tsutomu
Published: August 2023

Single-shot EPI (sshEPI) DWI still suffers from distortion and blurring. Multi-shot EPI (mshEPI) DWI called IRIS enables to reduce image distortion and blurring. A total of 142 patients with suspected prostate cancer (PC) underwent mpMRI including sshEPI DWI and IRIS under the same scan time. The image quality and diagnostic performance of the lesions were compared between sshEPI DWI and IRIS. IRIS improved image distortion and blurring compared to sshEPI DWI, and also suggested a similar or higher diagnostic performance compared to sshEPI DWI.
Semi-Quantitative Analysis of Dynamic Contrast-Enhanced Magnetic Resonance Lymphangiography in the Legs of Primary Lymphoedema Patients
Authors: Mills Michael , Van Zanten Malou , Pearce Julian , Ho Bernard , Gordon Kristiana , Mortimer Peter , Ostergaard Pia , Howe Franklyn
Published: August 2023

Despite its prevalence, methods for investigating lymphoedema (chronic tissue swelling due to abnormal lymphatic functioning) remain limited. Dynamic Contrast-Enhanced Magnetic Resonance Lymphangiography (DCE-MRL) allows identification of lymph vessels in both healthy and lymphoedematous limbs, however quantitative analyses are lacking. DCE-MRL data was acquired for 30 minutes in lymphoedematous (n=7) and healthy limbs (n=4), with estimates of lymphatic vessel signal characteristics compared between groups. Maximum enhancement compared to baseline was significantly increased in healthy volunteers, while other metrics were similar. Larger groups and longer imaging sessions are likely required to detect additional differences.