bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of Brain Activity during a Lower Extremity Sensorimotor Task using CEST MRI at 3T
Authors: Tain Rongwen , Ellingson Benjamin , Stark Craig , Guzman Catalina Raymond , Sharp Kelli , Smith Joanne
Published: August 2023

A recent animal study demonstrates that CEST MRI is a potential tool to detect neuronal activation. In this work, we study CEST effects in the secondary somatosensory cortex during rest and during a goal-directed lower extremity sensorimotor task (small amplitude left leg lifting) in 10 healthy participants. Significantly higher CEST effects were observed in participants performing the leg task in the secondary somatosensory cortex, but not in a prefrontal cortex control region. This indicates that CEST MRI is a potential tool to detect brain metabolism associated with neuronal activity in human subjects at 3T.
Amide proton transfer imaging for differentiation of glioblastoma from brain metastasis
Authors: Kaewumporn Utarat , Wongsawaeng Doonyaporn , Piyapittayanan Siriwan , Ngamsombat Chanon , Chaysiri Panid , Kittikornchaichan Janiya , Ningunha Kritdipha , Tisavipat Nanthasak , Itthimathin Titima , Rayaroji Ketkanok , Chawalparit Orasa
Published: August 2023

Until now, the differentiation between glioblastoma and brain metastasis still has some limitations and inconclusive findings.

This study aimed to use amide proton transfer (APT)-weighted imaging to differentiate glioblastoma from brain metastasis.

We found that by quantitative assessment, the APTw value in enhancing solid portion and peritumoral high FLAIR area of glioblastomas were significantly greater than that of brain metastases. The APTw color map also showed higher signal at the peritumoral high FLAIR area in glioblastomas than metastasis by visual assessment.
Machine Learning-Based Radiomics Predicting the IDH1 Genotype of Diffuse Gliomas
Authors: Zhao Qirui , Li Zongfang , Lu Yi , Bao Han , Hou Zujun , Chen Liuyang , Xie Wei , Wang Qing , Zhao Wei , Koh Tong-San , Nie Lisha
Published: August 2023

The current study aims to evaluate the value of susceptibility weighted imaging (SWI) and contrast-enhanced T1-weighted imaging (CE-T1WI) radiomics features in predicting isocitrate dehydrogenase1 (IDH1) genotype of diffuse gliomas and build prediction models. It was concluded that SWI and CE-T1WI radiomics features can effectively predict the IDH1 genotype of diffuse gliomas, and CE-T1WI performed better. By combining SWI with CE-T1WI radiomics features, the prediction performance can be improved.
Automated machine learning-based brain lesion segmentation on structural MRI acquired from traumatic brain injury patients
Authors: Yildiz Ilkay , Garner Rachael , Morris Michael , Tejeda Jesus , Real Courtney , Blanco Manuel , Vespa Paul , Duncan Dominique
Published: August 2023

Traumatic brain injury (TBI) can cause severe disorders, including post-traumatic epilepsy (PTE). Lesion segmentation is an MRI-based analysis to identify brain structures that correlate with PTE development post-TBI. Unfortunately, manual segmentation, considered the gold standard, is highly tedious and noisy. Thus, we propose the first automated machine-learning based lesion segmentation method for MRI of TBI patients enrolled in the Epilepsy Bioinformatics Study for Antiepileptogenic Therapy (EpiBioS4Rx). Experimental validation demonstrates considerable visual overlap of lesion predictions and ground-truths with 61% precision. Early and automated lesion segmentation via our approach can aid experts in MRI analysis and successful PTE identification following TBI.
Preferential utilization of acetate in human meningiomas
Authors: Ijare Omkar , Baskin David , Powell Suzanne , Pichumani Kumar
Published: August 2023

Meningiomas are the most frequently reported central nervous system (CNS) tumors, accounting for 37% of all CNS tumors. Atypical meningiomas (WHO grade-II) show increased cellular proliferation and recurrence. Currently, no chemotherapy is part of the standard of care for meningiomas, and surgery followed by radiotherapy is the mainstay of treatment. Metabolism is the key to many biological processes including tumorigenesis. Unravelling metabolic phenotypes of various histological subtypes of meningiomas will identify new targets for the therapeutic intervention of these tumors. Here, we investigate the in vivo metabolism of [U-13C]glucose and [1,2-13C]acetate in meningioma patients using 13C NMR based isotopomer analysis.
ITSS vasculature volume and Radiomics Features from MR SWI: Performance in Glioma Grading
Authors: Bhattacharjee Rupsa , Gupta Rakesh , Patir Rana , Vaishya Sandeep , Ahlawat Suneeta , Singh Anup
Published: August 2023

Majority of the glioma studies rely on using radiomic-features extracted only from conventional MRI and noticeably limited in SWI. Main objective of the current study is to evaluate the role of SWI in glioma grading aided by machine-learning (ML) methods, in terms of ITSS-vasculature-volume(IVV), radiomic features and by combining both. We conclude SWI to be the one of the useful sequences in the glioma-analysis as it contributes to calculate the IVV, which can singlehandedly improve the glioma grading. When IVV is combined with radiomic-analysis used in combination with PCA feature reduction and RF ML classifier, the performance is marginally improved.
Tissue Sodium Concentration Quantifies Cell Response after Radiation Therapy with Stereotactic Radiosurgery
Authors: Adlung Anne , Mohamed Sherif , Hoesl Michaela , Giordano Frank , Probst Eva Neumaier , Schad Lothar , Ruder Arne
Published: August 2023

We investigated TSC within Gross Tumor Volume (GTV), and surrounding tissue and healthy tissue (HR). 12 patients with a total of 14 GTV was included. 23Na MRI were acquired at three different time-points (2days pre-, 5days post-, 40days post-SRS). TSC was measured within GTV, HR and isodose-areas between 2 and 18Gy at all time-points. Results show changes in TSC within GTV shortly after SRS and subsequent TSC recovery. TSC was higher within higher isodose-areas showing a correlation of radiation exposure and TSC. Findings suggest that TSC might be able to quantify cell response to radiation of tumorous and healthy tissue.
Utility of T1WI and T2 FLAIR for Diagnosis of Parkinson’s Disease Using Radiomics
Authors: Wang Di , Lou Baohui , Wang Sicong , Wu Pu-Yeh , Li Chunmei , Chen Min
Published: August 2023

Radiomic features of bilateral RN and SN based on T1WI and T2 FLAIR from 100 PD patients and 100 healthy controls showed good performance in differentiation of PD, the radiomic model of combine T1WI and T2 FLAIR had best performance than individual T1WI and T2 FLAIR. Radiomics may provide MR imaging biomarkers for PD, and the routine MR sequence may help to diagnose PD using radiomics.
Development of noninvasive DCE based method to estimate tumor interstitial Fluid Pressure in Mouse Models for Pancreatic Ductal Adenocarcinoma
Authors: Paudyal Ramesh , LoCastro Eve , Russell James , Wolansky Ivan , Lekaye Carl , Deasy Joseph , Humm John , Shukla-Dave Amita
Published: August 2023

Pancreatic cancer accounts for about 3% of all cancer-related deaths in the US. An elevation of interstitial fluid pressure (IFP) is a major barrier to drug delivery in solid tumors. Noninvasive estimation of IFP as a biomarker in typically inaccessible tumors is a significant step toward assessing tumor response to therapy. We applied well-recognized fluid flow in porous media to mouse models of pancreatic ductal adenocarcinoma DCE-MRI data using extended Tofts' model-derived permeability maps with tumor-appropriate tumor geometry. Initial results suggest that after validation, IFP can be imaging biomarkers of early response to therapy.
Anatomical, functional and dynamic MRI features of the G144 GBM model developed in NOD-SCID mice
Authors: Arias-Ramos Nuria , Cardoso Ana M. , Jurado Amália S. , Castro M. Margarida C.A. , Pedroso de Lima Maria C. , López-Larrubia Pilar
Published: August 2023

Preclinical models are needed to study glioblastoma multiforme, the most lethal malignant brain tumor. Human G144-glioblastoma stem cells have been used in in vitro studies but there are few studies in vivo, especially using MRI approaches. We aimed to evaluate in vivo, for the first time to our knowledge, a G144 glioblastoma model by multiparametric-MRI. NOD-SCID mice were orthotopically injected with G144 cells, tumor was characterized by multiparametric-MRI and dynamic contrast enhancement studies. G144 tumors presented heterogeneous imaging pattern compared to other GBM models with higher contrast uptake areas and edema related features.
Intravoxel incoherent motion diffusion-weighted imaging for monitoring the anti-angiogenesis efficacy in a C6 glioma rat model
Authors: Hou Weishu , Li Xiaohu , Pan Hongli , Xu Man , Bi Sixing , Shen Yujun , Zhang Yong , Qian Yinfeng , Yu Yongqiang
Published: August 2023

The purpose of this study was to investigate the feasibility of intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) in evaluating early effects of antiangiogenic therapy in a C6 glioma rat model. Twenty-six glioma orthotopic rat models were successfully established 14-16 days after C6 cell inoculation and randomly divided into two groups. The rats in the treated group were administered with Bev while the rats in the control group were administered with vehicle. IVIM-DWI showed significantly decreased D* values and increased ADC and D values corresponding to histological staining in Bev treated tumors.
In vivo longitudinal characterization of hepatocellular carcinoma based on viscoelasticity and water diffusivity in an orthotopic mouse model
Authors: Garczyńska Karolina , Häckel Akvile , Schellenberger Eyk , Kühl Anja , Braun Jürgen , Savic Lynn , Sack Ingolf , Guo Jing
Published: August 2023

The biophysical properties of hepatocellular carcinoma (HCC) and surrounding liver tissue were investigated longitudinally in a syngeneic, orthotopic mouse model using noninvasive quantitative imaging. In vivo MR elastography (MRE) and diffusion weighted imaging (DWI) were conducted prior to cancer cell implantation and three times during tumor progression. Our preliminary results suggest the involvement of the surrounding liver in terms of changes in viscoelasticity and restricted water diffusion over 6 weeks post implantation, while the HCC appeared to be stiffer and less viscous than the liver at 6 weeks.
Ex vivo 7T MRI of resection specimen of oral cancer to improve margin control.
Authors: de Koning Klijs , Noorlag Rob , van der Toorn Annette , Breimer Gerben , Dankbaar Jan Willem , de Bree Remco , Philippens Marielle
Published: August 2023

We validated the measured resection margins of the surgical specimens of tongue carcinoma on 7T ex vivo MRI with histopathology using T2 weighted MRI. In 3D T2wTSE (250 μm3) with an acquisition time of 15-20 minutes, the resection margins was undestimated by 0.5 mm (+/- 1.3 mm). This will be developed into a clinical study with immediate re-resection during surgery to prevent adjuvant (chemo)radiotherapy, which is associated with radiation induced side effects.
QSM, R2* and correlation thereof as qMRI measures of iron and myelin reflect tissue changes in Huntington’s disease
Authors: Oros-Peusquens Ana-Maria , Dadsena Ravi , Dogan Imis , Reetz Kathrin , Shah N. Jon
Published: August 2023

QSM and R2* are quantitative MRI parameters sensitive to iron and myelin content, and their correlation provides further insight into the chemical form of iron. These are the tissue properties which are most affected by Huntington’s disease, besides volumetric changes. We investigate by multiparametric qMRI changes induced by HD in 18 gene-carriers by comparison to matched healthy controls. These qMRI changes are significant in several cortical and subcortical regions and correlate with clinical measures of HD, including CAG mutation length. Although the interpretation of correlations between parameters is not unambiguous, insights into tissue chemical and micro-structure are enabled.
Sub-Normothermic Ex-Vivo Perfusion of Porcine Kidney Grafts Improves Energy Metabolism: 31P-MRSI Analysis
Authors: Songeon Julien , Agius Thomas , Klauser Antoine , Longchamp Grégoire , Ruttimann Raphael , Corpataux Jean-Marc , Longchamp Alban , Lazeyras François
Published: August 2023

Improved preservation strategies for the storage of graft collected after circulatory death could increase the number of kidneys available and improve patient survival. Warm (22 and 37°C) ex-vivo perfusion has emerged as a feasible strategy for organ recovery, but the underlying mechanism remains elusive. Using phosphorus magnetic resonance spectroscopic imaging (31P-MRSI) and histological scoring, we evaluated kidney viability and adenosine triphosphate (ATP) production during sub-normothermic ex-vivo kidney perfusion (SNOP) versus hypothermic machine perfusion (HMP) in a porcine kidney autotransplantation model.
MR imaging of Zebrafish with mitochondria diseases
Authors: Magnitsky Sergey , Sharma Sonal , Falk Marni
Published: August 2023

We created a high-resolution MR imaging atlas of wt. and three mutants (OPA1, FBXL4 and SURF1) of Zebrafish models of human mitochondria disorders. Three age groups of animals were analyzed and organ volume was measured. Image analysis revealed that the brain and spinal cord were significantly smaller in OPA1 mutant than in wt. animals. This study showed that the MRI atlas is useful for the characterization of Zebrafish models. We demonstrated that high-resolution 3D MRI atlas provides comparable with the histology resolution, allows to observe and evaluate the entire animal, and requires less effort to create a histological atlas.
Longitudinal metabolic and morphometric characterization of a knock-in mouse model of SpinoCerebellar Ataxia Type 7
Authors: Pérot Jean-Baptiste , Niewiadomska-Cimicka Anna , Brouillet Emmanuel , Trottier Yvon , Flament Julien
Published: August 2023

SpinoCerebellar Ataxia Type 7 (SCA7) is an autosomal dominant degenerative disease defined by neurodegeneration of the retina and cerebellum. While gene silencing therapeutic strategy is developing, there is a need of biomarkers for evaluation of their efficacy. Here we characterize a recent knock-in mouse model of SCA7 with in-vivo longitudinal MRI and MRS. SCA7140Q/5Q display a wide range of phenotypes, including morphological and metabolic alterations in key brain structures. Our longitudinal protocol allowed better understanding of the chronology of these alterations and offers pertinent biomarkers for evaluation of therapies using the SCA7140Q/5Q model.
Diffusion magnetic resonance imaging in genetic and idiopathic dystonias
Authors: MacIver Claire , Jones Derek , Tax Chantal , Peall Kathryn
Published: August 2023

Dystonia is a hyperkinetic movement disorder involving repetitive or sustained muscle contractions. Its pathophysiology is poorly understood, limiting therapeutic advancement. A systematic literature review on diffusion MRI in dystonia was performed to gain insight into microstructural white matter changes that may contribute to pathology. Of 403 identified records, 40 met the criteria for inclusion. The most consistent diffusion abnormalities for both genetic and idiopathic dystonia forms were lower FA values or reduced number of tractography streamlines in regions connecting brainstem, cerebellum, basal ganglia and sensorimotor cortex, with some genotype and phenotype specific differences identified.
Data-driven heatmap clustering approach to analyzing structural connectomes
Authors: Reddick Wilburn , Teague Jordan , Song Ruitian , Glass John , Jacola Lisa
Published: August 2023

Heatmap differences between 336 patients treated for ALL and 59 age-similar controls were calculated for a limited set of reproducible edges and clustered using an agglomerative hierarchical clustering that identified four clusters with unique connectivity. Differences in edges demonstrated patterns of lower (group 2), higher (group 4), or mixed (group 1 & 3) connectivity relative to controls. Neurocognitive performance was substantially below normal on measures of memory (DSF – groups 2 & 3; DSB - group 1; Visual matching – group 2). This data driven approach was able to identify four distinct groups of patients with unique connectivity profiles and cognitive performance.
BIDScoin: A user-friendly application to convert imaging data to the Brain Imaging Data Structure
Authors: Zwiers Marcel , Pernet Cyril , Galassi Anthony , Oostenveld Robert
Published: August 2023

Sharing neuroimaging data is an important development that has the potential to be scaled up with the new Brain Imaging Data Structure (BIDS) standard. Existing tools to converting data to BIDS often require programming skills or are tailored to specific institutes, datasets or data formats. Here we introduce BIDScoin, a cross-platform, flexible, free and open-source converter that provides a graphical user interface to help users finding their way in the BIDS standard, and supports plugins to extend its functionality. We show its design and demonstrate how it can be applied to a downloadable tutorial dataset.
Multivariate analysis of morphometric and quantitative magnetic resonance imaging metrics in aging and Alzheimer’s disease
Authors: Bussy Aurelie , Patel Raihaan , Salaciak Alyssa , Farzin Sarah , Tullo Stephanie , Pelleieux Sandra , Villeneuve Sylvia , Poirier Judes , Breitner John , Devenyi Gabriel , Tardif Christine , Chakravarty M. Mallar
Published: August 2023

Morphometric and quantitative magnetic resonance imaging techniques have rarely been used simultaneously to characterise healthy aging and Alzheimer’s disease (AD) progression. Here, we are extracting four vertex-wise cortical metrics : cortical thickness, surface area, T1 value (myelin) and T2* values (iron). All these metrics were analysed using non-negative matrix factorization and linear models. Overall, cortical thinning seemed to be linked to both aging and AD progression, while decrease in myelin seemed to be a phenomenon mostly related to aging. No significant patterns of changes were seen in the prodromal phase of AD.
Characterising the impact of distortion correction in high-resolution 3D GRE R2* mapping at 7T.
Authors: Dymerska Barbara , Josephs Oliver , Callaghan Martina
Published: August 2023

R2*-mapping delivers quantitative information about tissue microstructure. We investigate the scale of image distortions in high-resolution, bipolar, multi-echo GRE acquisitions at 7T and their effects on R2*-mapping. We study reduction in variance by applying field map-based distortion correction while also considering the confounding effect of local smoothing. We show that for regions with signal displacement > 0.5 voxels the reduction in variance comes largely, not from smoothing, but from the appropriate repositioning of the tissue signal. Therefore, correcting distortions, also in sub-voxel regime, improves data consistency in bipolar GRE acquisitions, facilitating more robust R2*-mapping in high-resolution laminar studies for instance.
Analysis on Echo Placement for Multi-echo Proton Resonance Frequency Shift Thermometry
Authors: Nouwens Sven , Sumser Kemal , Paulides Maarten , de Jager Bram , Heemels Maurice
Published: August 2023

Proton resonance frequency shift based MR thermometry is widely used to non-invasively monitor thermal therapies in vivo. Multi-echo gradient-echo sequences are being studied to increase the effective temperature to noise ratio, however, choosing the optimal echo-times is non-trivial. We developed an optimization framework based on measurement noise models to compute the optimal echo placement for schemes that either correct or do not correct for the conductivity bias. In a 4-echo phantom experiment, we demonstrated a reduction in the noise standard deviation of 22% when comparing optimal to equidistant echo placements.
Comparisons of Bayesian against non-Bayesian algorithms in intravoxel incoherent motion (IVIM) diffusion-weighted imaging in breast cancer
Authors: Cheung Sai Man , Wu Wing Shan , Senn Nicholas , Sharma Ravi , McGoldrick Trevor , Gagliardi Tanja , Husain Ehab , Masannat Yazan , He Jiabao
Published: August 2023

Intravoxel incoherent motion (IVIM) model approximates the tissue perfusion as a form of pseudo-diffusion, extracted as fast diffusion component in diffusion weighted imaging (DWI). Despite the central role of tissue perfusion in the angiogenesis in cancer, the clinical application of IVIM is hampered due to the susceptibility to noise and tendency of overfitting bi-exponential decay function. Recent introduction of Bayesian algorithm significantly enhanced the robustness and accuracy of IVIM method, renewing its potential as a clinical tool. We therefore set out to examine current IVIM algorithms in the context of neoadjuvant chemotherapy on patients with breast cancer preceding the treatment.
Generalized Bloch model: a theory for pulsed magnetization transfer
Authors: Assländer Jakob , Gultekin Cem , Flassbeck Sebastian , Glaser Steffen , Sodickson Daniel
Published: August 2023

We introduce a classical model to describe magnetization transfer (MT). Like a quantum-mechanical description of spin dynamics and like the original Bloch equations, but unlike existing MT models, the proposed model is based on the algebra of angular momentum in the sense that it explicitly models the rotations induced by radio-frequency (RF) pulses. It unifies the original Bloch model, Henkelman's steady-state theory for magnetization transfer, and the commonly assumed rotation induced by hard, i.e. short, pulses, and describes experimental data better than previous models.
Reproducibility of 3D NOE-MTR in a in vivo healthy human brain at 7T
Authors: Benyard Blake , Nanga Ravi , Wilson Neil , Thakuri Deepa , Cember Abigail , Reddy Ravindeer
Published: August 2023

Nuclear Overhauser Effect (NOE) is an emerging technique to study mobile macromolecules such as lipids in the gray (GM) and white matter (WM) of the brain. In this work, we optimized the saturation pulse parameters of NOE Magnetization Transfer Ratio (MTR) MRI and investigated its reproducibility on a healthy human volunteer at 7 Telsa. We found that NOE-MTR of GM and WM regions of the brain was highly reproducible (COV<10%) over a three year time span. In addition, a saturation length of 3 to 4 sec provided optimal NOE-MTR contrast from both GM and WM regions of the brain.
Free-breathing 3D CEST MRI of Human Liver at 3T Using MR Multitasking
Authors: Han Pei , Cao Tianle , Cheema Karandeep , Lee Hsu-Lei , Han Fei , Wang Nan , Han Hui , Xie Yibin , Christodoulou Anthony , Li Debiao
Published: August 2023

We developed a 3D abdominal CEST MRI technique at 3T using MR Multitasking, which enables entire-liver coverage with free-breathing acquisition. By exploiting the correlation among images throughout the spatial, time, frequency offset, and respiration dimensions, the low-rank tensor framework shows the possibility to acquire the whole Z-spectrum of 53 frequency offsets within 11 min.
Fast WASAB1 post-processing for simultaneous B0 and B1 mapping for CEST imaging use in clinical routine
Authors: Papageorgakis Christos , Firippi Eleni , Gy Benoit , Boutelier Timothé , Khormi Ibrahim , Al-iedani Oun , Paton Bryan , Lechner-Scott Jeannette , Fazlollahi Amir , Ponsonby Anne-Louise , Liebig Patrick , Ramadan Saadallah , Zaiss Moritz , Casagranda Stefano
Published: August 2023

This work provides a new method for fast post-processing of MRI data acquired using the WASAB1 sequence for simultaneous B0 and B1 mapping, used in CEST imaging for field inhomogeneity corrections. We are proposing a new processing method with outstanding acceleration of the parameter estimation procedure, without compromising the stability of the estimation. The stability of the method is demonstrated on phantom data and in vivo 3 Tesla clinical data.
Developing 3D-printed phantoms for quality assurance and validation of quantitative DCE–MRI measurements
Authors: Sarwar Muhammad , Vallatos Antoine , Lau Cher Hon , Waldman Adam , Dimartino Simone , Thrippleton Michael
Published: August 2023

Difficulties in engineering accurate biomimetic phantoms make it challenging to validate MRI models. This is particularly true for quantitative vascular permeability measurements using dynamic contrast-enhanced (DCE-) MRI, where no robust controllable phantoms are available for validating novel techniques and harmonising multicentre results. We developed 3D-printed biomimetic vascular permeability phantoms with controllable properties and assessed their ability to interrogate common DCE model quantification approaches. Parameters such as blood flow, vascular permeability, plasma volume and extravascular volume were reproduced by adapted 3D-printed material and flow circuit properties. The resulting phantoms were shown to reproduce realistic DCE-MRI signals observed clinically.
MR-visibility and relaxation properties of 3-D printed FDM polymers
Authors: Tuomainen Teemu , Paajanen Antti , Nissi Mikko
Published: August 2023

Increasing availability and affordability of 3-D printers utilizing fused deposition modeling (FDM) have enabled their widespread use especially in pre-clinical MRI, allowing in-house design and manufacturing of elaborate coil housings, animal holders, sample holders, etc. Here, we investigated ten common and broadly available FDM polymers for their MRI-visibility at 9.4T. We utilized ultra-short echo time imaging sequences, specifically, single-point-imaging (SPI) and multi-band SWIFT to measure the relaxation properties of the different polymers. The findings support the selection of appropriate printing materials when either visibility or invisibility for ultra-short echo time imaging is required.
A protocol for the acceptance tests of an ultra-high field MR system, in compliance with new standard IEC 62464-1:2018
Authors: Biagi Laura , Cecchi Paolo , Tosetti Michela
Published: August 2023

The European Standard IEC 62464-1:2018 [1] describes the methodologies to carry out acceptance and constancy tests of an MR scanner. Its come into effect extends its applicability in the range of ultra-high field (UHF) tomographers. Here, we present a protocol, with an effective time of acquisition of about 11 hours, developed for the testing of a 7T MR system, in order to address all the requirements of the standard for the evaluation of essential image quality parameters. The protocol provided for the test of two different coil configurations, using proper phantoms.
Convection triggers local MR signal loss during proton beam irradiation of liquid water phantoms
Authors: Peter Juliane , Gantz Sebastian , Karsch Leonhard , Pawelke Jörg , Hoffmann Aswin
Published: August 2023

MRI-based proton beam visualisation in water has proven feasible in exploratory irradiation experiments performed on a first research prototype in-beam MRI system. Beam-induced convection was hypothesised to be implicated into MR signal loss observed within the beam volume. In this study, this hypothesis was tested in liquid water-filled phantoms by suppression of convection-induced motion using mechanical barriers and temperature control of water expansivity. In absence of convection-induced motion, no beam-induced signal changes occurred, supporting the hypothesis that convection triggers local MR signal loss during proton beam irradiation. The elucidation of the exact mechanism of convection-induced signal loss requires further investigation.
Sex-specific effects of prenatal tobacco exposure on cognitive and brain morphometry measures in preadolescent children
Authors: Rivera Pedro Rodriguez , Isaiah Amal , Ernst Thomas , Cloak Christine , Liang Huajun , Chang Linda
Published: August 2023

Prenatal tobacco exposure (PTE) can affect the offspring cognitive and brain development outcomes. Our study evaluated children who had PTE in the Adolescent Brain and Cognitive Development (ABCD) study and found poorer overall cognitive scores, especially working memory scores, lower cortical surface areas and subcortical volumes, with smaller surface areas in the posterior cingulate (PCC) and entorhinal cortices, the lingual and inferior parietal gyri, and abnormally smaller volumes in the thalamus and nucleus accumbens. Furthermore, we found that only PTE-girls had significantly smaller surface areas in the postcentral gyrus, while only PTE-boys had smaller volumes in the posterior corpus callosum.
Diffusion microstructure measurements across the brain and lifespan
Authors: Newman Benjamin , Druzgal T. Jason
Published: August 2023

Understanding how the brain develops, matures, ages, and declines is one of the fundamental questions facing neuroscience1–3. Recent advances in diffusion microstructure analysis have allowed for detailed descriptions of neuronal change. However, it is essential that findings from these studies are appropriately contextualized to general age-related changes in the brain4,5. This study uses 3-tissue constrained spherical deconvolution (3T-CSD) to examine the relationship between brain diffusion microstructure and chronological age in a number of gross anatomical structures, subcortical gray matter, and cortex while additionally evaluating lateral differences in microstructural measurements. The results should serve as a benchmark for diffusion microstructure studies.
Evaluating the feasibility of quantifying longitudinal microstructural changes in mild traumatic brain injury (mTBI) with MAP-MRI
Authors: Nadar Priyanka , Avram Alexandru , Marinelli Luca , Basser Peter
Published: August 2023

Mean Apparent Propagator (MAP) MRI, an expansion of diffusion tensor imaging (DTI), explicitly measures the distribution of net 3D displacements of diffusing water molecules, providing better delineation of crossing white matter fiber tracts. This characteristic may be useful in characterizing unseen microstructural damage in patients with mild traumatic brain injuries whose clinical imaging scans are otherwise normal. An image processing pipeline for using mean apparent propagator (MAP) MRI to analyze diffusion weighted images in mTBI patients has been validated in healthy controls and shown to generate reliable data for patient brain scans.
Advanced multimodal MRI detects premanifest and early-stage alterations in SCA1 and SCA3 with high sensitivity
Authors: Chandrasekaran Jayashree , Park Young Woo , Petit Emilien , Montcel Sophie Tezenas du , Povazan Michal , Banan Guita , Valabregue Romain , Ehses Philipp , Faber Jennifer , Joers James , Coupé Pierrick , Herrera Jose Vincente Manjón , Onyike Chiadi , Barker Peter , Schmahman Jeremy , Ratai Eva , Subramony S.H , Mareci Thomas , Bushara Khalaf , Paulson Henry , Durr Alexandra , Klockgether Thomas , Ashizawa Tetsuo , Lenglet Christophe , Oz Gulin
Published: August 2023

Spinocerebellar ataxias are rare inherited neurodegenerative diseases that cause degeneration in the cerebellum and brainstem. The multi-site READISCA clinical trial readiness study aims to validate MR biomarkers at early stages of SCA1 and SCA3. SCA gene carriers (including individuals at pre-ataxic and ataxic stage) and matched controls (total N=107) were scanned at 3T to obtain structural and diffusion MRI and MR spectroscopy. Medulla, pons, and cerebellar peduncles were the earliest sites of involvement in both SCAs. Neurochemical and microstructural abnormalities were detected with very high sensitivity (AUC>0.9 in ROC analyses) prior to ataxia onset.
A Deep Learning Approach for Automated Volume Delineation on Daily MRI Scans in Glioblastoma Patients
Authors: Breto Adrian , Cullison Kaylie , Jones Kolton , Zavala-Romero Olmo , Ford John , Mellon Eric , Stoyanova Radka
Published: August 2023

Identifying early progressors following treatment for Glioblastoma (GBM) is paramount in GBM management. MRI-RT platforms provide opportunity for daily MRI of patients. We identified early changes in tumor volume typically starting week 3 or 4 of treatment. We hypothesize tumor volume kinetics are associated with outcome and allow for adapting treatment. We develop a deep learning solution for automatic volume delineation on daily scans, allowing real time monitoring of tumor changes and reducing time burden of segmentation. We obtained DSC for tumor lesion and resection cavity on training and test datasets (mean±standard deviation) 0.87±0.128 and 0.9±0.122; 0.74±0.233 and 0.8±0.277, respectively.
AI-driven markers of IDH1 mutational status using microstructure-based characterization of peritumoral region in gliomas
Authors: Samani Zahra Riahi , Parker Drew , Brem Steven , Verma Ragini
Published: August 2023

We developed a novel, microstructure-based, voxel-wise map of the peritumoral region in glioma brain tumors using DTI-based free water volume fraction map and deep-learning. This novel map captures the infiltrative heterogeneity of peritumoral region and can differentiate between gliomas with distinct IDH1 mutation status (IDH-mutant vs. IDH-wildtype). Thus, this new derived map that incorporates microstructure information can be used as a new diffusion based radiomic feature for various oncological investigations involving mutation status.
Characterising hypoxia in rhabdomyosarcoma xenografts with oxygen-enhanced MRI
Authors: Boult Jessica , Roy Upasana , Bernauer Carolina , Box Carol , Howell Louise , Lepicard Elise , Jamin Yann , O'Connor James , Shipley Janet , Robinson Simon
Published: August 2023

Hypoxic gene signatures are prevalent in paediatric rhabdomyosarcomas and are important in conferring resistance to standard treatments. Oxygen-enhanced MRI (OE-MRI) and histological assessment of pimonidazole adduct formation show that xenografts derived from three human rhabdomyosarcoma cell lines exhibit high levels of hypoxia with differences in vascular perfusion evident between the models.

There is much interest in hypoxia-alleviating strategies to reduce tumour hypoxia for therapeutic gain, and these will be assessed in rhabdomyosarcoma models in vivo using OE-MRI. A reduction in hypoxia in response to atovaquone in spheroids derived from the same rhabdomyosarcoma cell lines in vitro has been confirmed.
Liver health outcome of chronic hepatic steatosis: an interim analysis of the Dallas Heart Study cohort
Authors: Mukherjee Sujoy , Berry Jarett , Duncker Carlos , Neeland Ian , Singal Amit , Topper Viktoria , Yokoo Takeshi
Published: August 2023

The natural history of hepatic steatosis and risk factors for the development of advanced chronic liver disease (CLD) are unknown. This interim analysis of 191 subjects in the Dallas Heart Study longitudinal cohort shows that having hepatic steatosis (defined as proton-density fat fraction >5%) at the baseline exam was significantly associated with development of advanced CLD (defined as corrected liver T1 ≥ 800msec) 10-20 years later, with CLD prevalence of 38.8% and 16.9% in the steatosis vs. non-steatosis cohort (p<0.001). The baseline overweight or obesity status also appears to be associated with advanced CLD, independent of having steatosis at baseline.
LIA (Liver Shear Stiffness, INR, Etiology) Score Predicts Risk of Further Decompensation in Patients with Decompensated Cirrhosis
Authors: Zhu Jie , Yi Zhuoya , Li Mengsi , Chen Qilong , Xiao Yuanqiang , Yin Ziying , Glaser Kevin , Chen Jun , Yin Meng , Ehman Richard , Wang Jin
Published: August 2023

In patients who have been clinically diagnosed with decompensated cirrhosis (DC), progression to more advanced decompensation is associated with high mortality. Therefore, the early detection of the risk of further decompensation is helpful to formulate individual treatment and follow-up schedules for patients with DC. Liver stiffness is a potential prognosis biomarker for patients with cirrhosis. This study evaluated MR elastography (MRE) as a tool to predict the risk of further decompensation. By integrating MRE-assessed liver stiffness with clinical information, we developed a risk score that is valuable for predicting further decompensation in patients with DC.
Comparison of Centralized R2* Mapping Algorithms to Vendor R2* Mapping in a Multi-Center, Multi-Vendor Liver Iron Overload Study
Authors: Simchick Gregory , Zhao Ruiyang , Yuan Qing , Ghasabeh Mounes , Ruschke Stefan , Karampinos Dimitrios , Harris David , Mattison Ryan , Jeng Michael , Pedrosa Ivan , Kanel Ihab , Vasanawala Sheryas , Yokoo Takeshi , Reeder Scott , Hernando Diego
Published: August 2023

Recently, a multi-center, multi-vendor study evaluating the reproducibility of R2* vs liver iron concentration (LIC) calibrations was completed, based on a centralized offline R2* reconstruction. However, the relationship between the offline reconstructed R2* maps and the online vendor-provided R2* maps remains unknown. In this work, subjects were recruited at four centers and imaged using 1.5T and 3T MRI scanners from three vendors. R2* maps were obtained using various offline reconstructions and compared to the online vendor reconstructions to determine R2* ranges of agreement. This may enable improved clinical interpretation of vendor R2* measurements using emerging offline R2*-LIC calibrations.
Efficient Non-Uniform Fourier Transform with embedded low-rank projection for fast model-based MRI reconstruction
Authors: Cencini Matteo , Peretti Luca , Tosetti Michela
Published: August 2023

Modern approaches to iterative imaging, such as model-based reconstruction, requires efficient implementations of Non-Uniform Fourier Transform to reach feasible reconstruction times. In addition, low-rank subspace projection is often used to reduce computational burden. While many implementations of NUFFT currently exists, they are not optimized for this kind of problems. Here, we propose a fast and memory-efficient NUFFT operator with embedded low-rank subspace projection. We demonstrate an order of magnitude of speed-up with comparable image quality compared to other high-level implementations.
Flow 2.0 - a flexible, scalable, cross-platform post-processing software for real-time phase contrast sequences
Authors: Pan Liu , Fall Sidy , Baledent Olivier
Published: August 2023

Real-time phase contrast sequences (RT-PC) has potential value as a scientific and clinical tool in quantifying the effects of respiration on cerebral circulation. To simplify its complicated post-processing process, we developed Flow 2.0 software, which provides a complete post-processing workflow including converting DICOM data, image segmentation, image processing, data extraction, background field correction, anti-aliasing filter, signal processing and analysis and a novel time-domain method for quantifying the effect of respiration on the cerebral circulation. This end-to-end software allows us to quickly, robustly and accurately perform batch process RT-PC and multivariate analysis of the effects of respiration on cerebral circulation.
Virtual Scanner 2.0: enabling the MR digital twin
Authors: Tong Gehua , Vaughan John , Geethanath Sairam
Published: August 2023

Virtual Scanner is an open-source MR platform for end-to-end simulation and serves as a digital twin for real MR scanners in hardware and software aspects. In this update, we present new functions including RF pulse design and simulation, hardware-incorporated Bloch simulation that takes into account B0 and B1- fields, and non-Cartesian reconstruction. Three Google Colab notebooks are provided to demonstrate these functions and enable users to perform virtual experiments in a zero-footprint manner. Furthermore, we demonstrate the digital twin concept in a development iteration case using the SPGR sequence.
Realistic Simulation of Body Composition MRI and Field-Strength Dependence
Authors: Yagiz Ecrin , Cui Sophia , Lee Nam , Tasdelen Bilal , Tian Ye , Nayak Krishna
Published: August 2023

MRI is used extensively for body composition assessment in large part due to the increasing prevalence of metabolic disease and obesity. In this work, we provide a framework for simulating body composition MRI, including non-Cartesian sequences and emerging low field strengths. This framework can be utilized to investigate the optimality of acquisition parameters (e.g., resolution, TE, sampling trajectory) and the performance of fat/water separated reconstruction algorithms.
A software tool to assess radiofrequency coil designs with respect to ultimate intrinsic performance limits
Authors: Montin Eros , Georgakis Ioannis , Zhang Bei , Lattanzi Riccardo
Published: August 2023

This work introduces POIROT (Performance Observer In Receive or Transmit), a web-based tool for the assessment of receive and transmit coil designs against ultimate intrinsic signal-to-noise ratio and transmit efficiency, respectively. It enables engineers, for the first time, to evaluate how good is a design and whether there is further room for improvement before building a prototype. POIROT currently includes ultimate intrinsic data for three numerical head models at different resolutions and magnetic field strengths. POIROT could be integrated with rapid numerical EM modeling tools to develop a pipeline for coil design optimization that uses ultimate performance as the benchmark.
A BIDS extension proposal for magnetic resonance spectroscopy data
Authors: Mikkelsen Mark , Wong Dickson , Bogner Wolfgang , Halchenko Yaroslav , Lamb Damon , Mullins Paul , Oeltzschner Georg , Wilson Martin
Published: August 2023

Magnetic resonance spectroscopy (MRS) studies can generate extensive and complex datasets. Datasets can be organized idiosyncratically across (and even within) labs. However, sharing data and reproducing results without the added challenge of parsing lab-specific file organization is paramount to open science. Sharing of MRS data that is independent of lab-specific practices would greatly aid transparency and reusability. Here, we present an extension to the Brain Imaging Data Structure (BIDS) specification for MRS data. MRS-BIDS adopts the established tenets of standardization of BIDS and applies them to MRS data while considering the nuances relevant to MRS methodology.
Study of potential immediate effects of neuronal activity on the MRI signal in humans
Authors: van Gelderen Peter , de Zwart Jacco , Duyn Jeff
Published: August 2023

A recent study has shown rapid MRI signals in response to whisker pad stimulation in mice that track electrical activity. We used rapid, high SNR imaging at 7 T to look for a possible direct effect of visual stimulation on MRI signal in human visual cortex. Two rapid stimulation protocols and variation of T1-weighting failed to generate observable signal changes above the 0.01% detection threshold, well below the previously reported effect size of 0.15%. This confirms the well-established difficulty in developing more direct measures of neuronal activity than available with BOLD-fMRI.
Non-steady-state sequences for multi-parametric MRI need to be evaluated in the context of gradient-encoding
Authors: Fuderer Miha , van der Heide Oscar , Liu Hongyan , van den Berg Cornelis , Sbrizzi Alessandro
Published: August 2023

In non-steady-state multi-parametric quantitative MRI (e.g. MR-STAT or MR Fingerprinting (MRF)), it is a non-trivial task to devise good sequences of time-varying flip angles. Recent work addresses this issue, albeit assuming a single-voxel approach, i.e. the k-space encoding is not taken into account when optimizing. In this work we show, using examples from MR-STAT reconstructions and using a Cramer-Rao based BLAKJac analysis, that two apparently similar sequences can have vastly different outcomes when applied in an actual (2-dimensional) measurement setup - showing that the context of encoding is very relevant.
Quantitative Assessment of Diffusion Weighted Imaging Near Metal Implants
Authors: Neri John , Koff Matthew , Koch Kevin , Tan Ek
Published: August 2023

Conventional echo-planar imaging (EPI) DWI suffers from substantial artifact when imaging orthopedic hardware. DWI with multi-acquisition with variable resonance image combination (MAVRIC) can reduce susceptibility artifact around metal implants. The purpose of this work was to evaluate the quantitative accuracy of DWI-MAVRIC near metal components using a diffusion phantom. DWI-MAVRIC sequences were acquired in the presence of no metal, cobalt-chromium, titanium, and stainless steel. It was found that DWI-MAVRIC can accurately measure apparent diffusion coefficient (ADC) in the presence of metal. Among tested metals, stainless steel creates the greatest artifact that prevented the acquisition of accurate ADC data.
Quantitative & qualitative evaluation of accelerated T2 mapping technique using Deep Learning reconstruction in knee cartilage
Authors: Carretero Laura , Fung Maggie , García-Polo Pablo , Litwiller Daniel , Lebel Marc , McKinnon Graeme C , Padrón Mario
Published: August 2023

MRI-based cartilage imaging shows biochemical and microstructural changes at early stages of osteoarthritis before changes become visible with structural MRI and arthroscopy. However, clinical application of T2 mapping is driven by high variability and suboptimal reproducibility, besides long examination times. The purpose of this study is to accelerate T2 mapping technique and apply a novel DL reconstruction method to develop a fast and robust way to access T2 relaxometry. Phantom and in-vivo testing demonstrated that DL reconstructed accelerated images provide increased consistency compared to conventional reconstruction and implies a great step into an extensive clinical adoption.
Comparison study between APT-weighted and relaxation-compensated CEST-MRI in human glioma at 3T
Authors: Kroh Florian , Breitling Johannes , von Knebel Doeberitz Nikolaus , Schlemmer Heinz-Peter , Ladd Mark , Bachert Peter , Paech Daniel , Goerke Steffen
Published: August 2023

Although the underlying mechanisms of APT-weighted (APTw) CEST-MRI are not completely understood, it has been shown to provide valuable information for brain tumor imaging at 3T. To gather more information about the mechanisms, the APTw signal was correlated to relaxation-compensated CEST contrasts in 21 postoperative human glioma patients. A correlation, although being only moderate, was found for the relaxation-compensated APT contrast in the contrast enhancing (CE) tumor region, but not for other tissues, nor rNOE or MT contrast. Differentiation of the CE tumor and normal appearing white matter was strongly dependent on the selective relaxation-compensated CEST evaluation method.
Reduced field of view CEST for high performance prostate imaging at 3T human scanner
Authors: Chai Xubin , Liu Chuyu , Wang Chu , Xue Rong , Song Xiaolei
Published: August 2023

For imaging small-sized organs like the prostate, reduced-field-of-view (rFOV) technique is useful for shortening scan time, increasing resolution and reducing artifacts caused by field inhomogeneity and motion. Herein on a 3T clinical scanner, rFOV CEST was obtained using an off-resonance saturation preparation (seconds long), followed by readouts at the crossing section of a 90 deg excitation slab and a 180 deg refocus slab that had an angle in between. For saturation powers of 0.7 uT and 2 uT, CEST contrast maps and quantitative curves suggested the rFOV-CEST outperformed the Traditional-FOV acquisitions, which has potential for prostate CEST imaging at 3T.
Generalized Framework for Homogeneous Ultra-High-Field Brain Imaging
Authors: Liebig Patrick , Herrler Juergen , Tomi-Tricot Raphael , Williams Sydney , Ding-Yuan Belinda , Hlou Majd , Chebrolu Venkata , Gadjimuradov Fasil , Hilbert Tom , Kober Tobias , Gumbrecht Rene , Heidemann Robin , Benkert Thomas , Rodgers Chris , Porter David , Dragonu Iulius , Nagel Armin , Malik Shaihan
Published: August 2023

7T MRI is affected by inhomogeneous transmit and receive B1 field that can impede the inherent gains in signal-to-noise ratio. pTx provides excellent results in correcting the transmit field and showed feasibility in a clinical setting as well1,2. Although multiple algorithms have been developed to correct for the receive profile or signal homogeneities in general, each algorithm has its own shortcomings. Here, we suggest combining prospective correction of the transmit field by pTx with a deep learning network to retrospectively correct for the remaining signal inhomogeneities (mainly receive field variations) in a generalized fashion.