bluuebunny/crossref_metadata_2025 huggingface dataset:
Differentiation of IDH-mutant Glioma Subtypes Using Unsupervised Dimensionality Reduction of MRI Biomarkers
Authors: Willms Klara , Zeevi Tal , Chadha Saahil , von Reppert Marc , Lost Jan , Tillmanns Niklas , Merkaj Sara , Huttner Anita , Aneja Sanjay , Aboian Mariam
Published: November 2024

Motivation: Radiomic features can potentially help distinguish subtypes of IDH-mutant gliomas that appear similar on MRI. Goal(s): The aim of this study was to evaluate whether imaging-based clustering of radiomic biomarkers of IDH-mutant gliomas may identify patterns or subgroups based on the 2021 CNS WHO classification. Approach: Dimensionality reduction techniques were applied to radiomic features of 179 patients of different sequence combinations to analyze the high dimensional feature space. Results: FLAIR and T1 post-contrast imaging revealed unique clusters, and survival analysis suggested potential differences amongst clusters. However, further research with a larger dataset is needed to determine whether the observed differences are significant. Impact: This study analyzed quantitative imaging biomarkers to differentiate IDH-mutant gliomas according to the 2021 WHO classification. The findings suggest that radiomic features may hold insights into potential survival differences among subtypes. Larger-scale research is required to further investigate these findings.
Textural changes in the amygdala are more sensitive than volumetric changes in cocaine use disorder patients undergoing therapy
Authors: Nandi Shounak , Poojar Pavan , Bachi Keren , Taufique Shilpa , Hurd Yasmin , Geethanath Sairam
Published: November 2024

Motivation: Neuroimaging improves treatment response classification in cocaine use disorder (CUD), often relying on brain morphometry to track changes. Multiple studies report that MRI textural changes predict earlier changes than volumetric changes in Alzheimer’s disease. We aim to apply textural analysis to multi-timepoint CUD MRI data. Goal(s): Our work investigates changes in the amygdala volume and texture in CUD patients undergoing repetitive transcranial magnetic stimulation (rTMS). Approach: We computed the volumetric and textural changes over time and compared the relative temporal sensitivities. Results: The relative temporal sensitivity of textural changes in the amygdala is higher than volumetric changes in CUD patients undergoing rTMS. Impact: Textural changes in MRI become noticeable before volumetric changes, offering additional insights into ongoing therapy complementary to clinical measures. This allows for personalized treatment, utilizing each individual's baseline data as their internal reference.
Subtype classification of Functional Pituitary Adenomas based on MRI Radiomics.
Authors: Ndimulunde Elizabeth , Lin Bing-Fong , Lu Chia-Feng , Lin Dao-Chen
Published: November 2024

Motivation: Pituitary adenomas (PAs) are a rare but clinically diverse group of tumors with varying hormone secretion profiles and clinical characteristics, comprising 15% of intracranial tumors. Typical classification of PAs relies on blood hormone levels as gold standard test, with a limited exploration into assessing hormone status using neuroimaging biomarkers. Goal(s): We aim to offer a practical MRI-based classification model, improving clinical PA management. Approach: Our study developed a machine learning model using MRI radiomics as image biomarkers for the classification of PAs focusing on six subtypes. Results: Our SVM model showed an accuracy of 0.65 based on MRI images. Impact: Our radiomics classification model promises to revolutionize MRI PA classification and diagnosis, enhancing clinical management and benefiting scientists, clinicians, and patients by enabling more accurate and efficient diagnostics and treatments.
Machine Learning-Based Classification of IDH Mutant Gliomas Using VASARI and Radiomics Features
Authors: Willms Klara , von Reppert Marc , Lost Jan , Tillmanns Niklas , Merkaj Sara , Schrickel Elisabeth , Memon Fatima , Aboian Mariam
Published: November 2024

Motivation: Diagnosis of molecular subtypes of IDH-mutant gliomas on MRI has presented a challenge in clinical practice. Goal(s): To classify IDH-mutant gliomas we compared different ML models using qualitative and quantitative features from preoperative MRI. Approach: Three models were compared, using only qualitative VASARI features as scored by two blinded neuroradiologists, the other used quantitative features from FLAIR and T1Gd and finally combining both in a third model. Results: The VASARI feature based model showed moderate diagnostic accuracies for different tumor entities, which was higher than the Radiomics only model. Combining both features improved results, emphasizing the importance of feature selection in clinical applications. Impact: This study demonstrates the potential of machine learning models in enhancing the accuracy of IDH-mutant glioma classification on preoperative MRI images.
Toward Optimal MRI Utilization: How Waste and Slack Turn Into Potential
Authors: Chu Sheena , Garrett John , Reeder Scott , Pirasteh Ali
Published: November 2024

Motivation: There are no standard metrics to measure clinical MRI utilization. This gap contributes to a lack of best practices for MRI utilization optimization. Goal(s): (1)Identify and standardize metrics relevant to MRI workflow; (2)demonstrate the use of these metrics to quantify MRI utilization; (3)identify opportunities for improvement in efficiency in a clinical MRI practice. Approach: Timepoint and summary metrics were defined to characterize MRI workflow. Data from two MRI facilities were analyzed using these metrics to characterize MRI utilization. Results: The defined standard set of metrics quantified MRI utilization and identified workflow areas that could be further optimized to improve MRI utilization. Impact: It is currently difficult to communicate key timepoint metrics that characterize the utilization of clinical MRI exams. The development of standardized language to characterize MR exam timepoint metrics can facilitate best practices for workflow improvement. Such tools are essential to improve the value of MR.
Applications of the likelihood function for dynamic contrast enhanced MRI
Authors: Landheer Karl , Preda Marilena , Cook Thomas , Walls Johnathon , Germino Mary , Noakes Leigh
Published: November 2024

Motivation: Least squares can provide biased and inefficient estimations of pharmokinetic parameters in certain circumstances. Goal(s): To develop a more efficient method to extract pharmokinetic parameters as well as the limit on the precision of those parameters. Approach: The likelihood function for multi-channel receive dynamic contrast enhanced MRI was used to develop a method to extract pharmokinetic parameters. Results: The proposed maximum likelihood estimator method has substantially less bias than the typical least squares method. For the input parameters investigated the maximum likelihood estimated pharmacokinetic parameters had standard deviations within 10% or less of their fundamental lower bound. Impact: The developed tool provides nearly efficient pharmokinetic estimations, thereby providing an improved method over the standard least squares approach, as well as demonstrating the limited utlility of future machine learning and other methods attempting to solve this problem.
Small voxel sizes reduce extravascular dephasing from large veins in gradient-echo BOLD fMRI at 7T: a simulation study
Authors: Berman Avery , Balasubramanian Mukund , Setsompop Kawin , Polimeni Jonathan
Published: November 2024

Motivation: Recent ultra-high-resolution gradient-echo BOLD-fMRI data demonstrate an unexpected reduction in sensitivity to large veins at 7T, suggesting that small voxels may experience less signal loss due to extravascular dephasing. Goal(s): To test whether a reduction in through-plane or in-plane dephasing with small voxels may measurably contribute to reduced large-vein influences in gradient-echo BOLD. Approach: We apply biophysical simulations of simplified vascular architecture, combined with realistic image encoding gradients. Results: While voxels adjacent to veins are still strongly influenced, smaller voxel sizes have reduced extravascular BOLD, which impacts cerebral cortical-depth profiles of activation. The direction of the imaging encoding gradients also affects these profiles. Impact: Rencelty available ultra-high-resolution fMRI improves spatial accuracy, and may also provide an unexpected improvement in neuronal specificity. We demonstrate that small-voxel gradient-echo BOLD achieves reduced unwanted contamination from large veins, potentially providing an fMRI method with high sensitivity AND specificity.
Investigating concurrent neuronal activities and hemodynamic signals with simultaneous fMRI and wild-field cortical optical imaging in mice
Authors: Pan Wen-Ju , Daley Lauren , Watters Harrison , Meyer-Baese Lisa , Keilholz Shella
Published: November 2024

Motivation: To identify the best sequence for future multimodal studies, the simultaneous fMRI and cortical optical imaging in mice were used for evaluation of consistency of neuronal activation with EPI or ZTE scans. Goal(s): The goal of this work is to establish a general framework for simultaneous fMRI and wide-field optical imaging. Approach: ZTE and EPI were evaluated during sensory stimulation and at rest with simultaneously wide field optical imaging. Results: High quality images were obtained from 7 mice, 4 with calcium indicators and three with voltage indicators. The localized neuronal activations at cortex have great consistency with both EPI and ZTE scans. Impact: The validation opens a pathway for further imaging cell-specific fluorescence activities. The integration of these two complementary neuroimaging modalities opens a broad range of future applications for systems level neuroscience and preclinical studies of pathological brain function.
Neighborhood disadvantage is associated with altered cortical connectivity in frontoparietal brain regions
Authors: Safai Apoorva , Tiwari Pallavi , Kind Amy , Bendlin Barbara , Ismail Marwa
Published: November 2024

Motivation: Neighborhood disadvantage measured using an area deprivation index(ADI) has shown to impact cognitive outcomes,with alterations in regional volumetric and cortical assessment. Connectivity based approaches could further identify cortical network patterns associated with cognitive decline and neighborhood disadvantageGoal(s): We evaluated associations between neighborhood disadvantage,cognitive impairment and changes in morphological similarity network(MSN)features. Approach: For unimpaired cohort(n=297)with lowest and highest ADI ranks,cortical thickness based MSN features were computed and associations between ADI,cognitive performance and network features were assessed using linear regression and mediation analysisResults: Disorganization of frontoparietal regions was associated with ADI and demonstrated marginal mediating effect between cognitive impairment and neighborhood disadvantage status. Impact: Our findings of association between neighborhood disadvantage status and cortical disorganization in Alzheimer’s-related fronto-parietal brain regions, support the impact of neighborhood disadvantage on cognitive outcomes, and provide a connectivity based mechanism that may explain risk for cognitive decline and dementia.
Alterations of functional segregation and integration in children with autism spectrum disorder: A resting-state MRI study.
Authors: Zhou Di , Hua Ting , Zhao Xiance , Tang Guangyu
Published: November 2024

Motivation: Neuroimaging analysis of brain functional changes can provide a new imaging perspective for understanding the neural mechanism and providing biomarkers for the clinical diagnosis of ASD. Goal(s): This study aimed to explore the brain functional changes in children with autism spectrum disorder (ASD). Approach: All subjects underwent brain resting state functional MRI (rs-fMRI) scans.The data were analyzed using various methods including functional segregation and functional integration. Results: The results showed the significant higher and lower activities in many brain regions, hypo-connectivity between different brain networks and only hyper-connectivity between DAN and DMN. Impact: The functional changes of the brain may be the pathogenesis for children with ASD accompanied, which could become the biomarkers in future clinical diagnosis.
Dysregulated functional network interactions in the brain of depression: From the perspective of the triple-network model
Authors: Xu Manxi , Qiu Yingwei , Ma Guolin
Published: November 2024

Motivation: Major Depressive Disorder (MDD) has a high incidence and disability rate. However, the etiology remains unclear, and objective diagnostic markers are lacking. Goal(s): We hypothesize the presence of static and dynamic abnormal connectivity patterns in three core networks of MDD patients. Approach: We employ static functional network connectivity (FNC) analysis, dynamic functional network connectivity (dFNC), the network interaction index (NII), and the dynamic functional network connectivity (dNII) to investigate interactions among Default Mode Network (DMN), Salience Network (SN), and Executive Control Network (ECN). Results: MDD patients have abnormal network functional interactions that can be captured by static and dynamic NII indicators. Impact: The abnormal network functional interactions deepen our understanding of the abnormal activity of the three networks in MDD patients, helps to reveal the pathogenesis of MDD, and provides ideas for its intervention.
Cortical Sulcus Depth Alterations in Patients with Tinnitus Before and After Sound Therapy: A Surface-Based Morphometry Study
Authors: Wei Xuan
Published: November 2024

Motivation: This study aimed to explore alterations in brain surface-based morphometry sulcal depth in patients with idiopathic tinnitus before and after 24 weeks of sound therapy. Goal(s): This study aimed to explore alterations in brain surface-based morphometry sulcal depth in patients with idiopathic tinnitus before and after 24 weeks of sound therapy. Approach: Thirty-three tinnitus patients underwent magnetic resonance imaging scans at baseline and after 24 weeks of sound therapy. Results: Compared to HCs, those in the tinnitus group at baseline had significantly lower sulcal depth in the left medial temporal cortex (MTC) and right somatosensory and motor cortex (SMC). Impact: The remodeling of sulcal depth after sound therapy is an indicator for effective sound therapy.
Altered functional connectivity of emotional circuits and default model network in postpartum women: A Resting-State fMRI Study
Authors: gao Yingli , zhang Kaihua , Lin Liangjie , Du Xiaoxia
Published: November 2024

Motivation: Resting-state functional connectivity can elucidate the brain intrinsic functional connectivity patterns of postpartum women, providing new evidence for functional plasticity in postpartum women. Goal(s): Our goal is to explore functional connectivity patterns of postpartum women. Approach: Postpartum women were imaged using rs-fMRI and compared with nonmothers by functional connectivity analysis. Results: Brain functional remodeling does occur in the postpartum women, as evidenced by changes in intrinsic functional connectivity patterns. Impact: We used rs-FC to demonstrate that brain functional placity in postpartum women during raising infants, providing new ideas and directions for studying the neural mechanisms of maternal behavior.
Contribution of coupling task-functional-MRI and kinematic to the analysis of motor function in healthy subjects
Authors: Belkacemi Zakaria , van Dokkum Liesjet , Troalen Thomas , Tchechmedjiev Andon , De Champfleur Nicolas Menjot , Laffont Isabelle , Mottet Denis , Le Bars Emmanuelle
Published: November 2024

Motivation: There is a lack of understanding of the mechanisms of post-stroke motor recovery. To date, fMRI brings information which are not linked to the movement characteristics. Goal(s): To investigate whether integration of kinematic in fMRI adds any value to the understanding of motor function. Approach: A block designed motor-task-fMRI experiment coupled with real-time motion-tracking was performed on sixteen healthy subjects. Post-processing consisted of a group-level analysis comparing the regression of the BOLD signal with action-rest onsets, and with the flexion velocity vector. Results: Using a wider cluster-size, kinematic approach allows retrieving regions found with conventional approach and additional regions involved in motor control. Impact: Coupling of fMRI with kinematics provides additional information on motor function and motor control. Post-stroke motor recovery is subject to variability and is linked to motor control. Coupling both measurements could provide better understanding of motor recovery at the individual-level.
Resting-state fMRI localization of tongue motor areas with a patient-based probabilistic functional atlas
Authors: Liu Ho-Ling , Teo Jian Ming , Tran Kevin , Jen Mu-Lan , Hou Ping , Noll Kyle , Ferguson Sherise , Prabhu Sujit , Wintermark Max , Kumar Vinodh
Published: November 2024

Motivation: To benefit patients who needs presurgical mapping of tongue motor areas but have limited tb-fMRI. Goal(s): To create a probabilistic tongue motor atlas and evaluate its use for guiding rs-fMRI seed-based correlation (SBC) analysis. Approach: Presurgical tb-fMRI of 30 brain tumor patients were used to create the atlas. This atlas was transferred to a different set of patients’ individual space for guiding rs-fMRI analysis. Locations of functional connectivity detected in the ipsilateral hemisphere were compared with tb-fMRI results. Results: A tongue motor atlas was developed, which can effectively guide the rs-fMRI analysis with results similar to when seeding based on the tb-fMRI activation. Impact: The probabilistic functional atlas enables automated seed-based analysis for rs-fMRI localization of tongue motor areas in patients undergoing brain tumor resection. It also provides a functional localizer which can be used for various quantitative image analyses of tongue motor areas.
Vessel-specific quantification of cerebral venous oxygenation with velocity encoding preparation and rapid acquisition
Authors: Lin Zixuan , Jiang Dengrong , Zhang Yi , Hsu Yi-Cheng , Lu Hanzhang , Wu Dan
Published: November 2024

Motivation: Non-invasive measurement of cerebral venous oxygenation (Yv) is of critical importance in numerous brain diseases. Goal(s): The present work proposed a fast method to quantify regional Yv map for both large and small veins, named T2-Relaxation-Under-Velocity-Encoding-and-Rapid Acquisition (TRU-VERA). Approach: It isolates blood spins from static tissue with velocity-encoding preparation, modulates the T2 weighting of venous signal with T2-preparation and utilizes a bSSFP readout to achieve fast acquisition with high resolution. Results: Venous T2 measured with TRU-VERA was highly correlated with T2 from TRUST and showed an excellent test-retest reproducibility with a CoV of 1.2% for large veins and 3.6% for small veins. Impact: The proposed TRU-VERA sequence is a promising method to for non-contrast and fast assessment of vessel-specific oxygenation, thus regional cerebral oxygen metabolism, in a number of diseases.
Longitudinal MRI Tracking of Transplanted Neural Progenitor Cells in the Spinal Cord Utilizing the Bright Ferritin Mechanism
Authors: Zhuang Keyu , Luo Zixiang , Kim Seong Jun , Vollett Kyle , Cheng Hai-Ying Mary , Khazaei Mohamad , Fehlings Michael , Cheng Hai-Ling Margaret
Published: November 2024

Motivation: A non-invasive imaging technology for monitoring cell survival and in-vivo migration after transplantation is critical to optimizing and translating stem cell-based therapies. Goal(s): To extend our previously reported bright-ferritin cell tracking platform to monitoring stem cell therapy, we investigated tracking human neural progenitor cells transplanted in the rat spinal cord. Approach: In-vitro assays of proliferation and differentiation, and imaging both in vitro on cell pellets and in vivo in rats were performed. Results: Monitoring rats on MRI over seven weeks confirmed the ability to assess cell retention and distribution in the rat spinal cord. Impact: Our bright-ferritin platform demonstrated no adverse effects on human neural progenitor cells. Stem cells injected in the rat spinal cord could be tracked longitudinally and on-demand via a bright T1-contrast on MRI.
Establishing a Standardized Healthy Reference Distribution for Multi-Site 129Xe Gas Exchange MRI Across Major Scanner Platforms
Authors: Leewiwatwong Suphachart , Bechtel Aryil , Mummy David , Zhang Shuo , Lu Junlan , Cleveland Zackary , Willmering Matthew , Parra-Robles Juan , Fain Sean , Hahn Andrew , Driehuys Bastiaan
Published: November 2024

Motivation: Quantitative 129Xe gas exchange MRI, conducted across different imaging centers and scanner platforms, requires consistent healthy reference distributions. Goal(s): To establish standardized reference values from an 18-30yr old multicenter healthy cohort for 129Xe gas exchange MRI. Approach: Participants from three research centers underwent pulmonary function tests and a standardized 129Xe MRI/MRS protocol. Data were processed centrally and corrected for T2*. Results: A balanced multicenter dataset revealed minimal variability between combined and site-specific reference distributions, validating the combined values for cross-center use. The distribution for 208-ppm excitation could be reliably transformed for 218-ppm excitation. Impact: This study provides robust cross-platform reference distributions for 129Xe gas exchange MRI, facilitating comparison of quantitative imaging in multi-center respiratory research.
129Xe MRI Ventilation Texture Features and Machine Learning to Predict Response to ICS/LAMA/LABA in Moderate Asthma
Authors: Mozaffaripour Ali , Tcherner Sam , Sharma Maksym , Kooner Harkiran , McIntosh Marrissa , Yamashita Cory , Parraga Grace
Published: November 2024

Motivation: 129Xe MRI ventilation texture features provide a way to generate quantitative spatial information about ventilation heterogeneity beyond ventilation defect percent, which is important in some asthma patients with patchy (and not obviously segmental or subsegmental) ventilation abnormalities. Goal(s): Machine-learning and 129Xe MRI ventilation texture-analysis were used to generate ventilation-imaging based models for predicting ICS/LAMA/LABA response. Approach: Machine-learning models trained on clinical measurements were compared with those trained on ventilation texture features. Results: MRI texture-based models outperformed clinical models for predicting 6-week response. The neighbourhood gray-tone difference matrix strength was the top-ranking texture feature, which significantly correlated with clinical measurements. Impact: 129Xe MRI ventilation texture features provided unique information about ventilation abnormalities and ventilation patchiness; when texture features were embedded in predictive models, these features outperformed clinical models explaining response to ICS/LAMA/LABA in moderate asthma.
Detection of low calcium channel activity in pig hearts with manganese-enhanced MRI
Authors: Nordhøy Wibeke , Kleppestø Magne , Storås Tryggve , Østensen Jonny
Published: November 2024

Motivation: Evaluate manganese-enhanced MRI (MEMRI) for heart failure assessment. Goal(s): Quantify the manganese uptake rate in the myocardium as an indicator of L-type calcium channel activity and T-tubule density. Approach: A high temporally-resolved dynamic SatRec sequence was used to track the Mangafodipir bolus instead of using the less precise, but higher spatially-resolved, conventional T1 mapping method that was used before and after the manganese administration. Results: Pigs have less dense T-tubule than humans leading to fewer L-type calcium channels and low Mn uptake in cardiomyocytes. Therefore, we believe that MEMRI can become a promising tool for assessing heart failure diseases in humans. Impact: Since pigs are often used in preclinical research, there are important differences to be aware of. The low Mn uptake proved their less dense T-tubule, showing that MEMRI may be a useful tool for studying heart failure in humans.
High Contrast MRI of the Prostate Using Divided Reverse Subtracted Inversion Recovery (drSIR) Sequences
Authors: Matern Philipp , Bonekamp David , Rauch Julian , Bydder Graeme , Kuder Tristan
Published: November 2024

Motivation: Divided reverse Subtracted Inversion Recovery (drSIR) has shown potential for brain MRI but has not yet been applied to the prostate. Goal(s): To produce prostate images with high $$$T_1$$$ contrast and highlight the junction between the peripheral and transitional zones by using two IR-TSE images with different inversion times (TIs). Approach: In healthy volunteers, the TIs that suppressed the peripheral and transitional zones as well as the tissue junction were determined, and the corresponding images were subtracted and divided pixelwise. Results: High $$$T_1$$$ contrast between the prostate zones was achieved without contrast agents and subtle $$$T_1$$$ heterogeneities were observed. Impact: High $$$T_1$$$ contrast with obvious distinction between the peripheral and the transitional zones of the prostate was achieved without contrast agents. The approach is likely to show lesions with high contrast and may improve the detection and delineation of tumors.
Single-patient analysis of quantitative T1 values at 7T reveals global abnormalities in epilepsy
Authors: Piredda Gian Franco , Hilbert Tom , Caneschi Samuele , Bonanno Gabriele , Seiffge David , Goeldlin Martina , Hoepner Robert , Schindler Kaspar , Vulliemoz Serge , Seeck Margitta , Ravano Veronica , Maréchal Bénédicte , Wiest Roland , Kober Tobias , Radojewski Piotr
Published: November 2024

Motivation: While widespread structural changes in epilepsy have been previously reported, the global secondary effects on the brain are yet to be fully understood. Goal(s): To investigate the presence of global abnormalities in quantitative T1 values in drug-resistant epilepsy at a single-patient level. Approach: Seventy-eight epilepsy patients were studied using 7T MRI, and a previously established quantitative T1 brain atlas of healthy subjects was used to calculate T1 deviations in patients. Results: Frontal and temporal gray matter exhibited the largest T1 alterations, with significant correlations observed between T1 deviations and the patients’ disease duration. These findings suggest widespread microstructural disruptions in epilepsy patients. Impact: The observed quantitative T1 changes reveal widespread microstructural disturbances in epilepsy patients that extend beyond the seizure onset zone. The proposed method may allow early diagnosis of previously undetectable microstructural abnormalities along brain areas involved into seizure formation and propagation.
Unsupervised MR2PET Synthesis Provides Pseudo-Normal Reference to Improve Epileptic Lesion Detection
Authors: Li Jiwei , Chen Wentao , Huang Hui , Yuan Siyu , Xu Xichen , Cai Bingyang , Cui Ya , Zhang Miao , Zhou Weimin , Luo Jie
Published: November 2024

Motivation: It is challenging to obtain demographically matched controls for every patient who underwent FDG PET examinations. Goal(s): We aim to generate pseudo-normal PET for each epilepsy patient leveraging recent progress in cross modality image translation. Approach: We employed diffusion model to learn the translation between T1w-MRI and FDG PET of healthy subjects, then generated pseudo-normal PET for a cohort of 104 patients with focal epilepsy, who underwent PET/MR scanning for presurgical evaluation. Results: Unsupervised SynDiff achieved comparable performance as supervised Pix2pixGAN in PET synthesis. Improved DICE coefficient and lesion detection were achieved using synthesized reference compared with traditional group reference. Impact: Imaging translation provides a personalized pseudo-normal reference for each epilepsy patient. Pseudo-normal PET is poised for potential adoption as an auxiliary tool to enhance the capability of PET imaging in detecting epileptic lesions within clinical settings.
Abnormal apparent diffusion coefficient of ultra-high b-values in the bilateral thalamus and striatum in MRI-negative refractory epilepsy
Authors: Tang Guixian , Cui Wei , Ling Xueying , Guo Qiang , Xu Hao
Published: November 2024

Motivation: Subcortical nuclei such as the thalamus and striatum have been shown to be related to seizure modulation and termination, especially in refractory epilepsy. Goal(s): This study aimed to assess AQP4 function reflected by the apparent diffusion coefficient (ADC) from ultra-high b-values (ADCuh) in MRI-negative refractory epilepsy. Approach: The eDWI parameters such as standard ADC (ADCst), pure water diffusion (D) and ADCuh were calculated from the 15 b-values. Results: ADCuh values in the bilateral thalamus, caudate nucleus, putamen and globus pallidus in MRI-negative refractory epilepsy were significantly higher than those in the healthy control subjects. Impact: The alterations of the ADCuh values in the bilateral thalamus and striatum may reflect abnormal AQP4 function in MRI-negative refractory epilepsy. ADCuh might be a useful measurement for evaluating subcortical nuclei related brain damage in epilepsy patients.
Spiral cardiac cine imaging with water/fat separation
Authors: Chao Tzu Cheng , Wang Dinghui , Pipe James , Leiner Tim
Published: November 2024

Motivation: Water/fat separation can be helpful to better distinguish adipose tissue, blood and myocardium in a cardiac cine series. However, inclusion of a multi-echo acquisition in the conventional bSSFP sequence can introduce artifacts and reduce temporal efficiency. Goal(s): To develop a fast and robust water/fat separation method for time-resolved cardiac cine imaging. Approach: A spoiled gradient echo sequence with spiral acquisition is proposed to perform the cine acquisition with retrospectively cardiac gating. Results: The image from the proposed method has shorter scan time, lower artifact level and lower RF deposition compared to a multi-echo bSSFP sequence. Impact: We demonstrate the feasibility of spiral cardiac cine imaging with water/fat separation, enabling faster scanning while preserving adequate contrast among adipose tissue, blood and myocardium. This sequence also has low RF deposition with much lower SAR level for the patient.
Parallel contrast imaging from multi-echo SSFP
Authors: Beitone Coraline , Chiew Mark , Miller Karla , Bangerter Neal , Lally Peter
Published: November 2024

Motivation: Multi-echo steady-state acquisitions (Dual/Triple Echo Steady State) allow for the acquisition of multi-contrast images, but only in a sequential manner, which is time-inefficient, and requires substantial gradient spoiling to avoid banding artifacts. Goal(s): Our goal was to introduce an alternative multi-contrast acquisition with parallel imaging capabilities. Approach: By exploiting the effects of partial RF spoiling in Fluctuating Equilibrium MR (FEMR) imaging, we devised a novel acquisition strategy enabling simultaneous acquisition of aliased multi-contrast images and their subsequent reconstruction via SENSE. Results: Implemented in 3D, our approach yields multiple images in one acquisition while providing flexibility over the acquired imaging contrasts. Impact: This new acquisition strategy offers more time-efficient multi-contrast imaging while also reducing gradient requirements in comparison to existing approaches, creating new opportunities for rapid quantitative imaging experiments in healthy and diseased tissue.
Design of a power independent of finite number of slices (PIFINS) pulse for simultaneous multi-slice imaging
Authors: Reich Jason , MacMillan Erin , Feldman Rebecca
Published: November 2024

Motivation: Simultaneous mutli-slice (SMS) techniques can reduce scan times. Power deposition from multiband pulses and outer slice signal from power independent of number of slices (PINS) pulses has hampered thoracic and cardiac SMS imaging. Goal(s): To reduce power deposition in thoracic and cardiac SMS imaging, thereby reducing scan times and motion artifacts. Approach: A power independent of finite number of slices (PIFINS) pulse was designed to excite any number of slices over a desired field of view with power deposition comparable to single-band pulse. Results: The PIFINS pulse was used to simultaneously acquire 3 slices in a cylindrical ACR phantom. Impact: Reducing scan time in thoracic and cardiac imaging reduces motion artifacts. Acceleration with simultaneous multi-slice has been hampered due to high power deposition. The new pulse presented here will enable SMS thoracic and cardiac imaging with reduced power deposition.
Pulseq on Philips MRI Systems: Unlocking and Validating Open-Source Sequences
Authors: Roos Thomas , Versteeg Edwin , Gosselink Mark , Hoogduin Hans , Klomp Dennis , Siero Jeroen , Wijnen Jannie
Published: November 2024

Motivation: Conventional MRI vendor-specific sequence development limits research transferability and reproducibility. Harmonized frameworks, like Pulseq, overcome these limitations - but Pulseq was not supported yet on Philips MRI scanners. Goal(s): To develop a fully-compliant Pulseq interpreter for Philips MRI systems, facilitating the use of open-source sequences previously incompatible with these platforms. Approach: Custom adaptation of Pulseq for the Philips R5.4 platform, followed by validation with standard imaging sequences using a field camera and phantom/in vivo scans, and comparison with native sequences. Results: Demonstration of the first Philips-compatible Pulseq interpreter, evidenced by successful scans at 7T, marking a leap in cross-vendor research capabilities. Impact: The successful adaptation of Pulseq sequences to Philips MRI system enables researchers to deploy and disseminate advanced MRI techniques universally, fostering cross-vendor collaboration and accelerating the evolution of MRI technology.
Partially spoiled non-balanced oscillating steady state imaging - A new T2-mapping approach
Authors: Köstler Herbert , Schad Oliver
Published: November 2024

Motivation: Determination of T2 typically depends on spin-echo based relaxometry. Partially spoiled non-balanced gradient echo imaging also allows T2-mapping but requires two data sets from two different steady states, making it prone to motion artefacts. Goal(s): To determine T2 from a single T2-weighted steady state. Approach: A combination of partial spoiling and oscillating steady state imaging was optimized using Bloch simulations, implemented on a human whole-body MR-scanner and tested on a test object and in vivo. Results: Partially spoiled oscillating steady state imaging allowed generating phase images similar to partially spoiled non-balanced SSFP imaging without the need to sequentially establish two different steady states. Impact: Partially spoiled gradient echo imaging allows T2-mapping without using large flip angles but requires data from two different steady states. By combining partial spoiling with oscillating steady state imaging T2 can be determined from one single oscillating steady state.
High-Resolution 3D Magnetization-Prepared GRE with Inherent Phase-cycling (iPC MP-GRE)
Authors: Peng Thomas , Ramin Jafari , Wu Can , Zhao Yansong , Peng Qi
Published: November 2024

Motivation: Magnetization-prepared (MP) 3D gradient-echo (GRE) MRI sequences suffer from T1 relaxation-induced artifacts, necessitating short echo train lengths. Paired phase-cycling (pPC) mitigates this but at the cost of doubled scan time. Goal(s): This research introduces inherent phase-cycling (iPC) to 3D MP-GRE sequences, aiming to eliminate T1-related artifacts without extending scan time.Approach: iPC combines random PC+ and PC- acquisitions within a single 3D sequence. It is demonstrated that iPC, coupled with compressed sensing reconstruction, achieves high-resolution imaging without scan time increase.Results: iPC significantly reduces ghosting and blurring artifacts compared to pPC, with potential applications in accelerated and artifact-free MRI.Impact: The iPC MP-GRE sequence improves image quality while reducing scan time and complexity. It promises faster, clearer diagnostic imaging, benefiting medical research and patient care, and opens doors to broader applications in quantitative parameter mapping and beyond.
Cluster Failure at (Ultra)high Resolution fMRI? Enhancing Accuracy in 7T Single-Subject Analysis Using Small Gaussian Kernels
Authors: Ceja Igor Tellez , Gladytz Thomas , Starke Ludger , Tabelow Karsten , Niendorf Thoralf , Reimann Henning
Published: November 2024

Motivation: Selecting the right Gaussian kernel size for fMRI lacks standardization. For the detection of subtle brain activations, smaller kernels are needed. However, their reliability in ensuring accurate and trustworthy results remains uncertain. Goal(s): Evaluate the effectiveness of small Gaussian filter kernel on fMRI data. Approach: Assessment of BOLD signal integrity, accuracy, and data normality- employing 7T fMRI simulated time series and resting-state data. Results: The study underscored the efficiency of smaller kernels in minimizing noise and upholding accurate signal detection. Residuals largely followed a Gaussian distribution. Impact: Our study provides factual support for using small Gaussian kernel sizes in 7T fMRI data for their reliability in both functionality and compliance with RFT requirements.
Enhanced neural activity detection in the fMRI using polar Fourier transform
Authors: Feizifar Babak , Ghaffarzadeh Sina , Makhsousi Faeze , Ghodrati Vahid , Nasiraei-Moghaddam Abbas
Published: November 2024

Motivation: Alternative distortion-reducing methods are needed since NUFFT reconstruction of modestly undersampled radial k-space creates streaking artifacts that influence the entire image and fMRI study's ROI.Goal(s): Our objective is to demonstrate that the ROI in our fMRI study is less exposed to aliasing artifacts when PFT reconstruction is used as opposed to NUFFT reconstruction. Approach: Radial-based fMRI images with 2x undersampling were reconstructed using PFT. The neural activity map was then compared to NUFFT-based reconstruction.Results: Compared to the NUFFT, our proposed approach achieved a qualitatively and quantitatively improved activation map thanks to the distinct artifact characteristic of the PFT. Impact: Global streaking artifacts in reconstructed images from undersampled radial k-space may seriously affect fMRI study ROI and lead to incorrect brain activity maps. This work used the PFT approach to reduce ROI aliasing artifact in fMRI studies.
Novel microstate method to identify fMRI networks and assess their dynamic temporal characteristics
Authors: Jann Kay , Wijesinghe Dilmini , Zhang Ru , Koenig Thomas , Wang Danny
Published: November 2024

Motivation: Implement a well-established method (microstate analysis) to characterize state and state-transitions from EEG to fMRI. Such an approach will provide information on dynamic network changes and could provide a novel way to assess brain function in health and disease. Goal(s): To provide a proof-of-concept that EEG-microstate analysis can be adapted to fMRI. Approach: Adapt EEG-microstate analysis to fMRI data and characterize dynamic brain network changes. Results: We demonstrate that this novel approach can identify distinct network states, their average duration, frequency of occurrence, total coverage of entire scan and transition probabilities between states. Impact: We provide proof-of-concept that commonly used EEG-microstate analysis can be adapted to characterize dynamic changes in brain network states in fMRI data. This novel analysis could provide novel insights in alterations of brain functionality in various disorders.
Compartmentalised reconstruction of cardiac 31P concentric ring MRSI at 7T
Authors: Mozes Ferenc , Tyler Andrew , Miller Jack , Clarke William , Valkovič Ladislav
Published: November 2024

Motivation: Cardiac 31P MRS allows the probing of metabolism in various heart diseases, however, commonly employed 3D MRSI techniques are slow even at 7 T. Goal(s): Our work aims to evaluate the use of compartment-based localised spectroscopy using a linear algebraic model (SLAM). Approach: 31P MRSI data was collected using concentric ring trajectory acquisitions and SLAM was used to reconstruct 31P signal from the myocardium. Results: We show increased SNR and reduced uncertainty in determining the cardiac PCr signal, in addition to also reducing the repeatability of PCr/ATP ratio measurements when compared to a 2.5 minute, NUFFT-reconstructed CRT protocol. Impact: Repeatable and high-SNR 31P acquisitions will allow the probing of cardiac energetics in patient populations that were previously unable to attend prolonged scan sessions at ultra-high field strengths.
Targeting Motor and Cognitive Impairments: Comparative Insights into STN-DBS and NAc-DBS Efficacy in Parkinson's Disease Model with Metabolism
Authors: Li Ssu-Ju , Lee Yi-Chun , Chen Ting-Chieh , Lo Yu-Chun , Chang Ching-Wen , Liang Yao-Wen , Lin Yi-Chen , Liu Yun-Ting , Lin Sheng-Huang , Chen You-Yin
Published: November 2024

Motivation: Addressing subthalamic nucleus deep brain stimulation (STN-DBS) limitations in Parkinson's Disease (PD), such as metabolic disorder and cognitive dysfunction. We explored nucleus accumbens deep brain stimulation (NAc-DBS) as an alternative, aiming to enhance motor, cognitive, and metabolic functions comprehensively. Goal(s): Investigate NAc-DBS effectiveness, bridging STN-DBS gaps, enhancing motor skills, and improving cognitive and metabolic functions in PD. Approach: Utilized behavioral tests, brain magnetic resonance imaging analysis, and bioenergetic analysis to evaluate NAc-DBS and STN-DBS impact on the MitoPark PD mouse model. Results: NAc-DBS significantly enhanced cognitive, motor functions, and energy metabolism, offering a promising therapeutic solution for PD patients. Impact: Our findings transform Parkinson's treatment, sheding a light to patients. The dual benefits of NAc-DBS inspire new inquiries, reshaping therapies with metabolic modulation. Improved outcomes redefine standards, offering hope for enhanced quality of life.
AwakeRodent, the multi-center, multi-species, multi-modality study!
Authors: Galteau Marie , Bo Binshi , Li Hui , Pei Mengchao , Xu Mengyang , Liang Zhifeng , Qin Qikai , Thompson Garth , Trouvé-Carpena Alejandro , Sempere-Ferràndez Alejandro , Canals Santiago , Tuset-Sanchis Luis , de Guzman A. Elizabeth , Hayward Andrew , Gozzi Alessandro , Gutierrez-Barragan Daniel , Naessens Daphne , Coolen Bram , Alles Lindy , Strijkers Gustav , Reneman Liesbeth , Dvořáková Lenka , Stenroos Petteri , Paasonen Jaakko , Gröhn Olli , Wang Ruoming , Chen Qian , Tian Xiangnan , Pei Mengchao , Liang Zhifeng , Ma Zhiwei , Moreno Andrea , Vrooman Roël , Grandjean Joanes
Published: November 2024

Motivation: To bring awareness on the heterogeneity in awake rodent functional imaging. We aim to identify protocol differences that optimize awake functional connectivity, reproducibility and collaboration. Goal(s): To aggregate awake rodent functional datasets, establish population parameters, provide evidence-based recommendations, compare functional Magnetic Resonance Imaging and functional Ultrasound, foster collaborations. Approach: We collect datasets from mice and rats, preprocess and run a seed-based analysis at the individual-level using RABIES. Group-level analysis is performed in Python, resulting in functional connectivity specificity maps. Results: We have gathered 5 mice-datasets and 4 rat-datasets totaling 122 scans with great variability in rodent characteristics, imaging methods, and experimental designs. Impact: Findings will empower researchers to refine awake rodent functional imaging, enhancing investigations into cognitive and behavioral processes, without the anesthesia confounds. This approach closely parallels human brain imaging, enhancing translational relevance and providing an accurate representation of conscious brain function.
Protocol for awake task free fMRI using freely behaving head fixed mice.
Authors: Vrooman Roël , Veltien Andor , Homberg Judith , Scheenen Tom , Grandjean Joanes
Published: November 2024

Motivation: To increase the translatability of preclinical imaging data, awake protocols have to be developed. Goal(s): Here we outline a protocol for awake task free fMRI using freely behaving head fixed mice. Approach: After headplate surgery and habituation to a holder containing a treadmill, mice are scanned up to 6 times. Results: The corticosterone and framewise displacement show that habituation seems to continue during scanning, suggesting that the habituation protocol needs to be lengthened. However, after dual regression analysis, activity within task free networks can be seen in the data, meaning that this protocol takes steps in the improvement of translatability of data. Impact: To increase the translatability of functional MRI data, development of awake protocols is necessary. This allows for removal of the confound of anesthesia as well as opening up the option for behavioral paradigms during scanning.
Astrocytic calcium signal bidirectionally regulated BOLD-fMRI signals in awake mice
Authors: Tong Chuanjun , Zou Yijuan , Xia Ying , Li Weishuai , Liang Zhifeng
Published: November 2024

Motivation: Previous study found brain-state dependent astrocytic calcium signals are related to positive and negative BOLD-fMRI signals. However, causal evidences regarding the contribution of astrocytes to BOLD signals is lacking. Goal(s): We aimed to provide causal evidences for the bidirectional contribution of astrocytic calcium activity on BOLD-fMRI signals. Approach: We applied simultaneous calcium imaging and awake mouse fMRI to detect distinct astrocytic signals (task-aligned vs. spontaneous) coupled to BOLD signals in three conditions, including no manipulation, activation and inhibition of S1BF astrocytes. Results: We found whisker stimulation-evoked astrocyte activity mainly contributes to positive BOLD signals, while state-specific astrocyte activity contributes to negative BOLD signals. Impact: We provide casual evidences that astrocytes bidirectionally regulated BOLD signals. Moreover, our results challenge the prevailing interpretation of the BOLD signal solely as an indicator of neuronal activity by highlighting the impact of arousal-specific involvement of astrocytes in neurovascular coupling.
Zero-echo time MB-SWIFT MRI responses to visual stimuli in a mouse model of demyelination and remyelination
Authors: Dvořáková Lenka , Salo Raimo , Stenroos Petteri , Paasonen Jaakko , Zehnder Tamara , Mueggler Thomas , Künnecke Basil , Gröhn Olli
Published: November 2024

Motivation: The changes in responses to sensory stimuli during demyelination and remyelination could help quantify neuro-functional deficits in neurodegenerative disorders. Goal(s): The goal of this study was to explore the capability of fMRI to detect changes in the functional response during both demyelination and remyelination. Approach: A genetic mouse model of widespread demyelination and remyelination was imaged with MB-SWIFT fMRI during visual stimulation. Results: We observed alterations in activation maps and fMRI responses to visual stimuli during demyelination. The function was restored during the remyelination phase. Impact: We show that zero echo time MB-SWIFT fMRI protocol with visual stimulation can detect myelination-associated differences in neuro-functional responses in mice and thus lends itself as a potential translational biomarker for disease and treatment monitoring in drug development.