Reproducible Research Practices in Magnetic Resonance Neuroimaging: A Review Informed by Advanced Language Models.

MRI has progressed significantly with the introduction of advanced computational methods and novel imaging techniques, but their wider adoption hinges on their reproducibility. This concise review synthesizes reproducible research insights from recent MRI articles to examine the current state of reproducibility in neuroimaging, highlighting key trends and challenges. It also provides a custom generative pretrained transformer (GPT) model, designed specifically for aiding in an automated analysis and synthesis of information pertaining to the reproducibility insights associated with the articles at the core of this review.

Repeat it without me: Crowdsourcing the T1 mapping common ground via the ISMRM reproducibility challenge.

PURPOSE: T1 mapping is a widely used quantitative MRI technique, but its tissue-specific values remain inconsistent across protocols, sites, and vendors. The ISMRM Reproducible Research and Quantitative MR study groups jointly launched a challenge to assess the reproducibility of a well-established inversion-recovery T1 mapping technique, using acquisition details from a seminal T1 mapping paper on a standardized phantom and in human brains. METHODS: The challenge used the acquisition protocol from Barral et al. (2010). Researchers collected T1 mapping data on the ISMRM/NIST phantom and/or in human brains. Data submission, pipeline development, and analysis were conducted using open-source platforms. Intersubmission and intrasubmission comparisons were performed. RESULTS: Eighteen submissions (39 phantom and 56 human datasets) on scanners by three MRI vendors were collected at 3 T (except one, at 0.35 T). The mean coefficient of variation was 6.1% for intersubmission phantom measurements, and 2.9% for intrasubmission measurements. For humans, the intersubmission/intrasubmission coefficient of variation was 5.9/3.2% in the genu and 16/6.9% in the cortex. An interactive dashboard for data visualization was also developed: https://rrsg2020.dashboards.neurolibre.org. CONCLUSION: The T1 intersubmission variability was twice as high as the intrasubmission variability in both phantoms and human brains, indicating that the acquisition details in the original paper were insufficient to reproduce a quantitative MRI protocol. This study reports the inherent uncertainty in T1 measures across independent research groups, bringing us one step closer to a practical clinical baseline of T1 variations in vivo.

The relaxometry hype cycle.

Relaxometry is a field with a glorious and controversial history, and no review will ever do it justice. It is full of egos and inventions, patents and lawsuits, high expectations and deep disillusionments. Rather than a paragraph dedicated to each of these, we want to give it an impressionistic overview, painted over with a coat of personal opinions and ruminations about the future of the field. For those unfamiliar with the Gartner hype cycle, here's a brief recap. The cycle starts with a technology trigger and goes through a phase of unrealistically inflated expectations. Eventually the hype dies down as implementations fail to deliver on their promise, and disillusionment sets in. Technologies that manage to live through the trough reach the slope of enlightenment, when there is a flurry of second and third generation products that make the initial promise feel feasible again. Finally, we reach the slope of productivity, where mainstream adoption takes off, and more incremental progress is made, eventually reaching steady state in terms of the technology's visibility. The entire interactive timeline can be viewed at https://qmrlab.org/relaxometry/.

The Canadian Open Neuroscience Platform-An open science framework for the neuroscience community.

The Canadian Open Neuroscience Platform (CONP) takes a multifaceted approach to enabling open neuroscience, aiming to make research, data, and tools accessible to everyone, with the ultimate objective of accelerating discovery. Its core infrastructure is the CONP Portal, a repository with a decentralized design, where datasets and analysis tools across disparate platforms can be browsed, searched, accessed, and shared in accordance with FAIR principles. Another key piece of CONP infrastructure is NeuroLibre, a preprint server capable of creating and hosting executable and fully reproducible scientific publications that embed text, figures, and code. As part of its holistic approach, the CONP has also constructed frameworks and guidance for ethics and data governance, provided support and developed resources to help train the next generation of neuroscientists, and has fostered and grown an engaged community through outreach and communications. In this manuscript, we provide a high-level overview of this multipronged platform and its vision of lowering the barriers to the practice of open neuroscience and yielding the associated benefits for both individual researchers and the wider community.

In-vivo along muscle fascicle strain heterogeneity is not affected by image registration parameters: Robustness testing of combined magnetic resonance-diffusion tensor imaging method.

Coupled with diffusion tractography, non-rigid registration of high-resolution anatomical MR images allows the calculation of local strains along human skeletal muscle fascicles in-vivo. A reference study (passively imposed lengthening of gastrocnemius medial muscle) reported local shortening and lengthening occurring along the same muscle fascicles. However, the robustness of strain amplitudes and distribution patterns should be studied, as the heterogeneity of local length changes has major implications for muscle function. Using a previous image set of human medial gastrocnemius (GM) we aimed at testing: (1) the consistency of our MRI-DTI analysis workflow against changes made to the software environments, (2) the hypothesis that non-rigid demons algorithm tuning parameters (16 paired combinations were tested) are not a significant determinant of muscle fiber direction strain heterogeneity caused by passive knee extension. A profoundly altered analysis workflow did reproduce the original results well, showing a general pattern of proximally lengthened and distally shortened muscle fascicles (strain amplitude range: 21%-67%). Hierarchical shift function analyses and pairwise comparison of strain distributions between 10 equal parts of the tracked GM fascicles confirmed the hypothesis showing no significant effects of tuning parameters determining the in-vivo deformation field inhomogeneity. The findings show the robustness of the MRI-DTI method, and confirming the hypothesis, also the consistency of along muscle fascicle strain heterogeneity patterns against parameter selection. However, the strain amplitudes do vary with parameter choices. New studies are indicated to determine optimal tuning parameters to achieve accurate strain amplitudes compared to exact strains.

Open and reproducible neuroimaging: From study inception to publication.

Empirical observations of how labs conduct research indicate that the adoption rate of open practices for transparent, reproducible, and collaborative science remains in its infancy. This is at odds with the overwhelming evidence for the necessity of these practices and their benefits for individual researchers, scientific progress, and society in general. To date, information required for implementing open science practices throughout the different steps of a research project is scattered among many different sources. Even experienced researchers in the topic find it hard to navigate the ecosystem of tools and to make sustainable choices. Here, we provide an integrated overview of community-developed resources that can support collaborative, open, reproducible, replicable, robust and generalizable neuroimaging throughout the entire research cycle from inception to publication and across different neuroimaging modalities. We review tools and practices supporting study inception and planning, data acquisition, research data management, data processing and analysis, and research dissemination. An online version of this resource can be found at https://oreoni.github.io. We believe it will prove helpful for researchers and institutions to make a successful and sustainable move towards open and reproducible science and to eventually take an active role in its future development.

qMRI-BIDS: An extension to the brain imaging data structure for quantitative magnetic resonance imaging data.

The Brain Imaging Data Structure (BIDS) established community consensus on the organization of data and metadata for several neuroimaging modalities. Traditionally, BIDS had a strong focus on functional magnetic resonance imaging (MRI) datasets and lacked guidance on how to store multimodal structural MRI datasets. Here, we present and describe the BIDS Extension Proposal 001 (BEP001), which adds a range of quantitative MRI (qMRI) applications to the BIDS. In general, the aim of qMRI is to characterize brain microstructure by quantifying the physical MR parameters of the tissue via computational, biophysical models. By proposing this new standard, we envision standardization of qMRI through multicenter dissemination of interoperable datasets. This way, BIDS can act as a catalyst of convergence between qMRI methods development and application-driven neuroimaging studies that can help develop quantitative biomarkers for neural tissue characterization. In conclusion, this BIDS extension offers a common ground for developers to exchange novel imaging data and tools, reducing the entrance barrier for qMRI in the field of neuroimaging.

Vendor-neutral sequences and fully transparent workflows improve inter-vendor reproducibility of quantitative MRI.

PURPOSE: We developed an end-to-end workflow that starts with a vendor-neutral acquisition and tested the hypothesis that vendor-neutral sequences decrease inter-vendor variability of T1, magnetization transfer ratio (MTR), and magnetization transfer saturation-index (MTsat) measurements. METHODS: We developed and deployed a vendor-neutral 3D spoiled gradient-echo (SPGR) sequence on three clinical scanners by two MRI vendors. We then acquired T1 maps on the ISMRM-NIST system phantom, as well as T1, MTR, and MTsat maps in three healthy participants. We performed hierarchical shift function analysis in vivo to characterize the differences between scanners when the vendor-neutral sequence is used instead of commercial vendor implementations. Inter-vendor deviations were compared for statistical significance to test the hypothesis. RESULTS: In the phantom, the vendor-neutral sequence reduced inter-vendor differences from 8% to 19.4% to 0.2% to 5% with an overall accuracy improvement, reducing ground truth T1 deviations from 7% to 11% to 0.2% to 4%. In vivo, we found that the variability between vendors is significantly reduced (p = 0.015) for all maps (T1, MTR, and MTsat) using the vendor-neutral sequence. CONCLUSION: We conclude that vendor-neutral workflows are feasible and compatible with clinical MRI scanners. The significant reduction of inter-vendor variability using vendor-neutral sequences has important implications for qMRI research and for the reliability of multicenter clinical trials.

CG-SENSE revisited: Results from the first ISMRM reproducibility challenge.

PURPOSE: The aim of this work is to shed light on the issue of reproducibility in MR image reconstruction in the context of a challenge. Participants had to recreate the results of "Advances in sensitivity encoding with arbitrary k-space trajectories" by Pruessmann et al. METHODS: The task of the challenge was to reconstruct radially acquired multicoil k-space data (brain/heart) following the method in the original paper, reproducing its key figures. Results were compared to consolidated reference implementations created after the challenge, accounting for the two most common programming languages used in the submissions (Matlab/Python). RESULTS: Visually, differences between submissions were small. Pixel-wise differences originated from image orientation, assumed field-of-view, or resolution. The reference implementations were in good agreement, both visually and in terms of image similarity metrics. DISCUSSION AND CONCLUSION: While the description level of the published algorithm enabled participants to reproduce CG-SENSE in general, details of the implementation varied, for example, density compensation or Tikhonov regularization. Implicit assumptions about the data lead to further differences, emphasizing the importance of sufficient metadata accompanying open datasets. Defining reproducibility quantitatively turned out to be nontrivial for this image reconstruction challenge, in the absence of ground-truth results. Typical similarity measures like NMSE of SSIM were misled by image intensity scaling and outlier pixels. Thus, to facilitate reproducibility, researchers are encouraged to publish code and data alongside the original paper. Future methodological papers on MR image reconstruction might benefit from the consolidated reference implementations of CG-SENSE presented here, as a benchmark for methods comparison.

An interactive meta-analysis of MRI biomarkers of myelin.

Several MRI measures have been proposed as in vivo biomarkers of myelin, each with applications ranging from plasticity to pathology. Despite the availability of these myelin-sensitive modalities, specificity and sensitivity have been a matter of discussion. Debate about which MRI measure is the most suitable for quantifying myelin is still ongoing. In this study, we performed a systematic review of published quantitative validation studies to clarify how different these measures are when compared to the underlying histology. We analyzed the results from 43 studies applying meta-analysis tools, controlling for study sample size and using interactive visualization (https://neurolibre.github.io/myelin-meta-analysis). We report the overall estimates and the prediction intervals for the coefficient of determination and find that MT and relaxometry-based measures exhibit the highest correlations with myelin content. We also show which measures are, and which measures are not statistically different regarding their relationship with histology.

A Cross-Sectional Study on the Impact of Arterial Stiffness on the Corpus Callosum, a Key White Matter Tract Implicated in Alzheimer's Disease.

BACKGROUND: Vascular risk factors such as arterial stiffness play an important role in the etiology of Alzheimer's disease (AD), presumably due to the emergence of white matter lesions. However, the impact of arterial stiffness to white matter structure involved in the etiology of AD, including the corpus callosum remains poorly understood. OBJECTIVE: The aims of the study are to better understand the relationship between arterial stiffness, white matter microstructure, and perfusion of the corpus callosum in older adults. METHODS: Arterial stiffness was estimated using the gold standard measure of carotid-femoral pulse wave velocity (cfPWV). Cognitive performance was evaluated with the Trail Making Test part B-A. Neurite orientation dispersion and density imaging was used to obtain microstructural information such as neurite density and extracellular water diffusion. The cerebral blood flow was estimated using arterial spin labelling. RESULTS: cfPWV better predicts the microstructural integrity of the corpus callosum when compared with other index of vascular aging (the augmentation index, the systolic blood pressure, and the pulse pressure). In particular, significant associations were found between the cfPWV, an alteration of the extracellular water diffusion, and a neuronal density increase in the body of the corpus callosum which was also correlated with the performance in cognitive flexibility. CONCLUSION: Our results suggest that arterial stiffness is associated with an alteration of brain integrity which impacts cognitive function in older adults.

Arterial stiffness cut-off value and white matter integrity in the elderly.

OBJECTIVE: Central artery stiffness is a confirmed predictor of cardiovascular health status that has been consistently associated with cognitive dysfunction and dementia. The European Society of Hypertension has established a threshold of arterial stiffness above which a cardiovascular event is likely to occur. However, the threshold at which arterial stiffness alters brain integrity has never been established. METHODS: The aim of this study is to determine the arterial stiffness cut-off value at which there is an impact on the white matter microstructure. This study has been conducted with 53 cognitively elderly without dementia. The integrity of the white matter was assessed using diffusion tensor metrics. Central artery stiffness was evaluated by measuring the carotid-femoral pulse wave velocity (cfPWV). The statistical analyses included 4 regions previously denoted vulnerable to increased central arterial stiffness (the corpus callosum, the internal capsule, the corona radiata and the superior longitudinal fasciculus). RESULTS: The results of this study call into question the threshold value of 10 m/s cfPWV established by the European Society of Hypertension to classify patients in neuro-cardiovascular risk groups. Our results suggest that the cfPWV threshold value would be approximately 8.5 m/s when the microstructure of the white matter is taken as a basis for comparison. CONCLUSIONS: Adjustment of the cfPWV value may be necessary for a more accurate distinction between lower and higher risk group of patients for white matter microstructural injury related to arterial stiffness. Targeting the highest risk group for prevention methods may, in turn, help preserve brain health and cognitive functions.

Arterial stiffness and white matter integrity in the elderly: A diffusion tensor and magnetization transfer imaging study.

BACKGROUND AND PURPOSE: The stiffness of large arteries and increased pulsatility can have an impact on the brain white matter (WM) microstructure, however those mechanisms are still poorly understood. The aim of this study was to investigate the association between central artery stiffness, axonal and myelin integrity in 54 cognitively unimpaired elderly subjects (65-75 years old). METHODS: The neuronal fiber integrity of brain WM was assessed using diffusion tensor metrics and magnetization transfer imaging as measures of axonal organization (Fractional anisotropy, Radial diffusivity) and state of myelination (Myelin volume fraction). Central artery stiffness was measured by carotid-femoral pulse wave velocity (cfPWV). Statistical analyses included 4 regions (the corpus callosum, the internal capsule, the corona radiata and the superior longitudinal fasciculus) which have been previously denoted as vulnerable to increased central artery stiffness. RESULTS: cfPWV was significantly associated with fractional anisotropy and radial diffusivity (p < 0.05, corrected for multiple comparisons) but not with myelin volume fraction. Findings from this study also show that improved executive function performance correlates with Fractional anisotropy positively (p < 0.05 corrected) as well as with myelin volume fraction and radial diffusivity negatively (p < 0.05 corrected). CONCLUSIONS: These findings suggest that arterial stiffness is associated with axon degeneration rather than demyelination. Controlling arterial stiffness may play a role in maintaining the health of WM axons in the aging brain.

Analysis of microcantilevers excited by pulsed-laser-induced photoacoustic waves.

This study presents a simulation-based analysis on the excitation of microcantilever in air using pulsed-laser-induced photoacoustic waves. A model was designed and coded to investigate the effects of consecutive photoacoustic waves, arising from a spherical light absorber illuminated by short laser pulses. The consecutiveness of the waves were adjusted with respect to the pulse repetition frequency of the laser to examine their cumulative effects on the oscillation of microcantilever. Using this approach, oscillation characteristics of two rectangular cantilevers with different resonant frequencies (16.9 kHz and 505.7 kHz) were investigated in the presence of the random oscillations. The results show that the effective responses of the microcantilevers to the consecutive photoacoustic waves provide steady-state oscillations, when the pulse repetition frequency matches to the fundamental resonant frequency or its lower harmonics. Another major finding is that being driven by the same photoacoustic pressure value, the high frequency cantilever tend to oscillate at higher amplitudes. Some of the issues emerging from these findings may find application area in atomic force microscopy actuation and photoacoustic signal detection.

Successful return to play following adductor longus proximal tendon rupture in professional soccer without re-injury at 12 months: A case report.

Treatment of total ruptures of adductor longus is challenging in professional sports. Time for return to pre-injury level as well as re-injury rates are of concern and surgical and conservative treatment approaches are debated; yet no consensus approach described for professional athletes. We present a case of a professional soccer player who experienced a rupture in his left adductor longus proximal tendon during a game and was treated conservatively. This case was followed-up during clinical assessment, imaging and strength testing until and after return to play. Primary outcome measure was the return to standard play condition at his pre-injury level without any functional deficits, measured by isokinetic testing. Second outcome measure was the recurrence. No recurrence was observed during the first year of follow-up. Total ruptures are very challenging for both the physician and the player to make a quick decision due to minimal or lack of pain. Functional outcomes are almost identical although operative treatments need longer time to return to play. This case report adds another example to the literature of a successful return to play after non-operative treatment of adductor longus rupture at elite level soccer.

Magnetic resonance and diffusion tensor imaging analyses indicate heterogeneous strains along human medial gastrocnemius fascicles caused by submaximal plantar-flexion activity.

Sarcomere length changes are central to force production and excursion of skeletal muscle. Previous modeling indicates non-uniformity of that if mechanical interaction of muscle with its surrounding muscular and connective tissues is taken into account. Hence, quantifying length changes along the fascicles of activated human muscle in vivo is crucial, but this is lacking due to technical complexities. Combining magnetic resonance imaging deformation analyses and diffusion tensor imaging tractography, the aim was to test the hypothesis that submaximal plantar flexion activity at 15% MVC causes heterogeneous length changes along the fascicles of human medial gastrocnemius (GM) muscle. A general fascicle strain distribution pattern shown for all subjects indicates that proximal track segments are shortened, whereas distal ones are lengthened (e.g., by 13% and 29%, respectively). Mean fiber direction strains of different tracts also shows heterogeneity (for up to 57.5% of the fascicles). Inter-subject variability of amplitude and distribution of fascicle strains is notable. These findings confirm the hypothesis and are solid indicators for the functionally dependent mechanics of human muscle, in vivo. Heterogeneity of fascicle strains can be explained by epimuscular myofascial force transmission. To the best of our knowledge, this is the first study, which quantified local deformations along human skeletal muscle fascicles caused by sustained submaximal activation. The present approach and indicated fascicle strain heterogeneity has numerous implications for muscle function in health and disease to estimate the muscle's contribution to the joint moment and excursion and to evaluate mechanisms of muscle injury and several treatment techniques.

Combined magnetic resonance and diffusion tensor imaging analyses provide a powerful tool for in vivo assessment of deformation along human muscle fibers.

Muscle fiber direction strain provides invaluable information for characterizing muscle function. However, methods to study this for human muscles in vivo are lacking. Using magnetic resonance (MR) imaging based deformation analyses and diffusion tensor (DT) imaging based tractography combined, we aimed to assess muscle fiber direction local tissue deformations within the human medial gastrocnemius (GM) muscle. Healthy female subjects (n=5, age=27±1 years) were positioned prone within the MR scanner in a relaxed state with the ankle angle fixed at 90°. The knee was brought to flexion (140.8±3.0°) (undeformed state). Sets of 3D high resolution MR, and DT images were acquired. This protocol was repeated at extended knee joint position (177.0±1.0°) (deformed state). Tractography and Demons nonrigid registration algorithm was utilized to calculate local deformations along muscle fascicles. Undeformed state images were also transformed by a synthetic rigid body motion to calculate strain errors. Mean strain errors were significantly smaller then mean fiber direction strains (lengthening: 0.2±0.1% vs. 8.7±8.5%; shortening: 3.3±0.9% vs. 7.5±4.6%). Shortening and lengthening (up to 23.3% and 116.7%, respectively) occurs simultaneously along individual fascicles despite imposed GM lengthening. Along-fiber shear strains confirm the presence of much shearing between fascicles. Mean fiber direction strains of different tracts also show non-uniform distribution. Inhomogeneity of fiber strain indicates epimuscular myofascial force transmission. We conclude that MR and DT imaging analyses combined provide a powerful tool for quantifying deformation along human muscle fibers in vivo. This can help substantially achieving a better understanding of normal and pathological muscle function and mechanisms of treatment techniques.