IntroductionNeuroimaging technology has experienced explosive growth and transformed the study of neural mechanisms across health and disease. However, given the diversity of sophisticated tools for handling neuroimaging data, the field faces challenges in method integration, particularly across multiple modalities and species. Specifically, researchers often have to rely on siloed approaches which limit reproducibility, with idiosyncratic data organization and limited software interoperability.MethodsTo address these challenges, we have developed Quantitative Neuroimaging Environment & Toolbox (QuNex), a platform for consistent end-to-end processing and analytics. QuNex provides several novel functionalities for neuroimaging analyses, including a “turnkey” command for the reproducible deployment of custom workflows, from onboarding raw data to generating analytic features.ResultsThe platform enables interoperable integration of multi-modal, community-developed neuroimaging software through an extension framework with a software development kit (SDK) for seamless integration of community tools. Critically, it supports high-throughput, parallel processing in high-performance compute environments, either locally or in the cloud. Notably, QuNex has successfully processed over 10,000 scans across neuroimaging consortia, including multiple clinical datasets. Moreover, QuNex enables integration of human and non-human workflows via a cohesive translational platform.DiscussionCollectively, this effort stands to significantly impact neuroimaging method integration across acquisition approaches, pipelines, datasets, computational environments, and species. Building on this platform will enable more rapid, scalable, and reproducible impact of neuroimaging technology across health and disease.

Neuroimaging technology has experienced explosive growth and has transformed the study of neural mechanisms across health and disease. However, given the diversity of sophisticated tools for handling neuroimaging data, the field faces challenges around method integration (1-3). Specifically, researchers often have to rely on siloed approaches which limit reproducibility, with idiosyncratic data organization and limited software interoperability. To address these challenges, we developed Quantitative Neuroimaging Environment & Toolbox (QuNex), a platform for consistent end-to-end processing and analytics. QuNex is engineered for reproducible deployment of custom workflows, from onboarding raw data to generating analytic features, in a single "turnkey" command. The platform enables inter-operable integration of multi-modal, community-developed neuroimaging software through an extension framework with a software development kit for seamless integration of community tools. Critically, it supports high-throughput, parallel processing in high-performance compute environments, either locally or in the cloud. Notably, QuNex has successfully processed over 10,000 scans across neuroimaging consortia (4), including multiple clinical datasets. Moreover, QuNex enables integration of non-human primate, rodent, and human workflows via a cohesive translational platform. Collectively, this effort stands to significantly impact neuroimaging method integration across acquisition approaches, pipelines, datasets, computational environments, and species. Building on this platform will enable more rapid, scalable, and reproducible impact of neuroimaging technology across health and disease.

Sustained neural activity during the delay phase of spatial working memory tasks is compelling evidence for the neural correlate of active storage and maintenance of spatial information, however, it does not provide insight into specific mechanisms of spatial coding. This activity may reflect a range of processes, such as maintenance of a stimulus position or a prepared motor response plan. The aim of our study was to examine neural evidence for the use of different coding strategies, depending on the characteristics and demands of a spatial working memory task. Thirty-one (20 women, 23 ± 5 years) and 44 (23 women, 21 ± 2 years) participants performed a spatial working memory task while we measured their brain activity using fMRI in two separate experiments. Participants were asked to remember the position of a briefly presented target stimulus and, after a delay period, to use a joystick to indicate either the position of the remembered target or an indicated non-matching location. The task was designed so that the predictability of the response could be manipulated independently of task difficulty and memory retrieval process. We were particularly interested in contrasting conditions in which participants (i) could use prospective coding of the motor response or (ii) had to rely on retrospective sensory information. Prospective motor coding was associated with activity in somatomotor, premotor, and motor cortices and increased integration of brain activity with and within the somatomotor network. In contrast, retrospective sensory coding was associated with increased activity in parietal regions and increased functional connectivity with and within secondary visual and dorsal attentional networks. The observed differences in activation levels, dynamics of differences over trial duration, and integration of information within and between brain networks provide compelling evidence for the use of complementary spatial working memory strategies optimized to meet task demands.

Multimodal neuroimaging using EEG and fMRI provides deeper insights into brain function by improving the spatial and temporal resolution of the acquired data. However, simultaneous EEG-fMRI inevitably compromises the quality of the EEG and fMRI signals due to the high degree of interaction between the two systems. Fluctuations in the magnetic flux flowing through the participant and the EEG system, whether due to movement within the magnetic field of the scanner or to changes in magnetic field strength, induce electrical potentials in the EEG recordings that mask the much weaker electrical activity of the neuronal populations. A number of different methods have been proposed to reduce MR artifacts. We present an overview of the most commonly used methods and an evaluation of the methods using three sets of diverse EEG data. We limited the evaluation to open-access and easy-to-use methods and a reference signal regression method using a set of six carbon-wire loops (CWL), which allowed evaluation of their added value. The evaluation was performed by comparing EEG signals recorded outside the MRI scanner with artifact-corrected EEG signals recorded simultaneously with fMRI. To quantify and evaluate the quality of artifact reduction methods in terms of the spectral content of the signal, we analyzed changes in oscillatory activity during a resting-state and a finger tapping motor task. The quality of artifact reduction in the time domain was assessed using data collected during a visual stimulation task. In the study we utilized hierarchical Bayesian probabilistic modeling for statistical inference and observed significant differences between the evaluated methods in the success of artifact reduction and associated signal quality in both the frequency and time domains. In particular, the CWL system proved superior to the other methods evaluated in improving spectral contrast in the alpha and beta bands and in recovering visual evoked responses. Based on the results of the evaluation study, we proposed guidelines for selecting the optimal method for MR artifact reduction.

The event-related potential method has proven to be a useful tool for studying the effects of gender information in language. Studies have shown that mismatch between the antecedent and the following referent triggers two ERP components, N400 and P600. In the present study, we investigated how grammatical gender affects the mental representation of the grammatical subject. A match-mismatch paradigm was used to investigate how masculine grammatical gender and gender-balanced forms (the explicit mention of masculine and feminine forms as word pairs) as role nouns affect the processing of the referent in Slovenian. The morphological complexity of Slovenian language required the use of anaphoric verbs instead of nouns/pronouns, on which previous research was based. The results showed that following both the gender-balanced and the masculine generic forms, P600 (but not N400) was observed in response to the feminine verb but not to the masculine verb. The P600 amplitude was smaller in the case of the gender-balanced form than in the case of the masculine generic form only. We have concluded that gender-balanced forms are more open to feminine continuations than masculine generic forms. This is the first ERP study in Slovenian to address the effects of processing grammatical gender, thus contributing to existing research on languages with grammatical gender. The great strength of the study is that it is one of the first ERP studies to test the mental inclusivity of gender-balanced forms.