A Comparison of Single- and Multi-Echo Processing of Functional MRI Data During Overt Autobiographical Recall

Harnessing slow event-related fMRI to investigate trial-level brain-behavior relationships during object identification

Understanding brain-behavior relationships is the core goal of cognitive neuroscience. However, these relationships-especially those related to complex cognitive and psychopathological behaviors-have recently been shown to suffer from very small effect sizes (0.1 or less), requiring potentially thousands of participants to yield robust findings. Here, we focus on a much more optimistic case utilizing task-based fMRI and a multi-echo acquisition with trial-level brain-behavior associations measured within participant. In a visual object identification task for which the behavioral measure is response time (RT), we show that while trial-level associations between BOLD and RT can similarly suffer from weak effect sizes, converting these associations to their corresponding group-level effects can yield robust peak effect sizes (Cohen's d = 1.0 or larger). Multi-echo denoising (Multi-Echo ICA or ME-ICA) yields larger effects than optimally combined multi-echo with no denoising, which is in turn an improvement over standard single-echo acquisition. While estimating these brain-behavior relationships benefits from the inclusion of a large number of trials per participant, even a modest number of trials (20-30 or more) yields robust group-level effect sizes, with replicable effects obtainable with relatively standard sample sizes (N = 20-30 participants per sample).

Breakthroughs and challenges for generating brain network-based biomarkers of treatment response in depression

Treatment outcomes widely vary for individuals diagnosed with major depressive disorder, implicating a need for deeper understanding of the biological mechanisms conferring a greater likelihood of response to a particular treatment. Our improved understanding of intrinsic brain networks underlying depression psychopathology via magnetic resonance imaging and other neuroimaging modalities has helped reveal novel and potentially clinically meaningful biological markers of response. And while we have made considerable progress in identifying such biomarkers over the last decade, particularly with larger, multisite trials, there are significant methodological and practical obstacles that need to be overcome to translate these markers into the clinic. The aim of this review is to review current literature on brain network structural and functional biomarkers of treatment response or selection in depression, with a specific focus on recent large, multisite trials reporting predictive accuracy of candidate biomarkers. Regarding pharmaco- and psychotherapy, we discuss candidate biomarkers, reporting that while we have identified candidate biomarkers of response to a single intervention, we need more trials that distinguish biomarkers between first-line treatments. Further, we discuss the ways prognostic neuroimaging may help to improve treatment outcomes to neuromodulation-based therapies, such as transcranial magnetic stimulation and deep brain stimulation. Lastly, we highlight obstacles and technical developments that may help to address the knowledge gaps in this area of research. Ultimately, integrating neuroimaging-derived biomarkers into clinical practice holds promise for enhancing treatment outcomes and advancing precision psychiatry strategies for depression management. By elucidating the neural predictors of treatment response and selection, we can move towards more individualized and effective depression interventions, ultimately improving patient outcomes and quality of life.

Processing, evaluating, and understanding FMRI data with afni_proc.py

FMRI data are noisy, complicated to acquire, and typically go through many steps of processing before they are used in a study or clinical practice. Being able to visualize and understand the data from the start through the completion of processing, while being confident that each intermediate step was successful, is challenging. AFNI's afni_proc.py is a tool to create and run a processing pipeline for FMRI data. With its flexible features, afni_proc.py allows users to both control and evaluate their processing at a detailed level. It has been designed to keep users informed about all processing steps: it does not just process the data, but also first outputs a fully commented processing script that the users can read, query, interpret, and refer back to. Having this full provenance is important for being able to understand each step of processing; it also promotes transparency and reproducibility by keeping the record of individual-level processing and modeling specifics in a single, shareable place. Additionally, afni_proc.py creates pipelines that contain several automatic self-checks for potential problems during runtime. The output directory contains a dictionary of relevant quantities that can be programmatically queried for potential issues and a systematic, interactive quality control (QC) HTML. All of these features help users evaluate and understand their data and processing in detail. We describe these and other aspects of afni_proc.py here using a set of task-based and resting-state FMRI example commands.

Improved Resting-State Functional MRI Using Multi-Echo Echo-Planar Imaging on a Compact 3T MRI Scanner with High-Performance Gradients

In blood-oxygen-level-dependent (BOLD)-based resting-state functional (RS-fMRI) studies, usage of multi-echo echo-planar-imaging (ME-EPI) is limited due to unacceptable late echo times when high spatial resolution is used. Equipped with high-performance gradients, the compact 3T MRI system (C3T) enables a three-echo whole-brain ME-EPI protocol with smaller than 2.5 mm isotropic voxel and shorter than 1 s repetition time, as required in landmark fMRI studies. The performance of the ME-EPI was comprehensively evaluated with signal variance reduction and region-of-interest-, seed- and independent-component-analysis-based functional connectivity analyses and compared with a counterpart of single-echo EPI with the shortest TR possible. Through the multi-echo combination, the thermal noise level is reduced. Functional connectivity, as well as signal intensity, are recovered in the medial orbital sulcus and anterior transverse collateral sulcus in ME-EPI. It is demonstrated that ME-EPI provides superior sensitivity and accuracy for detecting functional connectivity and/or brain networks in comparison with single-echo EPI. In conclusion, the high-performance gradient enabled high-spatial-temporal resolution ME-EPI would be the method of choice for RS-fMRI study on the C3T.

Evaluating the efficacy of multi-echo ICA denoising on model-based fMRI

fMRI is an indispensable tool for neuroscience investigation, but this technique is limited by multiple sources of physiological and measurement noise. These noise sources are particularly problematic for analysis techniques that require high signal-to-noise ratio for stable model fitting, such as voxel-wise modeling. Multi-echo data acquisition in combination with echo-time dependent ICA denoising (ME-ICA) represents one promising strategy to mitigate physiological and hardware-related noise sources as well as motion-related artifacts. However, most studies employing ME-ICA to date are resting-state fMRI studies, and therefore we have a limited understanding of the impact of ME-ICA on complex task or model-based fMRI paradigms. Here, we addressed this knowledge gap by comparing data quality and model fitting performance of data acquired during a visual population receptive field (pRF) mapping (N = 13 participants) experiment after applying one of three preprocessing procedures: ME-ICA, optimally combined multi-echo data without ICA-denoising, and typical single echo processing. As expected, multi-echo fMRI improved temporal signal-to-noise compared to single echo fMRI, with ME-ICA amplifying the improvement compared to optimal combination alone. However, unexpectedly, this boost in temporal signal-to-noise did not directly translate to improved model fitting performance: compared to single echo acquisition, model fitting was only improved after ICA-denoising. Specifically, compared to single echo acquisition, ME-ICA resulted in improved variance explained by our pRF model throughout the visual system, including anterior regions of the temporal and parietal lobes where SNR is typically low, while optimal combination without ICA did not. ME-ICA also improved reliability of parameter estimates compared to single echo and optimally combined multi-echo data without ICA-denoising. Collectively, these results suggest that ME-ICA is effective for denoising task-based fMRI data for modeling analyzes and maintains the integrity of the original data. Therefore, ME-ICA may be beneficial for complex fMRI experiments, including voxel-wise modeling and naturalistic paradigms.

Key considerations for child and adolescent MRI data collection

Cognitive neuroimaging researchers' ability to infer accurate statistical conclusions from neuroimaging depends greatly on the quality of the data analyzed. This need for quality control is never more evident than when conducting neuroimaging studies with children and adolescents. Developmental neuroimaging requires patience, flexibility, adaptability, extra time, and effort. It also provides us a unique, non-invasive way to understand the development of cognitive processes, individual differences, and the changing relations between brain and behavior over the lifespan. In this discussion, we focus on collecting magnetic resonance imaging (MRI) data, as it is one of the more complex protocols used with children and youth. Through our extensive experience collecting MRI datasets with children and families, as well as a review of current best practices, we will cover three main topics to help neuroimaging researchers collect high-quality datasets. First, we review key recruitment and retention techniques, and note the importance for consistency and inclusion across groups. Second, we discuss ways to reduce scan anxiety for families and ways to increase scan success by describing the pre-screening process, use of a scanner simulator, and the need to focus on participant and family comfort. Finally, we outline several important design considerations in developmental neuroimaging such as asking a developmentally appropriate question, minimizing data loss, and the applicability of public datasets. Altogether, we hope this article serves as a useful tool for those wishing to enter or learn more about developmental cognitive neuroscience.