ArticleHuman brain mapping2019
Exploring the impact of analysis software on task fMRI results.
Article in Human brain mapping, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 78 papers, 7 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
78 citing papers in PubMed, 7 syntheses or guidelines pooled it.
- Disrupted and reorganized connectivity of brain networks in multiple sclerosis: a systematic review and meta-analysis of resting-state functional MRI.Journal of neurology · 2026Pooled it
- Improving the Eligibility of Task-Based fMRI Studies for Meta-Analysis: A Review and Reporting Recommendations.Neuroinformatics · 2024Pooled it
- A Minimum Bayes Factor Based Threshold for Activation Likelihood Estimation.Neuroinformatics · 2023Pooled it
- In search of convergent regional brain abnormality in cognitive emotion regulation: A transdiagnostic neuroimaging meta-analysis.Human brain mapping · 2022Pooled it
- Networks underpinning emotion: A systematic review and synthesis of functional and effective connectivity.NeuroImage · 2021Pooled it
- Meta-analysis of neural systems underlying placebo analgesia from individual participant fMRI data.Nature communications · 2021Pooled it
- Functional MRI Studies in Friedreich's Ataxia: A Systematic Review.Frontiers in neurology · 2021Pooled it
- Effects of high-definition tDCS targeting individual motor hotspot with EMG-driven robotic hand training on upper extremity motor function: a pilot randomized controlled trial.Journal of neuroengineering and rehabilitation · 2024Trial
- Investigating the Contribution of Molecular-Enriched Functional Connectivity to Brain-Age Analysis.Human brain mapping · 2026Article
- Distinct and common subcortical functional connectivity revealed across three major psychiatric disorders.Psychological medicine · 2026Article
- Effect of database, pre-processing pipeline, and scan duration on rs-fMRI functional connectivity based treatment targets for TMS obtained using the Stanford Neuromodulation Therapy (SNT) protocol.Psychoradiology · 2026Article
- Age-Related Changes in Default Mode Network in Autism Spectrum Disorder: Insights From Effective Connectivity.Human brain mapping · 2025Article
- Investigating the Contribution of Molecular-Enriched Functional Connectivity to Brain-Age Analysis.bioRxiv : the preprint server for biology · 2025Article
- An attention-based fuzzy CNN-LTSM network for visual object recognition from fMRI images.Journal of computational neuroscience · 2025Article
- fNIRS reproducibility varies with data quality, analysis pipelines, and researcher experience.Communications biology · 2025Article
- NeuroDISK: An AI Approach to Automate Continuous Inquiry-Driven Discoveries in Neuroimaging Genetics.bioRxiv : the preprint server for biology · 2025Article
- Open-source platforms to investigate analytical flexibility in neuroimaging.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Pipeline variability: Friend or foe, depending on the goal: Comment on Germani et al. 2025.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Predicting Parkinson's disease trajectory using clinical and functional MRI features: A reproduction and replication study.PloS one · 2025Article
- On the validity of fMRI mega-analyses using data processed with different pipelines.Imaging neuroscience (Cambridge, Mass.) · 2025Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
A wealth of analysis tools are available to fMRI researchers in order to extract patterns of task variation and, ultimately, understand cognitive function. However, this "methodological plurality" comes with a drawback. While conceptually similar, two different analysis pipelines applied on the same dataset may not produce the same scientific results. Differences in methods, implementations across software, and even operating systems or software versions all contribute to this variability. Consequently, attention in the field has recently been directed to reproducibility and data sharing. In this work, our goal is to understand how choice of software package impacts on analysis results. We use publicly shared data from three published task fMRI neuroimaging studies, reanalyzing each study using the three main neuroimaging software packages, AFNI, FSL, and SPM, using parametric and nonparametric inference. We obtain all information on how to process, analyse, and model each dataset from the publications. We make quantitative and qualitative comparisons between our replications to gauge the scale of variability in our results and assess the fundamental differences between each software package. Qualitatively we find similarities between packages, backed up by Neurosynth association analyses that correlate similar words and phrases to all three software package's unthresholded results for each of the studies we reanalyse. However, we also discover marked differences, such as Dice similarity coefficients ranging from 0.000 to 0.684 in comparisons of thresholded statistic maps between software. We discuss the challenges involved in trying to reanalyse the published studies, and highlight our efforts to make this research reproducible.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.