ReviewHuman brain mapping2022
ENIGMA HALFpipe: Interactive, reproducible, and efficient analysis for resting-state and task-based fMRI data.
Review in Human brain mapping, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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
68 citing papers in PubMed.
- Rostral anterior cingulate network effective connectivity in depressed adolescents and associations with treatment response in a randomized controlled trial.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2022Trial
- Evidence that intrinsic brain connectivity moderates the association between gait and neurocognitive function in people living with HIV.Journal of neurovirology · 2026Article
- Reproducible human reward imaging phenotypes exhibit differential sensitivity to dopamine D2 receptor antagonism.Nature communications · 2026Article
- Evaluating clinical and neuroimaging predictors for cognitive-behavioral therapy outcome in obsessive-compulsive disorder.Scientific reports · 2026Article
- Dynamic changes in amygdala and insula responses to the onset and offset of conditioned stimuli during threat learning.Scientific reports · 2026Article
- The Salience of Psychotic Experiences: Neural Correlates in the General Population.Schizophrenia bulletin · 2026Article
- Association of glymphatic function with 40-Hz neural oscillations, systemic metabolic markers, and cognitive performance in healthy aging adults: An EEG and MRI study.Translational psychiatry · 2026Article
- Predicting stress response trajectories: Differential contributions of limbic and prefrontal regions to cortisol and affective responses.Translational psychiatry · 2026Article
- The ENIGMA MEG Pipeline: Automated cortically localized spectral analysis of multi-site resting state MEG datasets.bioRxiv : the preprint server for biology · 2026Article
- Dynamic and Static Resting-State Functional Connectivity of Canonical Networks in Military and Civilian Populations With Posttraumatic Stress Disorder and/or Mild Traumatic Brain Injury.Biological psychiatry. Cognitive neuroscience and neuroimaging · 2026Article
- Temporal Dynamics of Parkinson's Disease Tremor: Clinical and Neuroimaging Insights.Movement disorders : official journal of the Movement Disorder Society · 2026Article
- Brain-heart interactions in late-onset major depressive disorder revealed by multimodal HRV-driven fMRI.Communications biology · 2026Article
- ComBat Harmonization With and Without Empirical Bayes Estimation for Resting-State Functional Connectivity in Pediatric Mild Traumatic Brain Injury: a CARE4Kids Study.Research square · 2026Article
- Resting-State Functional Connectivity of the Amygdala and Hippocampus in PTSD: Results From the PGC-ENIGMA PTSD Working Group.The American journal of psychiatry · 2026Article
- Toward trustworthy clinical AI for obsessive-compulsive disorder: reliability, generalizability, and interpretability of a transformer model across the ENIGMA-OCD consortium.medRxiv : the preprint server for health sciences · 2026Article
- Towards a general-purpose foundation model for functional MRI analysis.Nature biomedical engineering · 2026Article
- Slow wave canonical activity deviation concept: Toward a slow wave-based EEG-fMRI reference map for health-associated network function.iScience · 2026Article
- Linking brain structure to stress reactivity: cingulate surface area predicts acute cortisol responses.Psychological medicine · 2026Article
- Abnormal functional connectivity patterns in temporal lobe epilepsy-An international ENIGMA-epilepsy study.Epilepsia open · 2026Article
- Effective Connectivity Identifies Divergent Cerebro-Cerebellar Network Organization in Schizophrenia.Cerebellum (London, England) · 2026Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
The reproducibility crisis in neuroimaging has led to an increased demand for standardized data processing workflows. Within the ENIGMA consortium, we developed HALFpipe (Harmonized Analysis of Functional MRI pipeline), an open-source, containerized, user-friendly tool that facilitates reproducible analysis of task-based and resting-state fMRI data through uniform application of preprocessing, quality assessment, single-subject feature extraction, and group-level statistics. It provides state-of-the-art preprocessing using fMRIPrep without the requirement for input data in Brain Imaging Data Structure (BIDS) format. HALFpipe extends the functionality of fMRIPrep with additional preprocessing steps, which include spatial smoothing, grand mean scaling, temporal filtering, and confound regression. HALFpipe generates an interactive quality assessment (QA) webpage to rate the quality of key preprocessing outputs and raw data in general. HALFpipe features myriad post-processing functions at the individual subject level, including calculation of task-based activation, seed-based connectivity, network-template (or dual) regression, atlas-based functional connectivity matrices, regional homogeneity (ReHo), and fractional amplitude of low-frequency fluctuations (fALFF), offering support to evaluate a combinatorial number of features or preprocessing settings in one run. Finally, flexible factorial models can be defined for mixed-effects regression analysis at the group level, including multiple comparison correction. Here, we introduce the theoretical framework in which HALFpipe was developed, and present an overview of the main functions of the pipeline. HALFpipe offers the scientific community a major advance toward addressing the reproducibility crisis in neuroimaging, providing a workflow that encompasses preprocessing, post-processing, and QA of fMRI data, while broadening core principles of data analysis for producing reproducible results. Instructions and code can be found at https://github.com/HALFpipe/HALFpipe.
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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.