Journal article

ENIGMA HALFpipe: Interactive, reproducible, and efficient analysis for resting-state and task-based fMRI data

Lea Waller, Susanne Erk, Elena Pozzi, Yara Toenders, Courtney Haswell, Marc Büttner, Paul Thompson, Lianne Schmaal, Rajendra Morey, Henrik Walter, Ilya Veer

Cold Spring Harbor Laboratory | Published : 2021

Abstract

The reproducibility crisis in neuroimaging has led to an increased demand for standardized data processing workflows. Within the ENIGMA consortium, we developed HALFpipe ( H armonized A na L ysis of F unctional MRI p i p e line), 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 pre..

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