Rodent fMRI Preprocessing with BIDS and RABIES: A Bilingual, Interactive Manual for Standardized, Reproducible Workflows

Background. Reproducibility remains a central challenge in rodent functional MRI (fMRI), and much of the difficulty arises at the preprocessing stage. Unlike human neuroimaging—where community standards are widely used—the preclinical community still lacks agreed-upon procedures for preprocessing and quality control [1]. As a result, many groups depend on locally built pipelines that fit their scanners and routines but hinder comparisons across studies and can reduce the robustness of reported effects [1]. The situation echoes the concerns voiced in human fMRI more than a decade ago, when divergent analytic choices triggered a coordinated effort toward standardization [1]. In response, the field established shared data formats and processing frameworks—most notably, the Brain Imaging Data Structure (BIDS) [2] and pipelines such as fMRIPrep [3]—and analogous initiatives are now being adapted to preclinical imaging. Contribution. We present a bilingual, interactive manual that consolidates essential guidance for bringing rodent fMRI workflows into alignment with best practices centered on BIDS and RABIES. The site provides concise modules, organized parameter tables, and direct links to OS-specific installation instructions (Windows, macOS, Linux), covering preprocessing, confound correction, quality control, and first-pass analyses in a didactic format consistent with community standards [1–4]. By drawing together materials otherwise dispersed across papers, documentation, and repositories—and combining them with hands-on experience—the manual lowers the learning curve and operationalizes standardization for reliable, shareable pipelines [1, 2, 4]. Availability. Spanish: https://view.genially.com/66bc6b92b3be66ad9babe23f; English: https://view.genially.com/68991da348e6bd6ccd3a065b. References [1] Desrosiers-Grégoire, G., Devenyi, G. A., Grandjean, J., & Chakravarty, M. M. (2024). A standardized image processing and data quality platform for rodent fMRI. Nature Communications, 15, Article 6708. https://doi.org/10.1038/s41467-024-50826-8 [2] Gorgolewski, K. J., Auer, T., Calhoun, V. D., et al. (2016). The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Scientific Data, 3, 160044. https://doi.org/10.1038/sdata.2016.44 [3] Esteban, O., Markiewicz, C. J., Blair, R. W., et al. (2019). fMRIPrep: a robust preprocessing pipeline for functional MRI. Nature Methods, 16(1), 111–116. https://doi.org/10.1038/s41592-018-0235-4 [4] Grandjean, J., Desrosiers-Gregoire, G., Anckaerts, C., et al. (2023). A consensus protocol for functional connectivity analysis in the rat brain. Nature Neuroscience, 26(4), 673–681. https://doi.org/10.1038/s41593-023-01286-8 How to cite the manual Martínez-Guerrero, A., Apablaza-Yevenes, D. E., Ibarra-Coronado, E. G., & Pérez-Torres, A. (2025). Rodent fMRI Preprocessing with BIDS and RABIES: A Bilingual, Interactive Manual for Standardized, Reproducible Workflows (v1.0). Zenodo. https://doi.org/10.5281/zenodo.16809121