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Brainana: an end-to-end preprocessing framework for macaque neuroimaging
Xingyu Liu1, Yijun Zhang2, Zi Yin3
1Department of Psychology, University of Pennsylvania, Philadelphia, PA 19104, USA.
Biorxiv : the Preprint Server for Biology
|June 22, 2026
Summary
Brainana is a new automated framework for processing macaque MRI data. This tool enhances reproducibility and accessibility for non-human primate neuroimaging research.
Area of Science:
- Neuroscience
- Medical Imaging
- Computational Biology
Background:
- Macaque MRI research connects systems neuroscience with cellular mechanisms.
- Current preprocessing tools for macaque neuroimaging are fragmented and difficult to integrate.
- Lack of standardized, reproducible preprocessing hinders macaque MRI data analysis and cross-study comparisons.
Purpose of the Study:
- To introduce Brainana, an automated and BIDS-compatible preprocessing framework for macaque neuroimaging.
- To address the fragmentation and reproducibility challenges in macaque MRI data processing.
- To facilitate scalable and accessible neuroimaging analysis for non-human primate research.
Main Methods:
- Brainana integrates structural and functional MRI preprocessing, cortical surface reconstruction, quality control, and atlas projection.
- It utilizes macaque-trained deep learning models for brain extraction and tissue segmentation.
- The framework is containerized for easy deployment and offers cloud access for users.
- Conformation methods standardize variable acquisitions, and surface reconstruction is optimized for macaque anatomy.
Main Results:
- Brainana successfully processed data from 23 imaging sites across heterogeneous scanners and protocols.
- It achieved accurate anatomical correspondence in 130 monkeys and generated reliable native-space cortical surfaces.
- The framework enabled localized task-evoked activations and reproducible resting-state functional connectivity.
- Processed data demonstrated consistency across variable resolutions and species.
Conclusions:
- Brainana provides a reproducible, scalable, and accessible solution for macaque MRI preprocessing.
- It supports cross-study comparisons and multimodal integration across different spatial scales.
- The framework empowers researchers to advance non-human primate systems neuroscience.
- Brainana standardizes macaque neuroimaging, enabling more robust and integrated research findings.
