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High-resolution Functional Magnetic Resonance Imaging Methods for Human Midbrain

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Published on: May 10, 2012

Neptune: a toolbox for spinal cord functional MRI data processing and quality assurance.

D Rangaprakash¹, Robert L Barry^1,2

¹Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA.

Biorxiv : the Preprint Server for Biology

|March 18, 2026

Summary

Neptune is a new, user-friendly MATLAB toolbox for spinal cord functional MRI (fMRI) data analysis. It offers advanced processing and quality control, benefiting neuroscientific and clinical research.

Keywords:

MATLAB toolbox Resting state spinal cord fMRI cervical spine fALFF functional connectivity user interface

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Area of Science:

Neuroimaging
Biomedical Engineering
Computational Neuroscience

Background:

Advancements in brain functional MRI (fMRI) rely on open-source software like SPM, AFNI, and FSL.
Spinal cord fMRI analysis faces unique challenges including distinct noise sources, anatomical distortions, and specialized processing needs.
Existing software is limited for spinal cord fMRI, necessitating tailored solutions for its complex data.

Purpose of the Study:

To introduce Neptune, a user-friendly, MATLAB-based toolbox specifically designed for spinal cord fMRI data processing.
To provide an enhanced, 19-step preprocessing pipeline and a 4-step postprocessing pipeline for fMRI connectivity modeling.
To offer novel quality control visualizations for thorough data assessment in an accessible webpage format.

Main Methods:

Development of Neptune, a MATLAB toolbox with a graphical user interface, requiring no programming knowledge.
Implementation of a 19-step preprocessing pipeline, building upon a previous 15-step method, with enhanced and new processing stages.
Integration of a 4-step postprocessing pipeline for functional connectivity modeling and generation of quality control visuals.

Main Results:

Neptune provides an easy-to-use interface for complex spinal cord fMRI analysis.
The toolbox includes advanced preprocessing and postprocessing pipelines with novel quality control features.
Demonstrated utility on 7T data, with integrated features from Spinal Cord Toolbox (SCT) and import/export compatibility with FSL and SPM.

Conclusions:

Neptune addresses the need for specialized software in spinal cord fMRI research.
Its open-source nature and ease of use are expected to benefit the spinal cord fMRI community.
Neptune facilitates neuroscientific and clinical research by simplifying spinal cord fMRI data analysis.