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

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.