freesurfer: Connecting the Freesurfer software with R

Area of Science:

• Neuroimaging Analysis
• Computational Neuroscience
• Bioinformatics

Background:

• Freesurfer is a widely adopted open-source software for neuroimaging data analysis.
• Processing and analyzing structural neuroimaging data, particularly T1-weighted images, is crucial in neuroscience research.
• Integrating neuroimaging tools with statistical programming environments enhances research workflows.

Purpose of the Study:

• To introduce the freesurfer R package, designed to streamline the use of Freesurfer within the R environment.
• To facilitate the processing of neuroanatomical images and the interpretation of Freesurfer outputs for R users.
• To enhance the accessibility and usability of Freesurfer's advanced neuroimaging analysis capabilities.

Main Methods:

• Development of an R package named freesurfer that acts as an interface to the Freesurfer command-line tools.
• Implementation of functions to perform operations on neuroimaging data (nifti format) directly within R.
• Design of functions to efficiently read and convert Freesurfer output files into R-compatible objects.

Main Results:

• The freesurfer package successfully enables R users to execute Freesurfer commands and process neuroimaging data.
• Users can now seamlessly convert and access Freesurfer outputs, including brain images, surfaces, and analysis tables, within their R sessions.
• The package simplifies complex neuroimaging workflows, making advanced analysis more manageable.

Conclusions:

• The freesurfer R package significantly lowers the barrier to entry for utilizing Freesurfer in R-based research.
• It promotes more integrated and efficient neuroimaging data analysis pipelines for researchers.
• This tool enhances the utility of Freesurfer for a broader range of neuroscientists and data analysts.