Abstract
Aim: To develop a modular software pipeline for robustly extracting 3D brain-surface models from MRIs for visualization or printing. No other end-to-end pipeline specialized for neuroimaging does this directly with an interchangeable combination of methods. Materials & methods: A software application was developed to dynamically generate Nipype workflows using interfaces from the Analysis of Functional NeuroImages, Advanced Normalization Tools, FreeSurfer, BrainSuite, Nighres and the FMRIB Software Library suites. The application was deployed for public use via the LONI pipeline environment. Results: In a small, head-to-head comparison test, a pipeline using FreeSurfer for both the skull stripping and cortical-mesh extraction stages earned the highest subjective quality scores. Conclusion: We have deployed a publicly available and modular software tool for extracting 3D models from brain MRIs to use in medical education.
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