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How to Measure Cortical Folding from MR Images: a Step-by-Step Tutorial to Compute Local Gyrification Index
Published on: January 2, 2012
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A subject-specific reversible folding model reveals geometry-driven white-matter organization.
Besm Osman1, Ruben Vink1, Andrei C Jalba1
1Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands.
Biorxiv : the Preprint Server for Biology
|December 19, 2025
Summary
This study introduces a novel brain folding simulation to reconstruct white matter tracts using only T1-weighted MRI scans. This geometry-driven approach accurately maps fiber orientation without diffusion data or machine learning.
Area of Science:
- Neuroimaging
- Computational Neuroscience
- Developmental Neuroscience
Background:
- Current tractography methods using diffusion data and seed maps lack anatomical accuracy.
- White matter fiber development is closely linked to cortical folding patterns during brain development.
Purpose of the Study:
- To develop a subject-specific cortical folding simulation framework to reconstruct white matter fiber organization.
- To investigate the mechanistic link between cortical geometry and fiber organization using a novel computational model.
Main Methods:
- Introduced a quasi-static, constraint-based model to simulate cortical folding trajectories from structural T1-weighted MRI.
- Reversed folding to a fetal-like configuration and then refolded to map volumetric deformation onto fiber organization.
- Validated the model with longitudinal fetal MRI and applied it to adult data.
Main Results:
- Simulated cortical folds demonstrated biologically plausible developmental paths.
- The model accurately reproduced diffusion-derived white matter orientation patterns and regional correspondence in adults.
- Generated realistic short-range U-fibers and long-range association/commissural pathways without diffusion input or machine learning.
Conclusions:
- Cortical geometry alone provides a powerful, anatomically grounded source for subject-specific white matter fiber orientation.
- This geometry-informed approach offers a new paradigm for tractography, reducing reliance on diffusion imaging.
- The framework opens new avenues for understanding brain development and improving tractography accuracy.

