deepmriprep: Voxel-based Morphometry (VBM) Preprocessing via Deep Neural Networks

TL;DR

deepmriprep is a GPU-accelerated neural network pipeline that preprocesses MRI data for VBM analysis, achieving speeds 37 times faster than traditional tools while maintaining high accuracy and facilitating large-scale neuroimaging studies.

Contribution

It introduces a deep neural network-based preprocessing pipeline for VBM that is significantly faster and equally accurate compared to existing methods like CAT12.

Findings

37x faster processing speed than CAT12

Over 95% agreement in tissue segmentation with ground truth

Strong correlation in VBM results across datasets

Abstract

Voxel-based Morphometry (VBM) has emerged as a powerful approach in neuroimaging research, utilized in over 7,000 studies since the year 2000. Using Magnetic Resonance Imaging (MRI) data, VBM assesses variations in the local density of brain tissue and examines its associations with biological and psychometric variables. Here, we present deepmriprep, a neural network-based pipeline that performs all necessary preprocessing steps for VBM analysis of T1-weighted MR images using deep neural networks. Utilizing the Graphics Processing Unit (GPU), deepmriprep is 37 times faster than CAT12, the leading VBM preprocessing toolbox. The proposed method matches CAT12 in accuracy for tissue segmentation and image registration across more than 100 datasets and shows strong correlations in VBM results. Tissue segmentation maps from deepmriprep have over 95% agreement with ground truth maps, and its non-linear registration, using supervised SYMNet, predicts smooth deformation fields comparable to CAT12. The high processing speed of deepmriprep enables rapid preprocessing of extensive datasets and thereby fosters the application of VBM analysis to large-scale neuroimaging studies and opens the door to real-time applications. Finally, deepmripreps straightforward, modular design enables researchers to easily understand, reuse, and advance the underlying methods, fostering further advancements in neuroimaging research. deepmriprep can be conveniently installed as a Python package and is publicly accessible at https://github.com/wwu-mmll/deepmriprep.