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

arXiv: https://arxiv.org/abs/2408.10656 · HTML: https://mlsanity.com/paper/2408.10656/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 54 references that are in the map.
- First posted on arXiv 20 Aug 2024.

## Builds on (most cited first, 18 of 18)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Instance Normalization: The Missing Ingredient for Fast Stylization](https://mlsanity.com/paper/1607.08022/) (2016)
- [VoxelMorph: A Learning Framework for Deformable Medical Image Registration](https://mlsanity.com/paper/1809.05231/) (2018)
- [Cyclical Learning Rates for Training Neural Networks](https://mlsanity.com/paper/1506.01186/) (2015)
- [Empirical Evaluation of Rectified Activations in Convolutional Network](https://mlsanity.com/paper/1505.00853/) (2015)
- [Deep Learning for Medical Image Analysis](https://mlsanity.com/paper/1708.08987/) (2017)
- [fastai: A Layered API for Deep Learning](https://mlsanity.com/paper/2002.04688/) (2020)
- [TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning](https://mlsanity.com/paper/2003.04696/) (2020)
- [SynthMorph: learning contrast-invariant registration without acquired images](https://mlsanity.com/paper/2004.10282/) (2020)
- [Automated brain extraction of multi-sequence MRI using artificial neural networks](https://mlsanity.com/paper/1901.11341/) (2019)
- [SynthStrip: Skull-Stripping for Any Brain Image](https://mlsanity.com/paper/2203.09974/) (2022)
- [Fast Symmetric Diffeomorphic Image Registration with Convolutional Neural Networks](https://mlsanity.com/paper/2003.09514/) (2020)
- [MONAI Label: A framework for AI-assisted Interactive Labeling of 3D Medical Images](https://mlsanity.com/paper/2203.12362/) (2022)
- [Can parametric statistical methods be trusted for fMRI based group studies?](https://mlsanity.com/paper/1511.01863/) (2015)
- [U-SegNet: Fully Convolutional Neural Network based Automated Brain tissue segmentation Tool](https://mlsanity.com/paper/1806.04429/) (2018)
- [Deepbet: Fast brain extraction of T1-weighted MRI using Convolutional Neural Networks](https://mlsanity.com/paper/2308.07003/) (2023)
- [Hierarchical multi-class segmentation of glioma images using networks with multi-level activation function](https://mlsanity.com/paper/1810.09488/) (2018)

## Abstract (arXiv)

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.