CEREBRUM: a fast and fully-volumetric Convolutional Encoder-decodeR for weakly-supervised sEgmentation of BRain strUctures from out-of-the-scanner MRI

TL;DR

This paper introduces CEREBRUM, a fast, fully-volumetric CNN for brain MRI segmentation that leverages global context and weak supervision, achieving superior accuracy and speed over existing methods.

Contribution

The work presents a novel end-to-end CNN architecture capable of processing entire MRI volumes at once, improving segmentation accuracy and efficiency over patch-based approaches.

Findings

Outperforms state-of-the-art segmentation methods in accuracy.

Segmentation is achieved in only a few seconds.

Expert surveys favor the proposed method over FreeSurfer.

Abstract

Many functional and structural neuroimaging studies call for accurate morphometric segmentation of different brain structures starting from image intensity values of MRI scans. Current automatic (multi-) atlas-based segmentation strategies often lack accuracy on difficult-to-segment brain structures and, since these methods rely on atlas-to-scan alignment, they may take long processing times. Recently, methods deploying solutions based on Convolutional Neural Networks (CNNs) are making the direct analysis of out-of-the-scanner data feasible. However, current CNN-based solutions partition the test volume into 2D or 3D patches, which are processed independently. This entails a loss of global contextual information thereby negatively impacting the segmentation accuracy. In this work, we design and test an optimised end-to-end CNN architecture that makes the exploitation of global spatial information computationally tractable, allowing to process a whole MRI volume at once. We adopt a weakly supervised learning strategy by exploiting a large dataset composed by 947 out-of-the-scanner (3 Tesla T1-weighted 1mm isotropic MP-RAGE 3D sequences) MR Images. The resulting model is able to produce accurate multi-structure segmentation results in only few seconds. Different quantitative measures demonstrate an improved accuracy of our solution when compared to state-of-the-art techniques. Moreover, through a randomised survey involving expert neuroscientists, we show that subjective judgements clearly prefer our solution with respect to the widely adopted atlas-based FreeSurfer software.