A Constrast-Agnostic Method for Ultra-High Resolution Claustrum Segmentation

The claustrum is a band-like gray matter structure located between putamen and insula whose exact functions are still actively researched. Its sheet-like structure makes it barely visible in in vivo Magnetic Resonance Imaging (MRI) scans at typical resolutions and neuroimaging tools for its study, including methods for automatic segmentation, are currently very limited. In this paper, we propose a contrast- and resolution-agnostic method for claustrum segmentation at ultra-high resolution (0.35 mm isotropic); the method is based on the SynthSeg segmentation framework (Billot et al., 2023), which leverages the use of synthetic training intensity images to achieve excellent generalization. In particular, SynthSeg requires only label maps to be trained, since corresponding intensity images are synthesized on the fly with random contrast and resolution. We trained a deep learning network for automatic claustrum segmentation, using claustrum manual labels obtained from 18 ultra-high resolution MRI scans (mostly ex vivo). We demonstrated the method to work on these 18 high resolution cases (Dice score = 0.632, mean surface distance = 0.458 mm, and volumetric similarity = 0.867 using 6-fold Cross Validation (CV)), and also on in vivo T1-weighted MRI scans at typical resolutions (~1 mm isotropic). We also demonstrated that the method is robust in a test-retest setting and when applied to multimodal imaging (T2-weighted, Proton Density and quantitative T1 scans). To the best of our knowledge this is the first accurate method for automatic ultra-high resolution claustrum segmentation, which is robust against changes in contrast and resolution. The method is released at https://github.com/chiara-mauri/claustrum_segmentation and as part of the neuroimaging package Freesurfer (Fischl, 2012).

Neurovascular Segmentation in sOCT with Deep Learning and Synthetic Training Data

Microvascular anatomy is known to be involved in various neurological disorders. However, understanding these disorders is hindered by the lack of imaging modalities capable of capturing the comprehensive three-dimensional vascular network structure at microscopic resolution. With a lateral resolution of $<=$20 {\textmu}m and ability to reconstruct large tissue blocks up to tens of cubic centimeters, serial-section optical coherence tomography (sOCT) is well suited for this task. This method uses intrinsic optical properties to visualize the vessels and therefore does not possess a specific contrast, which complicates the extraction of accurate vascular models. The performance of traditional vessel segmentation methods is heavily degraded in the presence of substantial noise and imaging artifacts and is sensitive to domain shifts, while convolutional neural networks (CNNs) require extensive labeled data and are also sensitive the precise intensity characteristics of the data that they are trained on. Building on the emerging field of synthesis-based training, this study demonstrates a synthesis engine for neurovascular segmentation in sOCT images. Characterized by minimal priors and high variance sampling, our highly generalizable method tested on five distinct sOCT acquisitions eliminates the need for manual annotations while attaining human-level precision. Our approach comprises two phases: label synthesis and label-to-image transformation. We demonstrate the efficacy of the former by comparing it to several more realistic sets of training labels, and the latter by an ablation study of synthetic noise and artifact models.

A Lightweight Causal Model for Interpretable Subject-level Prediction

Recent years have seen a growing interest in methods for predicting a variable of interest, such as a subject's diagnosis, from medical images. Methods based on discriminative modeling excel at making accurate predictions, but are challenged in their ability to explain their decisions in anatomically meaningful terms. In this paper, we propose a simple technique for single-subject prediction that is inherently interpretable. It augments the generative models used in classical human brain mapping techniques, in which cause-effect relations can be encoded, with a multivariate noise model that captures dominant spatial correlations. Experiments demonstrate that the resulting model can be efficiently inverted to make accurate subject-level predictions, while at the same time offering intuitive causal explanations of its inner workings. The method is easy to use: training is fast for typical training set sizes, and only a single hyperparameter needs to be set by the user. Our code is available at https://github.com/chiara-mauri/Interpretable-subject-level-prediction.