Robust thalamic nuclei segmentation from T1-weighted MRI

TL;DR

This paper introduces HIPS, a polynomial synthesis method that enhances standard T1-weighted MRI contrast to improve thalamic nuclei segmentation accuracy, outperforming CNN-based methods and enabling effective atrophy detection.

Contribution

The study presents HIPS, a novel fast preprocessing technique that synthesizes WMn-like contrast from T1w MRI, integrated into the THOMAS pipeline for improved segmentation.

Findings

HIPS improves intra-thalamic contrast and boundary delineation.

HIPS-THOMAS achieves higher Dice scores and lower volume errors.

HIPS-based segmentation effectively detects thalamic atrophy in clinical data.

Abstract

Accurate segmentation of thalamic nuclei, crucial for understanding their role in healthy cognition and in pathologies, is challenging to achieve on standard T1-weighted (T1w) magnetic resonance imaging (MRI) due to poor image contrast. White-matter-nulled (WMn) MRI sequences improve intrathalamic contrast but are not part of clinical protocols or extant databases. Here, we introduce Histogram-based polynomial synthesis (HIPS), a fast preprocessing step that synthesizes WMn-like image contrast from standard T1w MRI using a polynomial approximation. HIPS was incorporated into our Thalamus Optimized Multi-Atlas Segmentation (THOMAS) pipeline, developed and optimized for WMn MRI. HIPS-THOMAS was compared to a convolutional neural network (CNN)-based segmentation method and THOMAS modified for T1w images (T1w-THOMAS). The robustness and accuracy of the three methods were tested across different image contrasts, scanner manufacturers, and field strength. HIPS-synthesized images improved intra-thalamic contrast and thalamic boundaries, and their segmentations yielded significantly better mean Dice, lower percentage of volume error, and lower standard deviations compared to both the CNN method and T1w-THOMAS. Finally, using THOMAS, HIPS-synthesized images were as effective as WMn images for identifying thalamic nuclei atrophy in alcohol use disorders subjects relative to healthy controls, with a higher area under the ROC curve compared to T1w-THOMAS (0.79 vs 0.73).