# Robust thalamic nuclei segmentation from T1-weighted MRI

arXiv: https://arxiv.org/abs/2304.07167 · HTML: https://mlsanity.com/paper/2304.07167/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 14 Apr 2023.

## Built on by (most cited first, 2 of 2)

- [Comprehensive segmentation of deep grey nuclei from structural MRI data](https://mlsanity.com/paper/2503.21955/) (2025)
- [DeepThalamus: A novel deep learning method for automatic segmentation of brain thalamic nuclei from multimodal ultra-high resolution MRI](https://mlsanity.com/paper/2401.07751/) (2024)

## Abstract (arXiv)

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).