Segmenting Thalamic Nuclei: T1 Maps Provide a Reliable and Efficient Solution

TL;DR

This study evaluates various MRI contrasts for thalamic nuclei segmentation and finds T1 maps alone provide the most reliable and efficient input, outperforming other sequences.

Contribution

It systematically compares MRI contrasts and demonstrates that T1 maps are the best input for thalamic segmentation, guiding future imaging protocol choices.

Findings

T1 maps achieve high segmentation accuracy.

PD maps do not improve results.

T1 maps are the most reliable input for clinical and research use.

Abstract

Accurate thalamic nuclei segmentation is crucial for understanding neurological diseases, brain functions, and guiding clinical interventions. However, the optimal inputs for segmentation remain unclear. This study systematically evaluates multiple MRI contrasts, including MPRAGE and FGATIR sequences, quantitative PD and T1 maps, and multiple T1-weighted images at different inversion times (multi-TI), to determine the most effective inputs. For multi-TI images, we employ a gradient-based saliency analysis with Monte Carlo dropout and propose an Overall Importance Score to select the images contributing most to segmentation. A 3D U-Net is trained on each of these configurations. Results show that T1 maps alone achieve strong quantitative performance and superior qualitative outcomes, while PD maps offer no added value. These findings underscore the value of T1 maps as a reliable and efficient input among the evaluated options, providing valuable guidance for optimizing imaging protocols when thalamic structures are of clinical or research interest.