Vidal, Julie PDanet, LolaPéran, PatricePariente, JérémieBach Cuadra, MeritxellZahr, Natalie MBarbeau, Emmanuel JSaranathan, Manojkumar2024-04-112024-04-112024-03-28Vidal JP, Danet L, Péran P, Pariente J, Bach Cuadra M, Zahr NM, Barbeau EJ, Saranathan M. Robust thalamic nuclei segmentation from T1-weighted MRI using polynomial intensity transformation. Brain Struct Funct. 2024 Mar 28. doi: 10.1007/s00429-024-02777-5. Epub ahead of print. PMID: 38546872.1863-266110.1007/s00429-024-02777-538546872https://hdl.handle.net/20.500.14038/53280Accurate 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. In this study, we introduce histogram-based polynomial synthesis (HIPS), a fast preprocessing transform step that synthesizes WMn-like image contrast from standard T1w MRI using a polynomial approximation for intensity transformation. HIPS was incorporated into THalamus Optimized Multi-Atlas Segmentation (THOMAS) pipeline, a method developed and optimized for WMn MRI. HIPS-THOMAS was compared to a convolutional neural network (CNN)-based segmentation method and THOMAS modified for the use of T1w images (T1w-THOMAS). The robustness and accuracy of the three methods were tested across different image contrasts (MPRAGE, SPGR, and MP2RAGE), scanner manufacturers (PHILIPS, GE, and Siemens), and field strengths (3 T and 7 T). HIPS-transformed images improved intra-thalamic contrast and thalamic boundaries, and HIPS-THOMAS yielded significantly higher mean Dice coefficients and reduced volume errors compared to both the CNN method and T1w-THOMAS. Finally, all three methods were compared using the frequently travelling human phantom MRI dataset for inter- and intra-scanner variability, with HIPS displaying the least inter-scanner variability and performing comparably with T1w-THOMAS for intra-scanner variability. In conclusion, our findings highlight the efficacy and robustness of HIPS in enhancing thalamic nuclei segmentation from standard T1w MRI.en© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.Structural imagingTHOMASThalamic nuclei segmentationThalamusJournal ArticleBrain structure & function