LST-AI: A deep learning ensemble for accurate MS lesion segmentation

Tun Wiltgen, Julian McGinnis, Sarah Schlaeger, Florian Kofler, Cui Ci Voon, Achim Berthele, Daria Bischl, Lioba Grundl, Nikolaus Will, Marie Metz, David Schinz, Dominik Sepp, Philipp Prucker, Benita Schmitz-Koep, Claus Zimmer, Bjoern Menze, Daniel Rueckert, Bernhard Hemmer, Jan Kirschke, Mark MühlauBenedikt Wiestler

Research output: Contribution to journalArticlepeer-review


Automated segmentation of brain white matter lesions is crucial for both clinical assessment and scientific research in multiple sclerosis (MS). Over a decade ago, we introduced an engineered lesion segmentation tool, LST. While recent lesion segmentation approaches have leveraged artificial intelligence (AI), they often remain proprietary and difficult to adopt. As an open-source tool, we present LST-AI, an advanced deep learning-based extension of LST that consists of an ensemble of three 3D U-Nets. LST-AI explicitly addresses the imbalance between white matter (WM) lesions and non-lesioned WM. It employs a composite loss function incorporating binary cross-entropy and Tversky loss to improve segmentation of the highly heterogeneous MS lesions. We train the network ensemble on 491 MS pairs of T1-weighted and FLAIR images, collected in-house from a 3T MRI scanner, and expert neuroradiologists manually segmented the utilized lesion maps for training. LST-AI also includes a lesion location annotation tool, labeling lesions as periventricular, infratentorial, and juxtacortical according to the 2017 McDonald criteria, and, additionally, as subcortical. We conduct evaluations on 103 test cases consisting of publicly available data using the Anima segmentation validation tools and compare LST-AI with several publicly available lesion segmentation models. Our empirical analysis shows that LST-AI achieves superior performance compared to existing methods. Its Dice and F1 scores exceeded 0.62, outperforming LST, SAMSEG (Sequence Adaptive Multimodal SEGmentation), and the popular nnUNet framework, which all scored below 0.56. Notably, LST-AI demonstrated exceptional performance on the MSSEG-1 challenge dataset, an international WM lesion segmentation challenge, with a Dice score of 0.65 and an F1 score of 0.63—surpassing all other competing models at the time of the challenge. With increasing lesion volume, the lesion detection rate rapidly increased with a detection rate of >75% for lesions with a volume between 10 mm3 and 100 mm3. Given its higher segmentation performance, we recommend that research groups currently using LST transition to LST-AI. To facilitate broad adoption, we are releasing LST-AI as an open-source model, available as a command-line tool, dockerized container, or Python script, enabling diverse applications across multiple platforms.

Original languageEnglish
Article number103611
JournalNeuroImage: Clinical
StatePublished - Jan 2024


  • Artificial Intelligence
  • Deep Learning
  • Lesion Segmentation
  • Magnetic Resonance Imaging
  • Multiple Sclerosis
  • White Matter Lesions


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