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Jan Kirschke

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4 papers

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YNIMG Journal 2025 Journal Article

Towards quantitative intensity analysis of conventional T1-weighted images in multiple sclerosis

Tun Wiltgen
Julian McGinnis
Ronja Berg
Cui Ci Voon
Oula Puonti
Katrin Giglhuber
Carl Ganter
Claus Zimmer

Conventional T1-weighted (T1w) magnetic resonance imaging (MRI) is commonly used in multiple sclerosis (MS) morphometry and volumetry research. However, arbitrary intensity scales preclude interpretation of signal values across patients, sites, and time. This requires quantitative MRI techniques, which are not always available. This study assessed T1w image intensity scaling methods, relying on extracerebral reference regions, for quantitative analysis of brain MRI in MS. In total, 701 people with a diagnosis of radiologically isolated syndrome, clinically isolated syndrome, or MS were included. Four intensity scaling strategies were applied: 1) MRI signal modeling, 2) linear scaling with reference regions, 3) z-score standardization, and 4) none (only bias field correction). Methods were evaluated using variance analysis, R1 map comparison, and normal-appearing white matter (NAWM) intensity group comparison, using mean and coefficient of variation (CoV), between low (≤3) and high (>3) expanded disability status scale (EDSS) scores. Statistical analysis was conducted using Pearson's r, two-sided Welch two-sample t-test, ANCOVA, and Cohen's d. Linear scaling with temporal fatty tissue achieved the most consistent variance reduction and strong correlation with R1 maps (r = 0.84). R1 values in NAWM were significantly lower in people with high compared to low EDSS scores (d = -0.351). Similarly, group differences in mean NAWM intensity of fat-scaled images were significant (d = -0.252). The largest group differences were found in NAWM CoV in bias field-corrected T1w images (d = 0.818). Linear scaling with fatty tissue most accurately reproduced the results obtained with R1 maps. Changes in MS NAWM appear to increase intensity variability detectable in conventional T1w images.

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YNICL Journal 2024 Journal Article

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

Tun Wiltgen
Julian McGinnis
Sarah Schlaeger
Florian Kofler
CuiCi Voon
Achim Berthele
Daria Bischl
Lioba Grundl

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.

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YNICL Journal 2023 Journal Article

Lesion location across diagnostic regions in multiple sclerosis

Viola Pongratz
Matthias Bussas
Paul Schmidt
Sophia Grahl
Christiane Gasperi
Malek El Husseini
Laura Harabacz
Viktor Pineker

BACKGROUND: Lesions in the periventricular, (juxta)cortical, and infratentorial region, as visible on brain MRI, are part of the diagnostic criteria for Multiple sclerosis (MS) whereas lesions in the subcortical region are currently only a marker of disease activity. It is unknown whether MS lesions follow individual spatial patterns or whether they occur in a random manner across diagnostic regions. AIM: First, to describe cross-sectionally the spatial lesion patterns in patients with MS. Second, to investigate the spatial association of new lesions and lesions at baseline across diagnostic regions. METHODS: Experienced neuroradiologists analyzed brain MRI (3D, 3T) in a cohort of 330 early MS patients. Lesions at baseline and new solitary lesions after two years were segmented (manually and by consensus) and classified as periventricular, (juxta)cortical, or infratentorial (diagnostic regions) or subcortical-with or without Gadolinium-enhancement. Gadolinium enhancement of lesions in the different regions was compared by Chi square test. New lesions in the four regions served as dependent variable in four zero-inflated Poisson models each with the six independent variables of lesions in the four regions at baseline, age and gender. RESULTS: At baseline, lesions were most often observed in the subcortical region (mean 13.0 lesions/patient), while lesion volume was highest in the periventricular region (mean 2287 µl/patient). Subcortical lesions were less likely to show gadolinium enhancement (3.1 %) than juxtacortical (4.3 %), periventricular (5.3 %) or infratentorial lesions (7.2 %). Age was inversely correlated with new periventricular, juxtacortical and subcortical lesions. New lesions in the periventricular, juxtacortical and infratentorial region showed a significant autocorrelative behavior being positively related to the number of lesions in the respective regions at baseline. New lesions in the subcortical region showed a different behavior with a positive association with baseline periventricular lesions and a negative association with baseline infratentorial lesions. CONCLUSION: Across regions, new lesions do not occur randomly; instead, new lesions in the periventricular, juxtacortical and infratentorial diagnostic region are associated with that at baseline. Lesions in the subcortical regions are more closely related to periventricular lesions. Moreover, subcortical lesions substantially contribute to lesion burden in MS but are less likely to show gadolinium enhancement (than lesions in the diagnostic regions).

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YNICL Journal 2019 Journal Article

Automated segmentation of changes in FLAIR-hyperintense white matter lesions in multiple sclerosis on serial magnetic resonance imaging

Paul Schmidt
Viola Pongratz
Pascal Küster
Dominik Meier
Jens Wuerfel
Carsten Lukas
Barbara Bellenberg
Frauke Zipp

Longitudinal analysis of white matter lesion changes on serial MRI has become an important parameter to study diseases with white-matter lesions. Here, we build on earlier work on cross-sectional lesion segmentation; we present a fully automatic pipeline for serial analysis of FLAIR-hyperintense white matter lesions. Our algorithm requires three-dimensional gradient echo T1- and FLAIR- weighted images at 3 Tesla as well as available cross-sectional lesion segmentations of both time points. Preprocessing steps include lesion filling and intrasubject registration. For segmentation of lesion changes, initial lesion maps of different time points are fused; herein changes in intensity are analyzed at the voxel level. Significance of lesion change is estimated by comparison with the difference distribution of FLAIR intensities within normal appearing white matter. The method is validated on MRI data of two time points from 40 subjects with multiple sclerosis derived from two different scanners (20 subjects per scanner). Manual segmentation of lesion increases served as gold standard. Across all lesion increases, voxel-wise Dice coefficient (0.7) as well as lesion-wise detection rate (0.8) and false-discovery rate (0.2) indicate good overall performance. Analysis of scans from a repositioning experiment in a single patient with multiple sclerosis did not yield a single false positive lesion. We also introduce the lesion change plot as a descriptive tool for the lesion change of individual patients with regard to both number and volume. An open source implementation of the algorithm is available at http://www.statistical-modeling.de/lst.html.

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