SF2Former: Amyotrophic lateral sclerosis identification from multi-center MRI data using spatial and frequency fusion transformer

Kushol, Rafsanjany; Luk, Collin; Dey, Avyarthana; Benatar, Michael; Briemberg, Hannah; Dionne, Annie; Dupré, Nicolas; Frayne, Richard; Genge, Angela; Gibson, Summer; Graham, Simon J.; Seres, Peter; Welsh, Robert C.; Wilman, Alan H.; Zinman, Lorne; Kalra, Sanjay; Yang, Yee‐Hong

doi:10.1016/j.compmedimag.2023.102279

Cited by 6 publications

(3 citation statements)

References 28 publications

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“…The degeneration of nerve cells in brain regions such as the hippocampus, substantia nigra, and corticospinal tract, which are regarded as identifiable regions of interest in the pathogenesis of AD, PD, and ALS, respectively, were captured within the range of selected coronal slices given as input to the ADDFormer and other 2D models used in our study. A recent study similar to the ADDFormer network also demonstrates outstanding performance in the context of ALS classification 43 .…”

Section: Discussionmentioning

confidence: 91%

Effects of MRI scanner manufacturers in classification tasks with deep learning models

Kushol,

Parnianpour,

Wilman

et al. 2023

Sci Rep

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Deep learning has become a leading subset of machine learning and has been successfully employed in diverse areas, ranging from natural language processing to medical image analysis. In medical imaging, researchers have progressively turned towards multi-center neuroimaging studies to address complex questions in neuroscience, leveraging larger sample sizes and aiming to enhance the accuracy of deep learning models. However, variations in image pixel/voxel characteristics can arise between centers due to factors including differences in magnetic resonance imaging scanners. Such variations create challenges, particularly inconsistent performance in machine learning-based approaches, often referred to as domain shift, where the trained models fail to achieve satisfactory or improved results when confronted with dissimilar test data. This study analyzes the performance of multiple disease classification tasks using multi-center MRI data obtained from three widely used scanner manufacturers (GE, Philips, and Siemens) across several deep learning-based networks. Furthermore, we investigate the efficacy of mitigating scanner vendor effects using ComBat-based harmonization techniques when applied to multi-center datasets of 3D structural MR images. Our experimental results reveal a substantial decline in classification performance when models trained on one type of scanner manufacturer are tested with data from different manufacturers. Moreover, despite applying ComBat-based harmonization, the harmonized images do not demonstrate any noticeable performance enhancement for disease classification tasks.

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Section: Discussionmentioning

confidence: 91%

Effects of MRI scanner manufacturers in classification tasks with deep learning models

Kushol,

Parnianpour,

Wilman

et al. 2023

Sci Rep

Self Cite

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“…The development of a Domain Shift Analyzer for MRI (DSMRI) which was designed explicitly for multicenter MRI datasets ( Kushol et al, 2023a , b ) allows for the identification of NDD as demonstrated for ALS cases ( Kushol et al, 2023c ), thus offering the possibility to investigate neuroimaging modalities like functional MRI (fMRI) and DTI within a similar environment.…”

Section: Postprocessing-related Contributions To Results Of Dti Studi...mentioning

confidence: 99%

Toward diffusion tensor imaging as a biomarker in neurodegenerative diseases: technical considerations to optimize recordings and data processing

Müller,

Kassubek

2024

Front. Hum. Neurosci.

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Neuroimaging biomarkers have shown high potential to map the disease processes in the application to neurodegenerative diseases (NDD), e.g., diffusion tensor imaging (DTI). For DTI, the implementation of a standardized scanning and analysis cascade in clinical trials has potential to be further optimized. Over the last few years, various approaches to improve DTI applications to NDD have been developed. The core issue of this review was to address considerations and limitations of DTI in NDD: we discuss suggestions for improvements of DTI applications to NDD. Based on this technical approach, a set of recommendations was proposed for a standardized DTI scan protocol and an analysis cascade of DTI data pre-and postprocessing and statistical analysis. In summary, considering advantages and limitations of the DTI in NDD we suggest improvements for a standardized framework for a DTI-based protocol to be applied to future imaging studies in NDD, towards the goal to proceed to establish DTI as a biomarker in clinical trials in neurodegeneration.

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“…These datasets are valuable resources that can improve the generalizability and representativeness of research, producing more robust and reliable findings. Additionally, multi-site databases make it easier to investigate rare disorders, assess novel imaging techniques, and establish clinical benchmarks [ 4 ]. However, despite their potential advantages, multi-center MRI datasets introduce significant challenges due to a phenomenon known as “domain shift" [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

DSMRI: Domain Shift Analyzer for Multi-Center MRI Datasets

Kushol,

Wilman,

Kalra

et al. 2023

Diagnostics

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In medical research and clinical applications, the utilization of MRI datasets from multiple centers has become increasingly prevalent. However, inherent variability between these centers presents challenges due to domain shift, which can impact the quality and reliability of the analysis. Regrettably, the absence of adequate tools for domain shift analysis hinders the development and validation of domain adaptation and harmonization techniques. To address this issue, this paper presents a novel Domain Shift analyzer for MRI (DSMRI) framework designed explicitly for domain shift analysis in multi-center MRI datasets. The proposed model assesses the degree of domain shift within an MRI dataset by leveraging various MRI-quality-related metrics derived from the spatial domain. DSMRI also incorporates features from the frequency domain to capture low- and high-frequency information about the image. It further includes the wavelet domain features by effectively measuring the sparsity and energy present in the wavelet coefficients. Furthermore, DSMRI introduces several texture features, thereby enhancing the robustness of the domain shift analysis process. The proposed framework includes visualization techniques such as t-SNE and UMAP to demonstrate that similar data are grouped closely while dissimilar data are in separate clusters. Additionally, quantitative analysis is used to measure the domain shift distance, domain classification accuracy, and the ranking of significant features. The effectiveness of the proposed approach is demonstrated using experimental evaluations on seven large-scale multi-site neuroimaging datasets.

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SF2Former: Amyotrophic lateral sclerosis identification from multi-center MRI data using spatial and frequency fusion transformer

Cited by 6 publications

References 28 publications

Effects of MRI scanner manufacturers in classification tasks with deep learning models

Effects of MRI scanner manufacturers in classification tasks with deep learning models

Toward diffusion tensor imaging as a biomarker in neurodegenerative diseases: technical considerations to optimize recordings and data processing

DSMRI: Domain Shift Analyzer for Multi-Center MRI Datasets

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