Negligible effect of brain MRI data preprocessing for tumor segmentation

• URL: http://arxiv.org/abs/2204.05278v4
• Date: Mon, 23 Oct 2023 15:51:12 GMT
• Title: Negligible effect of brain MRI data preprocessing for tumor segmentation
• Authors: Ekaterina Kondrateva and Polina Druzhinina and Alexandra Dalechina and Svetlana Zolotova and Andrey Golanov and Boris Shirokikh and Mikhail Belyaev and Anvar Kurmukov
• Abstract summary: We conduct experiments on three publicly available datasets and evaluate the effect of different preprocessing steps in deep neural networks. Our results demonstrate that most popular standardization steps add no value to the network performance. We suggest that image intensity normalization approaches do not contribute to model accuracy because of the reduction of signal variance with image standardization.
• Score: 36.89606202543839
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Magnetic resonance imaging (MRI) data is heterogeneous due to differences in device manufacturers, scanning protocols, and inter-subject variability. A conventional way to mitigate MR image heterogeneity is to apply preprocessing transformations such as anatomy alignment, voxel resampling, signal intensity equalization, image denoising, and localization of regions of interest. Although a preprocessing pipeline standardizes image appearance, its influence on the quality of image segmentation and on other downstream tasks in deep neural networks has never been rigorously studied. We conduct experiments on three publicly available datasets and evaluate the effect of different preprocessing steps in intra- and inter-dataset training scenarios. Our results demonstrate that most popular standardization steps add no value to the network performance; moreover, preprocessing can hamper model performance. We suggest that image intensity normalization approaches do not contribute to model accuracy because of the reduction of signal variance with image standardization. Finally, we show that the contribution of skull-stripping in data preprocessing is almost negligible if measured in terms of estimated tumor volume. We show that the only essential transformation for accurate deep learning analysis is the unification of voxel spacing across the dataset. In contrast, inter-subjects anatomy alignment in the form of non-rigid atlas registration is not necessary and intensity equalization steps (denoising, bias-field correction and histogram matching) do not improve models' performance. The study code is accessible online https://github.com/MedImAIR/brain-mri-processing-pipeline

Related papers

• A Unified Model for Compressed Sensing MRI Across Undersampling Patterns [69.19631302047569]
  Deep neural networks have shown great potential for reconstructing high-fidelity images from undersampled measurements. Our model is based on neural operators, a discretization-agnostic architecture. Our inference speed is also 1,400x faster than diffusion methods.
  arXiv  Detail & Related papers  (2024-10-05T20:03:57Z)
• Deep Learning Based Speckle Filtering for Polarimetric SAR Images. Application to Sentinel-1 [51.404644401997736]
  We propose a complete framework to remove speckle in polarimetric SAR images using a convolutional neural network. Experiments show that the proposed approach offers exceptional results in both speckle reduction and resolution preservation.
  arXiv  Detail & Related papers  (2024-08-28T10:07:17Z)
• Deformation-aware GAN for Medical Image Synthesis with Substantially Misaligned Pairs [0.0]
  We propose a novel Deformation-aware GAN (DA-GAN) to dynamically correct the misalignment during the image synthesis based on inverse consistency. Experimental results show that DA-GAN achieved superior performance on a public dataset with simulated misalignments and a real-world lung MRI-CT dataset with respiratory motion misalignment.
  arXiv  Detail & Related papers  (2024-08-18T10:29:35Z)
• On Sensitivity and Robustness of Normalization Schemes to Input Distribution Shifts in Automatic MR Image Diagnosis [58.634791552376235]
  Deep Learning (DL) models have achieved state-of-the-art performance in diagnosing multiple diseases using reconstructed images as input. DL models are sensitive to varying artifacts as it leads to changes in the input data distribution between the training and testing phases. We propose to use other normalization techniques, such as Group Normalization and Layer Normalization, to inject robustness into model performance against varying image artifacts.
  arXiv  Detail & Related papers  (2023-06-23T03:09:03Z)
• Realistic Data Enrichment for Robust Image Segmentation in Histopathology [2.248423960136122]
  We propose a new approach, based on diffusion models, which can enrich an imbalanced dataset with plausible examples from underrepresented groups. Our method can simply expand limited clinical datasets making them suitable to train machine learning pipelines.
  arXiv  Detail & Related papers  (2023-04-19T09:52:50Z)
• Uncertainty-aware GAN with Adaptive Loss for Robust MRI Image Enhancement [3.222802562733787]
  Conditional generative adversarial networks (GANs) have shown improved performance in learning photo-realistic image-to-image mappings. This paper proposes a GAN-based framework that (i)models an adaptive loss function for robustness to OOD-noisy data and (ii)estimates the per-voxel uncertainty in the predictions. We demonstrate our method on two key applications in medical imaging: (i)undersampled magnetic resonance imaging (MRI) reconstruction (ii)MRI modality propagation.
  arXiv  Detail & Related papers  (2021-10-07T11:29:03Z)
• About Explicit Variance Minimization: Training Neural Networks for Medical Imaging With Limited Data Annotations [2.3204178451683264]
  Variance Aware Training (VAT) method exploits this property by introducing the variance error into the model loss function. We validate VAT on three medical imaging datasets from diverse domains and various learning objectives.
  arXiv  Detail & Related papers  (2021-05-28T21:34:04Z)
• Segmentation-Renormalized Deep Feature Modulation for Unpaired Image Harmonization [0.43012765978447565]
  Cycle-consistent Generative Adversarial Networks have been used to harmonize image sets between a source and target domain. These methods are prone to instability, contrast inversion, intractable manipulation of pathology, and steganographic mappings which limit their reliable adoption in real-world medical imaging. We propose a segmentation-renormalized image translation framework to reduce inter-scanner harmonization while preserving anatomical layout.
  arXiv  Detail & Related papers  (2021-02-11T23:53:51Z)
• Improved Slice-wise Tumour Detection in Brain MRIs by Computing Dissimilarities between Latent Representations [68.8204255655161]
  Anomaly detection for Magnetic Resonance Images (MRIs) can be solved with unsupervised methods. We have proposed a slice-wise semi-supervised method for tumour detection based on the computation of a dissimilarity function in the latent space of a Variational AutoEncoder. We show that by training the models on higher resolution images and by improving the quality of the reconstructions, we obtain results which are comparable with different baselines.
  arXiv  Detail & Related papers  (2020-07-24T14:02:09Z)
• Data Consistent CT Reconstruction from Insufficient Data with Learned Prior Images [70.13735569016752]
  We investigate the robustness of deep learning in CT image reconstruction by showing false negative and false positive lesion cases. We propose a data consistent reconstruction (DCR) method to improve their image quality, which combines the advantages of compressed sensing and deep learning. The efficacy of the proposed method is demonstrated in cone-beam CT with truncated data, limited-angle data and sparse-view data, respectively.
  arXiv  Detail & Related papers  (2020-05-20T13:30:49Z)

This list is automatically generated from the titles and abstracts of the papers in this site.

This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.