In this paper, we present ClinicaDL, an open-source software platform that aims at enhancing the reproducibility and rigor of research for deep learning in neuroimaging. We first provide an overview of the software platform and then focus on recent advances. Features of the software aim at addressing three key issues in the field: the lack of reproducibility, the methodological flaws that plague many published studies and the difficulties using neuroimaging datasets for people with little expertise in this application area. Key existing functionalities include automatic data splitting, checking for data leakage, standards for data organization and results storing, continuous integration and integration with Clinica for preprocessing, amongst others. The most prominent recent features are as follows. We now provide various data augmentation and synthetic data generation functions (both standard and advanced ones including motion and hypometabolism simulation). Continuous integration test data are now versioned using DVC (data version control). Tools for generating validation splits have been made more generic. We made major improvements regarding usability and performance. We now support multi-GPU training and automatic mixed precision (to exploit tensor cores). We created a graphical interface to easily generate training specifications. We allow tracking of experiments through standard tools (MLflow, Weights&Biases). We believe that ClinicaDL can contribute to enhance the trustworthiness of research in deep learning for neuroimaging. Moreover, its functionalities and coding practices may serve as inspiration for the whole medical imaging community, beyond neuroimaging.
KEYWORDS: Image segmentation, Education and training, Feature fusion, Deep learning, Medical imaging, Heart, Spleen, Data modeling, Parkinson disease, Fourier transforms
Deep models have been shown to tend to fit the target function from low to high frequencies (a phenomenon called the frequency principle of deep learning). One may hypothesize that such property can be leveraged for better training of deep learning models, in particular for segmentation tasks where annotated datasets are often small. In this paper, we exploit this property to propose a new training method based on frequency-domain disentanglement. It consists of three main stages. First, it disentangles the image into high- and low-frequency components. Then, the segmentation network model learns them separately (the approach is general and can use any segmentation network as backbone). Finally, feature fusion is performed to complete the downstream task. The method was applied to the segmentation of the red and dentate nuclei in Quantitative Susceptibility Mapping (QSM) data and to three tasks of the Medical Segmentation Decathlon (MSD) challenge under different training sample sizes. For segmenting the red and dentate nuclei and the heart, the proposed approach resulted in considerable improvements over the baseline (respectively between 8 and 16 points of Dice and between 5 and 8 points). On the other hand, there was no improvement for the spleen and the hippocampus. We believe that these intriguing results, which echo theoretical work on the frequency principle of deep learning, are of interest for discussion at the conference. The source code is publicly available at: https://github.com/GuanghuiFU/frequency_disentangled_learning.
The recent advent of clinical data warehouses (CDWs) has facilitated the sharing of very large volumes of medical data for research purposes. MRIs can be affected by various artefacts such as motion, noise or poor contrast that can severely degrade the overall quality of an image. In CDWs, a large amount of MRIs are unusable because corrupted by these diverse artefacts. Given the huge number of MRIs present in CDWs, manually detecting these artefacts becomes an impractical task. Therefore, it is necessary to develop an automated tool that can efficiently identify and exclude corrupted images. We previously proposed an approach for the detection of motion artefacts in 3D T1-weighted brain MRIs. In this paper, we propose to extend our work to two other types of artefacts: poor contrast and noise. We rely on a transfer learning approach, which leverages synthetic artefact generation, and comprises two steps: model pre-training on research data using synthetic artefacts, followed by a fine-tuning step, where we generalise the pre-trained models to clinical routine data relying on the manual labelling of 5000 images. The main objectives of our study were two-fold: to be able to exclude images with severe artefacts and to detect moderate artefacts. Our approach excelled in meeting the first objective, achieving a balanced accuracy of over 84% for the detection of severe noise and very poor contrast, which closely matched the performance of human annotators. Nevertheless, performance in the pursuit of the second objective was less satisfactory and inferior to that of the human annotators. Overall, our framework will be useful for taking full advantage of MRIs present in CDWs.
Clinical data warehouses (CDWs) contain the medical data of millions of patients and represent a great opportunity to develop computational tools. MRIs are particularly sensitive to patient movements during image acquisition, which will result in artefacts (blurring, ghosting and ringing) in the reconstructed image. As a result, a significant number of MRIs in CDWs are unusable because corrupted by these artefacts. Since their manual detection is impossible due to the number of scans, it is necessary to develop a tool to automatically exclude images with motion in order to fully exploit CDWs. In this paper, we propose a CNN for the automatic detection of motion in 3D T1-weighted brain MRI. Our transfer learning approach, based on synthetic motion generation, consists of two steps: a pre-training on research data using synthetic motion, followed by a fine-tuning step to generalise our pre-trained model to clinical data, relying on the manual labelling of 5500 images. The objectives were both (1) to be able to exclude images with severe motion, (2) to detect mild motion artefacts. Our approach achieved excellent accuracy for the first objective with a balanced accuracy nearly similar to that of the annotators (balanced accuracy<80%). However, for the second objective, the performance was weaker and substantially lower than that of human raters. Overall, our framework will be useful to take advantage of CDWs in medical imaging and to highlight the importance of a clinical validation of models trained on research data.
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