KEYWORDS: Education and training, Positron emission tomography, Magnetic resonance imaging, Multiple sclerosis, White matter, Scanners, Neurological disorders, In vivo imaging, Gallium nitride, Design and modelling
Multiple sclerosis (MS) is a demyenalinating inflammatory neurological disease. In vivo biomarkers of myelin content are of major importance for patient care and clinical trials. Positron Emission Tomography (PET) with Pittsburgh Compound B (PiB) provides a specific myelin marker. However, it is not available in clinical routine. In this paper, we propose a method to generate myelin maps by synthesizing PiB PET from clinical routine MRI sequences (T1-weighted and FLAIR). To that purpose, we introduce a new curriculum learning strategy for training generative adversarial networks (GAN). Specifically, we design a curricular approach for training the discriminator: training starts with only lesion patches and random patches (from anywhere in the white matter) are progressively introduced. We relied on two distinct cohorts of MS patients acquired each on a different scanner and in a different country. One cohort was used for training/validation and the other one for testing. We found that the synthetic PiB PET was strongly correlated to the ground-truth both at the lesion level (r = 0.70, p < 10−5) and the patient level (r = 0.74, p < 10−5). Moreover, the correlations were stronger when using the curricular learning strategy compared to starting the discriminator training from random patches. Our results demonstrate the interest of this new curriculum learning strategy for PET image synthesis. Even though further evaluations are needed, our approach has the potential to provide a useful biomarker for clinical routine follow-up of patients with MS.
KEYWORDS: Quality control, Image segmentation, Education and training, Data modeling, Deep learning, Medical imaging, Brain, Visualization, Performance modeling, Multiple sclerosis
The establishment of automated image segmentation methods in medical imaging allows the analysis of very large datasets. However, visual quality control (QC) of segmentation results is impractical in large datasets, hence the need for automatic QC. In this paper, we introduce a novel automatic approach for QC of segmentation results. We developed a QC deep learning model (referred to as QC model) that, for a given patient, predicts the accuracy of the corresponding automatic segmentation (in our work the Dice score) provided by a deep learning segmentation model (referred to as segmentation model) in the absence of a ground truth annotation. To train the QC model, we introduce data augmentation by using the early epochs of the segmentation model. These early epochs allow us to feed the training of the QC model with examples of poor segmentation. We applied our approach to the QC of automatic segmentation of the choroid plexuses of the brain from MRI in controls and patients with multiple sclerosis. However, the method is generic and could be used with any segmentation model. The experiments showed that the proposed approach is very effective for predicting the segmentation accuracy with a correlation coefficient of 0.92, an R2 of 0.763, a mean absolute error (MAE) of 0.078, and a mean squared error (MSE) of 0.009. Overall, this work shall provide a valuable tool for the automatic QC of segmentation results.
Choroid plexuses (CP) are structures of the brain ventricles which produce most of the cerebrospinal fluid (CSF). Several postmortem and in vivo studies have pointed towards their role in the inflammatory processes in multiple sclerosis (MS). Automatic segmentation of CP from MRI thus has high value for studying their characteristics in large cohorts of patients. To the best of our knowledge, the only freely available tool for CP segmentation is FreeSurfer but its accuracy for this specific structure is poor. In this paper, we propose to automatically segment CP from non-contrast enhanced T1-weighted MRI. To that end, we introduce a new model called ”Axial-MLP” based on an assembly of Axial multi-layer perceptrons (MLPs). This is inspired by recent works which showed that the self-attention layers of Transformers can be replaced with MLPs. This approach is systematically compared with a standard 3D U-Net, nnU-Net, Freesurfer and FastSurfer. For our experiments, we make use of a dataset of 141 subjects (44 controls and 97 patients with MS). We show that all the tested deep learning (DL) methods outperform FreeSurfer (Dice around 0.7 for DL vs 0.33 for FreeSurfer). Axial-MLP is competitive with U-Nets even though it is slightly less accurate. The conclusions of our paper are two-fold: 1) the studied deep learning methods could be useful tools to study CP in large cohorts of MS patients; 2) Axial-MLP is a potentially viable alternative to convolutional neural networks for such tasks, although it could benefit from further improvements. An implementation is available at https://github.com/aramis-lab/axial-mlp.
Multiple sclerosis (MS) is a white matter (WM) disease characterized by the formation of WM lesions, which can be visualized by magnetic resonance imaging (MRI). The fluid-attenuated inversion recovery (FLAIR) MRI pulse sequence is used clinically and in research for the detection of WM lesions. However, in clinical settings, some MRI pulse sequences could be missed because of various constraints. The use of the three-dimensional fully convolutional neural networks is proposed to predict FLAIR pulse sequences from other MRI pulse sequences. In addition, the contribution of each input pulse sequence is evaluated with a pulse sequence-specific saliency map. This approach is tested on a real MS image dataset and evaluated by comparing this approach with other methods and by assessing the lesion contrast in the synthetic FLAIR pulse sequence. Both the qualitative and quantitative results show that this method is competitive for FLAIR synthesis.
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