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.
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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