Sina Amirrajab

Focal cortical dysplasia (FCD) is among the leading causes of drug-resistant focal epilepsy and can be challenging to detect on routine MRI due to the subtle and heterogeneous appearance of lesions. Motivated by the scarcity of clinically representative cohorts, we investigate the feasibility of simulating FCD-like lesions in healthy MRI using a composition of hand-crafted image transformations. We develop Syn-thFCD , a phenomenological FCD simulator, and create 2,164 synthetic examples from healthy controls in the heterogeneous FOMO300k dataset. We then pretrain deep learning (DL) segmentation models on synthetic lesions and fine-tune them on real FCD cases from the University Hospital Bonn (UHB) cohort. Comprehensive evaluations show consistent improvements across simulator presets, with detection-rate gains of up to 18.5 percentage points over training from scratch and 7.4 points over self-supervised pretraining, while achieving state-of-the-art segmentation performance (0.366 DSC) on the challenging held-out UHB benchmark. These findings suggest that simulation-based synthetic data generation can bridge existing radiological knowledge and advances in DL to provide meaningful supervisory signals that could ultimately aid the detection of underrepresented and diagnostically challenging cases.

Out-of-distribution (OOD) detection is crucial for the safety and reliability of artificial intelligence algorithms, especially in the medical domain. In the context of the Medical OOD (MOOD) detection challenge 2023, we propose a pipeline that combines a histogram-based method and a diffusion-based method. The histogram-based method is designed to accurately detect homogeneous anomalies in the toy examples of the challenge, such as blobs with constant intensity values. The diffusion-based method is based on one of the latest methods for unsupervised anomaly detection, called DDPM-OOD. We explore this method and propose extensive post-processing steps for pixel-level and sample-level anomaly detection on brain MRI and abdominal CT data provided by the challenge. Our results show that the proposed DDPM method is sensitive to blur and bias field samples, but faces challenges with anatomical deformation, black slice, and swapped patches. These findings suggest that further research is needed to improve the performance of DDPM for OOD detection in medical images.

This literature review presents a comprehensive overview of machine learning (ML) applications in proton MR spectroscopy (MRS). As the use of ML techniques in MRS continues to grow, this review aims to provide the MRS community with a structured overview of the state‐of‐the‐art methods. Specifically, we examine and summarize studies published between 2017 and 2023 from major journals in the MR field. We categorize these studies based on a typical MRS workflow, including data acquisition, processing, analysis, and artificial data generation. Our review reveals that ML in MRS is still in its early stages, with a primary focus on processing and analysis techniques, and less attention given to data acquisition. We also found that many studies use similar model architectures, with little comparison to alternative architectures. Additionally, the generation of artificial data is a crucial topic, with no consistent method for its generation. Furthermore, many studies demonstrate that artificial data suffers from generalization issues when tested on in vivo data. We also conclude that risks related to ML models should be addressed, particularly for clinical applications. Therefore, output uncertainty measures and model biases are critical to investigate. Nonetheless, the rapid development of ML in MRS and the promising results from the reviewed studies justify further research in this field.

We propose a method for synthesizing cardiac magnetic resonance (MR) images with plausible heart pathologies and realistic appearances for the purpose of generating labeled data for the application of supervised deep-learning (DL) training. The image synthesis consists of label deformation and label-to-image translation tasks. The former is achieved via latent space interpolation in a VAE model, while the latter is accomplished via a label-conditional GAN model. We devise three approaches for label manipulation in the latent space of the trained VAE model; i) intra-subject synthesis aiming to interpolate the intermediate slices of a subject to increase the through-plane resolution, ii) inter-subject synthesis aiming to interpolate the geometry and appearance of intermediate images between two dissimilar subjects acquired with different scanner vendors, and iii) pathology synthesis aiming to synthesize a series of pseudo-pathological synthetic subjects with characteristics of a desired heart disease. Furthermore, we propose to model the relationship between 2D slices in the latent space of the VAE prior to reconstruction for generating 3D-consistent subjects from stacking up 2D slice-by-slice generations. We demonstrate that such an approach could provide a solution to diversify and enrich an available database of cardiac MR images and to pave the way for the development of generalizable DL-based image analysis algorithms. We quantitatively evaluate the quality of the synthesized data in an augmentation scenario to achieve generalization and robustness to multi-vendor and multi-disease data for image segmentation. Our code is available at https://github.com/sinaamirrajab/CardiacPathologySynthesis

We propose a method for synthesizing cardiac magnetic resonance (MR) images with plausible heart pathologies and realistic appearances for the purpose of generating labeled data for the application of supervised deep-learning (DL) training. The image synthesis consists of label deformation and label-to-image translation tasks. The former is achieved via latent space interpolation in a VAE model, while the latter is accomplished via a label-conditional GAN model. We devise three approaches for label manipulation in the latent space of the trained VAE model; i) \textbf{intra-subject synthesis} aiming to interpolate the intermediate slices of a subject to increase the through-plane resolution, ii) \textbf{inter-subject synthesis} aiming to interpolate the geometry and appearance of intermediate images between two dissimilar subjects acquired with different scanner vendors, and iii) \textbf{pathology synthesis} aiming to synthesize a series of pseudo-pathological synthetic subjects with characteristics of a desired heart disease. Furthermore, we propose to model the relationship between 2D slices in the latent space of the VAE prior to reconstruction for generating 3D-consistent subjects from stacking up 2D slice-by-slice generations. We demonstrate that such an approach could provide a solution to diversify and enrich an available database of cardiac MR images and to pave the way for the development of generalizable DL-based image analysis algorithms. We quantitatively evaluate the quality of the synthesized data in an augmentation scenario to achieve generalization and robustness to multi-vendor and multi-disease data for image segmentation. Our code is available at https://github.com/sinaamirrajab/CardiacPathologySynthesis.