Browsing by Author "Yurt, Mahmut"
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Item Open Access Deep learning for multi-contrast MRI synthesis(2021-07) Yurt, MahmutMagnetic resonance imaging (MRI) possesses the unique versatility to acquire images under a diverse array of distinct tissue contrasts. Multi-contrast images, in turn, better delineate tissues, accumulate diagnostic information, and enhance radiological analyses. Yet, prolonged, costly exams native to multi-contrast pro-tocols often impair the diversity, resulting in missing images from some contrasts. A promising remedy against this limitation arises as image synthesis that recovers missing target contrast images from available source contrast images. Learning-based models demonstrated remarkable success in this source-to-target mapping due to their prowess in solving even the most demanding inverse problems. Main-stream approaches proposed for synthetic MRI were typically subjected to a model training to perform either one-to-one or many-to-one mapping. One-to-one models manifest elevated sensitivity to detailed features of the given source, but they perform suboptimally when source-target images are poorly linked. Meanwhile, many-to-one counterparts pool information from multiple sources, yet this comes at the expense of losing detailed features uniquely present in cer-tain sources. Furthermore, regardless of the mapping, they both innately demand large training sets of high-quality source and target images Fourier-reconstructed from Nyquist-sampled acquisitions. However, time and cost considerations put significant challenges in compiling such datasets. To address these limitations, here we first propose a novel multi-stream model that task-adaptively fuses unique and shared image features from a hybrid of multiple one-to-one streams and a single many-to-one stream. We then introduce a novel semi-supervised learning framework based on selective tensor loss functions to learn high-quality image synthesis directly from a training dataset of undersampled acquisitions, bypass-ing the undesirable data requirements of deep learning. Demonstrations on brain MRI images from healthy subjects and glioma patients indicate the superiority of the proposed approaches against state-of-the-art baselines.Item Open Access Deep MRI reconstruction with generative vision transformer(Springer, 2021) Korkmaz, Yılmaz; Yurt, Mahmut; Dar, Salman Ul Hassan; Özbey, Muzaffer; Çukur, TolgaSupervised training of deep network models for MRI reconstruction requires access to large databases of fully-sampled MRI acquisitions. To alleviate dependency on costly databases, unsupervised learning strategies have received interest. A powerful framework that eliminates the need for training data altogether is the deep image prior (DIP). To do this, DIP inverts randomly-initialized models to infer network parameters most consistent with the undersampled test data. However, existing DIP methods leverage convolutional backbones, suffering from limited sensitivity to long-range spatial dependencies and thereby poor model invertibility. To address these limitations, here we propose an unsupervised MRI reconstruction based on a novel generative vision transformer (GVTrans). GVTrans progressively maps low-dimensional noise and latent variables onto MR images via cascaded blocks of cross-attention vision transformers. Cross-attention mechanism between latents and image features serve to enhance representational learning of local and global context. Meanwhile, latent and noise injections at each network layer permit fine control of generated image features, improving model invertibility. Demonstrations are performed for scan-specific reconstruction of brain MRI data at multiple contrasts and acceleration factors. GVTrans yields superior performance to state-of-the-art generative models based on convolutional neural networks (CNNs).Item Open Access GRJointNET: 3B eksik nokta bulutları için sinerjistik tamamlama ve parça bölütleme(IEEE, 2021-07-19) Gürses, Yiğit; Taşpınar, Melisa; Yurt, Mahmut; Özer, SedatÜç boyutlu (3B) nokta bulutları üzerinde bölütleme yapmak, otonom sistemler için önemli ve gerekli bir işlemdir. Bölütleme algoritmalarının başarısı, üzerinde işlem yapılan nokta bulutlarının niteliğine (çözünürlük, tamlık vb.) bağlıdır. Dolayısıyla, nokta bulutundaki mevcut eksiklikler, nokta bulutu tabanlı uygulamaların başarısını düşürmektedir. Bu konuda, güncel bir çalısma olan GRNet, eksik nokta bulutlarını tamamlamaya odaklanan başarılı bir algoritmadır, ancak bölütleme yeteneği yoktur. Biz bu çalışmada, GRNet üzerine geliştirdigimiz derin öğrenme tabanlı GRJointNet algoritmasını sunmaktayız. GRJointNet hem bir nokta bulutundaki eksik noktaları tamamlamakta, hem de onun yapamadığı parça bölütlemesini de yapmaktadır. Bu işlemler elde ettikleri verileri birbirlerini desteklemek için kullanmaktadır. ShapeNet-Part veri kümesinde yapılmış deneylerimiz, GRJointNet algoritmasının nokta bulutu tamamlamada GRNet’den daha başarılı olduğunu göstermektedir. Aynı zamanda, GRNet bölütleme yapamazken, GRJointNet bu özelliği de kazanmıştır. Dolayısıyla bu çalışma nokta bulutlarının 3B bilgisayarlı görüde kullanışlılığını arttırmak adına umut vadetmektedir.Item Restricted Hamit Fendoğlu'nun hayatı ve 1970-1980 yılları arasında Türk siyasetine etkisi(Bilkent University, 2016) Arabacı, Büşra; Yurt, Mahmut; Yazar, Onurcan; Akgün, Cemil; Akdağlı, YunusItem Open Access Image synthesis in multi-contrast MRI with conditional generative adversarial networks(IEEE, 2019-10) Dar, Salman UH.; Yurt, Mahmut; Çukur, Tolga; Karacan, L.; Erdem, A.; Erdem, E.Acquiring images of the same anatomy with multiple different contrasts increases the diversity of diagnostic information available in an MR exam. Yet, the scan time limitations may prohibit the acquisition of certain contrasts, and some contrasts may be corrupted by noise and artifacts. In such cases, the ability to synthesize unacquired or corrupted contrasts can improve diagnostic utility. For multi-contrast synthesis, the current methods learn a nonlinear intensity transformation between the source and target images, either via nonlinear regression or deterministic neural networks. These methods can, in turn, suffer from the loss of structural details in synthesized images. Here, in this paper, we propose a new approach for multi-contrast MRI synthesis based on conditional generative adversarial networks. The proposed approach preserves intermediate-to-high frequency details via an adversarial loss, and it offers enhanced synthesis performance via pixel-wise and perceptual losses for registered multi-contrast images and a cycle-consistency loss for unregistered images. Information from neighboring cross-sections are utilized to further improve synthesis quality. Demonstrations on T 1 - and T 2 - weighted images from healthy subjects and patients clearly indicate the superior performance of the proposed approach compared to the previous state-of-the-art methods. Our synthesis approach can help improve the quality and versatility of the multi-contrast MRI exams without the need for prolonged or repeated examinations.Item Open Access mustGAN: multi-stream generative adversarial networks for MR image synthesis(Elsevier BV, 2021-05) Yurt, Mahmut; Dar, Salman Uh; Erdem, A.; Erdem, E.; Oğuz, Kader K.; Çukur, TolgaMulti-contrast MRI protocols increase the level of morphological information available for diagnosis. Yet, the number and quality of contrasts are limited in practice by various factors including scan time and patient motion. Synthesis of missing or corrupted contrasts from other high-quality ones can alleviate this limitation. When a single target contrast is of interest, common approaches for multi-contrast MRI involve either one-to-one or many-to-one synthesis methods depending on their input. One-to-one methods take as input a single source contrast, and they learn a latent representation sensitive to unique features of the source. Meanwhile, many-to-one methods receive multiple distinct sources, and they learn a shared latent representation more sensitive to common features across sources. For enhanced image synthesis, we propose a multi-stream approach that aggregates information across multiple source images via a mixture of multiple one-to-one streams and a joint many-to-one stream. The complementary feature maps generated in the one-to-one streams and the shared feature maps generated in the many-to-one stream are combined with a fusion block. The location of the fusion block is adaptively modified to maximize task-specific performance. Quantitative and radiological assessments on T1,- T2-, PD-weighted, and FLAIR images clearly demonstrate the superior performance of the proposed method compared to previous state-of-the-art one-to-one and many-to-one methods.Item Open Access Prior-Guided image reconstruction for accelerated multi-contrast MRI via generative adversarial networks(IEEE, 2020) Dar, Salman U.H.; Yurt, Mahmut; Shahdloo, Mohammad; Ildız, Muhammed Emrullah; Tınaz, Berk; Çukur, TolgaMulti-contrast MRI acquisitions of an anatomy enrich the magnitude of information available for diagnosis. Yet, excessive scan times associated with additional contrasts may be a limiting factor. Two mainstream frameworks for enhanced scan efficiency are reconstruction of undersampled acquisitions and synthesis of missing acquisitions. Recently, deep learning methods have enabled significant performance improvements in both frameworks. Yet, reconstruction performance decreases towards higher acceleration factors with diminished sampling density at high-spatial-frequencies, whereas synthesis can manifest artefactual sensitivity or insensitivity to image features due to the absence of data samples from the target contrast. In this article, we propose a new approach for synergistic recovery of undersampled multi-contrast acquisitions based on conditional generative adversarial networks. The proposed method mitigates the limitations of pure learning-based reconstruction or synthesis by utilizing three priors: shared high-frequency prior available in the source contrast to preserve high-spatial-frequency details, low-frequency prior available in the undersampled target contrast to prevent feature leakage/loss, and perceptual prior to improve recovery of high-level features. Demonstrations on brain MRI datasets from healthy subjects and patients indicate the superior performance of the proposed method compared to pure reconstruction and synthesis methods. The proposed method can help improve the quality and scan efficiency of multi-contrast MRI exams.Item Open Access Progressively volumetrized deep generative models for data-efficient contextual learning of MR image recovery(Elsevier BV, 2022-05) Yurt, Mahmut; Özbey, Muzaffer; Dar, Salman U.H.; Tınaz, Berk; Oğuz, Kader K.; Çukur, TolgaMagnetic resonance imaging (MRI) offers the flexibility to image a given anatomic volume under a multi- tude of tissue contrasts. Yet, scan time considerations put stringent limits on the quality and diversity of MRI data. The gold-standard approach to alleviate this limitation is to recover high-quality images from data undersampled across various dimensions, most commonly the Fourier domain or contrast sets. A primary distinction among recovery methods is whether the anatomy is processed per volume or per cross-section. Volumetric models offer enhanced capture of global contextual information, but they can suffer from suboptimal learning due to elevated model complexity. Cross-sectional models with lower complexity offer improved learning behavior, yet they ignore contextual information across the longitu- dinal dimension of the volume. Here, we introduce a novel progressive volumetrization strategy for gen- erative models (ProvoGAN) that serially decomposes complex volumetric image recovery tasks into suc- cessive cross-sectional mappings task-optimally ordered across individual rectilinear dimensions. Provo-GAN effectively captures global context and recovers fine-structural details across all dimensions, while maintaining low model complexity and improved learning behavior. Comprehensive demonstrations on mainstream MRI reconstruction and synthesis tasks show that ProvoGAN yields superior performance to state-of-the-art volumetric and cross-sectional models.Item Open Access ResViT: residual vision transformers for multimodal medical ımage synthesis(Institute of Electrical and Electronics Engineers Inc., 2022-04-18) Dalmaz, Onat; Yurt, Mahmut; Çukur, TolgaGenerative adversarial models with convolutional neural network (CNN) backbones have recently been established as state-of-the-art in numerous medical image synthesis tasks. However, CNNs are designed to perform local processing with compact filters, and this inductive bias compromises learning of contextual features. Here, we propose a novel generative adversarial approach for medical image synthesis, ResViT, that leverages the contextual sensitivity of vision transformers along with the precision of convolution operators and realism of adversarial learning. ResViT’s generator employs a central bottleneck comprising novel aggregated residual transformer (ART) blocks that synergistically combine residual convolutional and transformer modules. Residual connections in ART blocks promote diversity in captured representations, while a channel compression module distills task-relevant information. A weight sharing strategy is introduced among ART blocks to mitigate computational burden. A unified implementation is introduced to avoid the need to rebuild separate synthesis models for varying source-target modality configurations. Comprehensive demonstrations are performed for synthesizing missing sequences in multi-contrast MRI, and CT images from MRI. Our results indicate superiority of ResViT against competing CNN- and transformer-based methods in terms of qualitative observations and quantitative metrics.Item Open Access Semi-supervised learning of MRI synthesis without fully-sampled ground truths(IEEE, 2022-08-16) Yurt, Mahmut; Dalmaz, Onat; Dar, Salman; Özbey, Muzaffer; Tınaz, Berk; Oğuz, Kader; Çukur, TolgaLearning-based translation between MRI contrasts involves supervised deep models trained using high-quality source- and target-contrast images derived from fully-sampled acquisitions, which might be difficult to collect under limitations on scan costs or time. To facilitate curation of training sets, here we introduce the first semi-supervised model for MRI contrast translation (ssGAN) that can be trained directly using undersampled k-space data. To enable semi-supervised learning on undersampled data, ssGAN introduces novel multi-coil losses in image, k-space, and adversarial domains. The multi-coil losses are selectively enforced on acquired k-space samples unlike traditional losses in single-coil synthesis models. Comprehensive experiments on retrospectively undersampled multi-contrast brain MRI datasets are provided. Our results demonstrate that ssGAN yields on par performance to a supervised model, while outperforming single-coil models trained on coil-combined magnitude images. It also outperforms cascaded reconstruction-synthesis models where a supervised synthesis model is trained following self-supervised reconstruction of undersampled data. Thus, ssGAN holds great promise to improve the feasibility of learning-based multi-contrast MRI synthesis.Item Open Access Unsupervised MRI reconstruction via zero-shot learned adversarial transformers(Institute of Electrical and Electronics Engineers Inc., 2022-01-27) Korkmaz, Yilmaz; Dar, Salman U.H.; Yurt, Mahmut; Özbey, Muzaffer; Çukur, TolgaSupervised reconstruction models are characteristically trained on matched pairs of undersampled and fully-sampled data to capture an MRI prior, along with supervision regarding the imaging operator to enforce data consistency. To reduce supervision requirements, the recent deep image prior framework instead conjoins untrained MRI priors with the imaging operator during inference. Yet, canonical convolutional architectures are suboptimal in capturing long-range relationships, and priors based on randomly initialized networks may yield suboptimal performance. To address these limitations, here we introduce a novel unsupervised MRI reconstruction method based on zero-Shot Learned Adversarial TransformERs (SLATER). SLATER embodies a deep adversarial network with cross-attention transformers to map noise and latent variables onto coil-combined MR images. During pre-training, this unconditional network learns a high-quality MRI prior in an unsupervised generative modeling task. During inference, a zero-shot reconstruction is then performed by incorporating the imaging operator and optimizing the prior to maximize consistency to undersampled data. Comprehensive experiments on brain MRI datasets clearly demonstrate the superior performance of SLATER against state-of-the-art unsupervised methods.