Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention最新文献

This work investigates the use of configuration state imaging together with deep neural networks to develop quantitative MRI techniques for deployment in an interventional setting. A physics modeling technique for inhomogeneous fields and heterogeneous tissues is presented and used to evaluate the theoretical capability of neural networks to estimate parameter maps from configuration state signal data. All tested normalization strategies achieved similar performance in estimating $T_2$ and $T_2^{*}$ . Varying network architecture and data normalization had substantial impacts on estimated flip angle and $T_1$ , highlighting their importance in developing neural networks to solve these inverse problems. The developed signal modeling technique provides an environment that will enable the development and evaluation of physics-informed machine learning techniques for MR parameter mapping and facilitate the development of quantitative MRI techniques to inform clinical decisions during MR-guided treatments.

Higher-order properties of functional magnetic resonance imaging (fMRI) induced connectivity have been shown to unravel many exclusive topological and dynamical insights beyond pairwise interactions. Nonetheless, whether these fMRI-induced higher-order properties play a role in disentangling other neuroimaging modalities' insights remains largely unexplored and poorly understood. In this work, by analyzing fMRI data from the Human Connectome Project Young Adult dataset using persistent homology, we discovered that the volume-optimal persistence homological scaffolds of fMRI-based functional connectomes exhibited conservative topological reconfigurations from the resting state to attentional task-positive state. Specifically, while reflecting the extent to which each cortical region contributed to functional cycles following different cognitive demands, these reconfigurations were constrained such that the spatial distribution of cavities in the connectome is relatively conserved. Most importantly, such level of contributions covaried with powers of aperiodic activities mostly within the theta-alpha (4-12 Hz) band measured by magnetoencephalography (MEG). This comprehensive result suggests that fMRI-induced hemodynamics and MEG theta-alpha aperiodic activities are governed by the same functional constraints specific to each cortical morpho-structure. Methodologically, our work paves the way toward an innovative computing paradigm in multimodal neuroimaging topological learning. The code for our analyses is provided in https://github.com/ngcaonghi/scaffold_noise.

Deep learning models generating structural brain MRIs have the potential to significantly accelerate discovery of neuroscience studies. However, their use has been limited in part by the way their quality is evaluated. Most evaluations of generative models focus on metrics originally designed for natural images (such as structural similarity index and Fréchet inception distance). As we show in a comparison of 6 state-of-the-art generative models trained and tested on over 3000 MRIs, these metrics are sensitive to the experimental setup and inadequately assess how well brain MRIs capture macrostructural properties of brain regions (a.k.a., anatomical plausibility). This shortcoming of the metrics results in inconclusive findings even when qualitative differences between the outputs of models are evident. We therefore propose a framework for evaluating models generating brain MRIs, which requires uniform processing of the real MRIs, standardizing the implementation of the models, and automatically segmenting the MRIs generated by the models. The segmentations are used for quantifying the plausibility of anatomy displayed in the MRIs. To ensure meaningful quantification, it is crucial that the segmentations are highly reliable. Our framework rigorously checks this reliability, a step often overlooked by prior work. Only 3 of the 6 generative models produced MRIs, of which at least 95% had highly reliable segmentations. More importantly, the assessment of each model by our framework is in line with qualitative assessments, reinforcing the validity of our approach. The code of this framework is available via https://github.com/jiaqiw01/MRIAnatEval.git.

In resource-limited settings, portable ultra-low-field (uLF, i.e., 0.064T) magnetic resonance imaging (MRI) systems expand accessibility of radiological scanning, particularly for low-income areas as well as underserved populations like neonates and infants. However, compared to high-field (HF, e.g., ≥ 1.5T) systems, inferior image quality in uLF scanning poses challenges for research and clinical use. To address this, we introduce Super-Field Network (SFNet), a custom swinUNETRv2 with generative adversarial network components that uses uLF MRIs to generate super-field (SF) images comparable to HF MRIs. We acquired a cohort of infant data (n=30, aged 0-2 years) with paired uLF-HF MRI data from a resource-limited setting with an underrepresented population in research. To enhance the small dataset, we present a novel use of latent diffusion to create dual-channel (uLF-HF) paired MRIs. We compare SFNet with state-of-the-art synthesis methods by HF-SF image similarity perceptual scores and by automated HF and SF segmentations of white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF). The best performance was achieved by SFNet trained on the latent diffusion enhanced dataset yielding state-of-the-art results in Fréchet inception distance at 9.08 ± 1.21, perceptual similarity at 0.11 ± 0.01, and PSNR at 22.64 ± 1.31. True HF and SF segmentations had a strong overlap with Dice similarity coefficients of 0.71 ± 0.1, 0.79 ± 0.2, and 0.73 ± 0.08 for WM, GM, and CSF, respectively, in the developing infant brain with incomplete myelination, and displayed 166%, 107%, and 106% improvement over respective uLF-based segmentation metrics. SF MRI supports health equity by enhancing the clinical use of uLF imaging systems and improving the diagnostic capabilities of low-cost portable MRI systems in resource-limited settings and for underserved populations. Our code is made openly available at https://github.com/AustinTapp/SFnet.

Graph neural networks (GNNs) are proficient machine learning models in handling irregularly structured data. Nevertheless, their generic formulation falls short when applied to the analysis of brain connectomes in Alzheimer's Disease (AD), necessitating the incorporation of domain-specific knowledge to achieve optimal model performance. The integration of AD-related expertise into GNNs presents a significant challenge. Current methodologies reliant on manual design often demand substantial expertise from external domain specialists to guide the development of novel models, thereby consuming considerable time and resources. To mitigate the need for manual curation, this paper introduces a novel self-guided knowledge-infused multimodal GNN to autonomously integrate domain knowledge into the model development process. We propose to conceptualize existing domain knowledge as natural language, and devise a specialized multimodal GNN framework tailored to leverage this uncurated knowledge to direct the learning of the GNN submodule, thereby enhancing its efficacy and improving prediction interpretability. To assess the effectiveness of our framework, we compile a comprehensive literature dataset comprising recent peer-reviewed publications on AD. By integrating this literature dataset with several real-world AD datasets, our experimental results illustrate the effectiveness of the proposed method in extracting curated knowledge and offering explanations on graphs for domain-specific applications. Furthermore, our approach successfully utilizes the extracted information to enhance the performance of the GNN.

Low-dose computed tomography (LDCT) reduces the risks of radiation exposure but introduces noise and artifacts into CT images. The Feature Pyramid Network (FPN) is a conventional method for extracting multi-scale feature maps from input images. While upper layers in FPN enhance semantic value, details become generalized with reduced spatial resolution at each layer. In this work, we propose a Gradient Guided Co-Retention Feature Pyramid Network (G2CR-FPN) to address the connection between spatial resolution and semantic value beyond feature maps extracted from LDCT images. The network is structured with three essential paths: the bottom-up path utilizes the FPN structure to generate the hierarchical feature maps, representing multi-scale spatial resolutions and semantic values. Meanwhile, the lateral path serves as a skip connection between feature maps with the same spatial resolution, while also functioning feature maps as directional gradients. This path incorporates a gradient approximation, deriving edge-like enhanced feature maps in horizontal and vertical directions. The top-down path incorporates a proposed co-retention block that learns the high-level semantic value embedded in the preceding map of the path. This learning process is guided by the directional gradient approximation of the high-resolution feature map from the bottom-up path. Experimental results on the clinical CT images demonstrated the promising performance of the model. Our code is available at: https://github.com/liz109/G2CR-FPN.

Prenatal drug exposure, which occurs during a time of extraordinary and critical brain development, is typically associated with cognitive, behavioral, and physiological deficits during infancy, childhood, and adolescence. Early identifying infants with prenatal drug exposures and associated biomarkers using neuroimages can help inform earlier, more effective, and personalized interventions to greatly improve later cognitive outcomes. To this end, we propose a novel deep learning model called disentangled hybrid volume-surface transformer for identifying individual infants with prenatal drug exposures. Specifically, we design two distinct branches, a volumetric network for learning non-cortical features in 3D image space, and a surface network for learning features on the highly convoluted cortical surface manifold. To better capture long-range dependency and generate highly discriminative representations, image and surface transformers are respectively employed for the volume and surface branches. Then, a disentanglement strategy is further proposed to separate the representations from two branches into complementary variables and common variables, thus removing redundant information and boosting expressive capability. After that, the disentangled representations are concatenated to a classifier to determine if there is an existence of prenatal drug exposures. We have validated our method on 210 infant MRI scans and demonstrated its superior performance, compared to ablated models and state-of-the-art methods.

Histology slide digitization is becoming essential for telepathology (remote consultation), knowledge sharing (education), and using the state-of-the-art artificial intelligence algorithms (augmented/automated end-to-end clinical workflows). However, the cumulative costs of digital multi-slide high-speed brightfield scanners, cloud/on-premises storage, and personnel (IT and technicians) make the current slide digitization workflows out-of-reach for limited-resource settings, further widening the health equity gap; even single-slide manual scanning commercial solutions are costly due to hardware requirements (high-resolution cameras, high-spec PC/workstation, and support for only high-end microscopes). In this work, we present a new cloud slide digitization workflow for creating scanner-quality whole-slide images (WSIs) from uploaded low-quality videos, acquired from cheap and inexpensive microscopes with built-in cameras. Specifically, we present a pipeline to create stitched WSIs while automatically deblurring out-of-focus regions, upsampling input 10X images to 40X resolution, and reducing brightness/contrast and light-source illumination variations. We demonstrate the WSI creation efficacy from our workflow on World Health Organization-declared neglected tropical disease, Cutaneous Leishmaniasis (prevalent only in the poorest regions of the world and only diagnosed by sub-specialist dermatopathologists, rare in poor countries), as well as other common pathologies on core biopsies of breast, liver, duodenum, stomach and lymph node. The code and pretrained models will be accessible via our GitHub (https://github.com/nadeemlab/DeepLIIF), and the cloud platform will be available at https://deepliif.org for uploading microscope videos and downloading/viewing WSIs with shareable links (no sign-in required) for telepathology and knowledge sharing.

Delineating the normative developmental profile of functional connectome is important for both standardized assessment of individual growth and early detection of diseases. However, functional connectome has been mostly studied using functional connectivity (FC), where undirected connectivity strengths are estimated from statistical correlation of resting-state functional MRI (rs-fMRI) signals. To address this limitation, we applied regression dynamic causal modeling (rDCM) to delineate the developmental trajectories of effective connectivity (EC), the directed causal influence among neuronal populations, in whole-brain networks from infancy to adolescence (0-22 years old) based on high-quality rs-fMRI data from Baby Connectome Project (BCP) and Human Connectome Project Development (HCP-D). Analysis with linear mixed model demonstrates significant age effect on the mean nodal EC which is best fit by a "U" shaped quadratic curve with minimal EC at around 2 years old. Further analysis indicates that five brain regions including the left and right cuneus, left precuneus, left supramarginal gyrus and right inferior temporal gyrus have the most significant age effect on nodal EC (p < 0.05, FDR corrected). Moreover, the frontoparietal control (FPC) network shows the fastest increase from early childhood to adolescence followed by the visual and salience networks. Our findings suggest complex nonlinear developmental profile of EC from infancy to adolescence, which may reflect dynamic structural and functional maturation during this critical growth period.

Fréchet Inception Distance (FID) is a widely used metric for assessing synthetic image quality. It relies on an ImageNet-based feature extractor, making its applicability to medical imaging unclear. A recent trend is to adapt FID to medical imaging through feature extractors trained on medical images. Our study challenges this practice by demonstrating that ImageNet-based extractors are more consistent and aligned with human judgment than their RadImageNet counterparts. We evaluated sixteen StyleGAN2 networks across four medical imaging modalities and four data augmentation techniques with Fréchet distances (FDs) computed using eleven ImageNet or RadImageNet-trained feature extractors. Comparison with human judgment via visual Turing tests revealed that ImageNet-based extractors produced rankings consistent with human judgment, with the FD derived from the ImageNet-trained SwAV extractor significantly correlating with expert evaluations. In contrast, RadImageNet-based rankings were volatile and inconsistent with human judgment. Our findings challenge prevailing assumptions, providing novel evidence that medical image-trained feature extractors do not inherently improve FDs and can even compromise their reliability. Our code is available at https://github.com/mckellwoodland/fid-med-eval.