Research on multi-path dense networks for MRI spinal segmentation.
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ABSTRACT:
SUBMITTER: Liang S
PROVIDER: S-EPMC7954354 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Automatic segmentation of abdominal anatomy on computed tomography (CT) images can support diagnosis, treatment planning, and treatment delivery workflows. Segmentation methods using statistical models and multi-atlas label fusion (MALF) require inter-subject image registrations, which are challenging for abdominal images, but alternative methods without registration have not yet achieved higher accuracy for most abdominal organs. We present a registration-free deep-learning-based segmentation algorithm for eight organs that are relevant for navigation in endoscopic pancreatic and biliary procedures, including the pancreas, the gastrointestinal tract (esophagus, stomach, and duodenum) and surrounding organs (liver, spleen, left kidney, and gallbladder). We directly compared the segmentation accuracy of the proposed method to the existing deep learning and MALF methods in a cross-validation on a multi-centre data set with 90 subjects. The proposed method yielded significantly higher Dice scores for all organs and lower mean absolute distances for most organs, including Dice scores of 0.78 versus 0.71, 0.74, and 0.74 for the pancreas, 0.90 versus 0.85, 0.87, and 0.83 for the stomach, and 0.76 versus 0.68, 0.69, and 0.66 for the esophagus. We conclude that the deep-learning-based segmentation represents a registration-free method for multi-organ abdominal CT segmentation whose accuracy can surpass current methods, potentially supporting image-guided navigation in gastrointestinal endoscopy procedures.
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Project description:Defining myocardial contours is often the most time-consuming portion of dynamic cardiac MRI image analysis. Displacement encoding with stimulated echoes (DENSE) is a quantitative MRI technique that encodes tissue displacement into the phase of the complex MRI images. Cine DENSE provides a time series of these images, thus facilitating the non-invasive study of myocardial kinematics. Epicardial and endocardial contours need to be defined at each frame on cine DENSE images for the quantification of regional displacement and strain as a function of time. This work presents a reliable and effective two-dimensional semi-automated segmentation technique that uses the encoded motion to project a manually-defined region of interest through time. Contours can then easily be extracted for each cardiac phase. This method boasts several advantages, including, (1) parameters are based on practical physiological limits, (2) contours are calculated for the first few cardiac phases, where it is difficult to visually distinguish blood from myocardium, and (3) the method is independent of the shape of the tissue delineated and can be applied to short- or long-axis views, and on arbitrary regions of interest. Motion-guided contours were compared to manual contours for six conventional and six slice-followed mid-ventricular short-axis cine DENSE datasets. Using an area measure of segmentation error, the accuracy of the segmentation algorithm was shown to be similar to inter-observer variability. In addition, a radial segmentation error metric was introduced for short-axis data. The average radial epicardial segmentation error was 0.36+/-0.08 and 0.40+/-0.10 pixels for slice-followed and conventional cine DENSE, respectively, and the average radial endocardial segmentation error was 0.46+/-0.12 and 0.46+/-0.16 pixels for slice following and conventional cine DENSE, respectively. Motion-guided segmentation employs the displacement-encoded phase shifts intrinsic to DENSE MRI to accurately propagate a single set of pre-defined contours throughout the remaining cardiac phases.
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Project description:Extent of resection after surgery is one of the main prognostic factors for patients diagnosed with glioblastoma. To achieve this, accurate segmentation and classification of residual tumor from post-operative MR images is essential. The current standard method for estimating it is subject to high inter- and intra-rater variability, and an automated method for segmentation of residual tumor in early post-operative MRI could lead to a more accurate estimation of extent of resection. In this study, two state-of-the-art neural network architectures for pre-operative segmentation were trained for the task. The models were extensively validated on a multicenter dataset with nearly 1000 patients, from 12 hospitals in Europe and the United States. The best performance achieved was a 61% Dice score, and the best classification performance was about 80% balanced accuracy, with a demonstrated ability to generalize across hospitals. In addition, the segmentation performance of the best models was on par with human expert raters. The predicted segmentations can be used to accurately classify the patients into those with residual tumor, and those with gross total resection.
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Project description:Breast cancer detection largely relies on imaging characteristics and the ability of clinicians to easily and quickly identify potential lesions. Magnetic resonance imaging (MRI) of breast tumors has recently shown great promise for enabling the automatic identification of breast tumors. Nevertheless, state-of-the-art MRI-based algorithms utilizing deep learning techniques are still limited in their ability to accurately separate tumor and healthy tissue. Therefore, in the current work, we propose an automatic and accurate two-stage U-Net-based segmentation framework for breast tumor detection using dynamic contrast-enhanced MRI (DCE-MRI). This framework was evaluated using T2-weighted MRI data from 160 breast tumor cases, and its performance was compared with that of the standard U-Net model. In the first stage of the proposed framework, a refined U-Net model was utilized to automatically delineate a breast region of interest (ROI) from the surrounding healthy tissue. Importantly, this automatic segmentation step reduced the impact of the background chest tissue on breast tumors' identification. For the second stage, we employed an improved U-Net model that combined a dense residual module based on dilated convolution with a recurrent attention module. This model was used to accurately and automatically segment the tumor tissue from healthy tissue in the breast ROI derived in the previous step. Overall, compared to the U-Net model, the proposed technique exhibited increases in the Dice similarity coefficient, Jaccard similarity, positive predictive value, sensitivity, and Hausdorff distance of 3%, 3%, 3%, 2%, and 16.2, respectively. The proposed model may in the future aid in the clinical diagnosis of breast cancer lesions and help guide individualized patient treatment.
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Project description:Aiming to address dense small object tracking, we propose an image-to-trajectory framework including tracking and detection, where Track-Oriented Multiple Hypothesis Tracking(TOMHT) is revised for tracking. Unlike common cases of multi-object tracking, merged detections and the greater number of objects make dense small object tracking a more challenging problem. Firstly, we handle frequent merged detections through the aspects of detection and hypothesis selection. To tackle merged detection, we revise Local Contrast Method(LCM) and propose a multi-appearance variant, which exploits tree-like topological information and realizes one threshold for one object. Meanwhile, one-to-many constraint is employed via the proposed extended 0-1 programming, which enables hypothesis selection to handle track exclusions caused by merged detections. Secondly, to alleviate the high complexity caused by dense objects, we consider batch optimization and more rigorous and precise pruning technologies. Specifically, we propose autocorrelation based motion score test and two-stage hypotheses pruning. Experimental results are presented to verify the strength of our methods, which indicates speed and performance advantages of our tracker.
| S-EPMC6209235 | biostudies-literature
Project description:The spinal cord is an essential and vulnerable component of the central nervous system. Differentiating and localizing the spinal cord internal structure (i.e., gray matter vs. white matter) is critical for assessment of therapeutic impacts and determining prognosis of relevant conditions. Fortunately, new magnetic resonance imaging (MRI) sequences enable clinical study of the in vivo spinal cord's internal structure. Yet, low contrast-to-noise ratio, artifacts, and imaging distortions have limited the applicability of tissue segmentation techniques pioneered elsewhere in the central nervous system. Additionally, due to the inter-subject variability exhibited on cervical MRI, typical deformable volumetric registrations perform poorly, limiting the applicability of a typical multi-atlas segmentation framework. Thus, to date, no automated algorithms have been presented for the spinal cord's internal structure. Herein, we present a novel slice-based groupwise registration framework for robustly segmenting cervical spinal cord MRI. Specifically, we provide a method for (1) pre-aligning the slice-based atlases into a groupwise-consistent space, (2) constructing a model of spinal cord variability, (3) projecting the target slice into the low-dimensional space using a model-specific registration cost function, and (4) estimating robust segmentation susing geodesically appropriate atlas information. Moreover, the proposed framework provides a natural mechanism for performing atlas selection and initializing the free model parameters in an informed manner. In a cross-validation experiment using 67 MR volumes of the cervical spinal cord, we demonstrate sub-millimetric accuracy, significant quantitative and qualitative improvement over comparable multi-atlas frameworks, and provide insight into the sensitivity of the associated model parameters.
| S-EPMC4009677 | biostudies-other
Project description:BackgroundAutomated segmentation of spinal magnetic resonance imaging (MRI) plays a vital role both scientifically and clinically. However, accurately delineating posterior spine structures is challenging.MethodsThis retrospective study, approved by the ethical committee, involved translating T1-weighted and T2-weighted images into computed tomography (CT) images in a total of 263 pairs of CT/MR series. Landmark-based registration was performed to align image pairs. We compared two-dimensional (2D) paired - Pix2Pix, denoising diffusion implicit models (DDIM) image mode, DDIM noise mode - and unpaired (SynDiff, contrastive unpaired translation) image-to-image translation using "peak signal-to-noise ratio" as quality measure. A publicly available segmentation network segmented the synthesized CT datasets, and Dice similarity coefficients (DSC) were evaluated on in-house test sets and the "MRSpineSeg Challenge" volumes. The 2D findings were extended to three-dimensional (3D) Pix2Pix and DDIM.Results2D paired methods and SynDiff exhibited similar translation performance and DCS on paired data. DDIM image mode achieved the highest image quality. SynDiff, Pix2Pix, and DDIM image mode demonstrated similar DSC (0.77). For craniocaudal axis rotations, at least two landmarks per vertebra were required for registration. The 3D translation outperformed the 2D approach, resulting in improved DSC (0.80) and anatomically accurate segmentations with higher spatial resolution than that of the original MRI series.ConclusionsTwo landmarks per vertebra registration enabled paired image-to-image translation from MRI to CT and outperformed all unpaired approaches. The 3D techniques provided anatomically correct segmentations, avoiding underprediction of small structures like the spinous process.Relevance statementThis study addresses the unresolved issue of translating spinal MRI to CT, making CT-based tools usable for MRI data. It generates whole spine segmentation, previously unavailable in MRI, a prerequisite for biomechanical modeling and feature extraction for clinical applications.Key points• Unpaired image translation lacks in converting spine MRI to CT effectively. • Paired translation needs registration with two landmarks per vertebra at least. • Paired image-to-image enables segmentation transfer to other domains. • 3D translation enables super resolution from MRI to CT. • 3D translation prevents underprediction of small structures.
| S-EPMC10643734 | biostudies-literature
Project description:ObjectiveIncreased subcutaneous and visceral adipose tissue (SAT/VAT) volume is associated with risk for cardiometabolic diseases. This work aimed to develop and evaluate automated abdominal SAT/VAT segmentation on longitudinal MRI in adults with overweight/obesity using attention-based competitive dense (ACD) 3D U-Net and 3D nnU-Net with full field-of-view volumetric multi-contrast inputs.Materials and methods920 adults with overweight/obesity were scanned twice at multiple 3 T MRI scanners and institutions. The first scan was divided into training/validation/testing sets (n = 646/92/182). The second scan from the subjects in the testing set was used to evaluate the generalizability for longitudinal analysis. Segmentation performance was assessed by measuring Dice scores (DICE-SAT, DICE-VAT), false negatives (FN), and false positives (FP). Volume agreement was assessed using the intraclass correlation coefficient (ICC).ResultsACD 3D U-Net achieved rapid (< 4.8 s/subject) segmentation with high DICE-SAT (median ≥ 0.994) and DICE-VAT (median ≥ 0.976), small FN (median ≤ 0.7%), and FP (median ≤ 1.1%). 3D nnU-Net yielded rapid (< 2.5 s/subject) segmentation with similar DICE-SAT (median ≥ 0.992), DICE-VAT (median ≥ 0.979), FN (median ≤ 1.1%) and FP (median ≤ 1.2%). Both models yielded excellent agreement in SAT/VAT volume versus reference measurements (ICC > 0.997) in longitudinal analysis.DiscussionACD 3D U-Net and 3D nnU-Net can be automated tools to quantify abdominal SAT/VAT volume rapidly, accurately, and longitudinally in adults with overweight/obesity.
| S-EPMC11316694 | biostudies-literature
Project description:DesignProspective diagnostic study.ObjectivesAnatomical evaluation and graduation of the severity of spinal stenosis is essential in degenerative cervical spine disease. In clinical practice, this is subjectively categorized on cervical MRI lacking an objective and reliable classification. We implemented a fully-automated quantification of spinal canal compromise through 3D T2-weighted MRI segmentation.SettingMedical Center - University of Freiburg, Germany.MethodsEvaluation of 202 participants receiving 3D T2-weighted MRI of the cervical spine. Segments C2/3 to C6/7 were analyzed for spinal cord and cerebrospinal fluid space volume through a fully-automated segmentation based on a trained deep convolutional neural network. Spinal canal narrowing was characterized by relative values, across sever segments as adapted Maximal Canal Compromise (aMCC), and within the index segment as adapted Spinal Cord Occupation Ratio (aSCOR). Additionally, all segments were subjectively categorized by three observers as "no", "relative" or "absolute" stenosis. Computed scores were applied on the subjective categorization.Results798 (79.0%) segments were subjectively categorized as "no" stenosis, 85 (8.4%) as "relative" stenosis, and 127 (12.6%) as "absolute" stenosis. The calculated scores revealed significant differences between each category (p ≤ 0.001). Youden's Index analysis of ROC curves revealed optimal cut-offs to distinguish between "no" and "relative" stenosis for aMCC = 1.18 and aSCOR = 36.9%, and between "relative" and "absolute" stenosis for aMCC = 1.54 and aSCOR = 49.3%.ConclusionThe presented fully-automated segmentation algorithm provides high diagnostic accuracy and objective classification of cervical spinal stenosis. The calculated cut-offs can be used for convenient radiological quantification of the severity of spinal canal compromise in clinical routine.
| S-EPMC11230899 | biostudies-literature
Project description:Recently, low-field magnetic resonance imaging (MRI) has gained renewed interest to promote MRI accessibility and affordability worldwide. The presented M4Raw dataset aims to facilitate methodology development and reproducible research in this field. The dataset comprises multi-channel brain k-space data collected from 183 healthy volunteers using a 0.3 Tesla whole-body MRI system, and includes T1-weighted, T2-weighted, and fluid attenuated inversion recovery (FLAIR) images with in-plane resolution of ~1.2 mm and through-plane resolution of 5 mm. Importantly, each contrast contains multiple repetitions, which can be used individually or to form multi-repetition averaged images. After excluding motion-corrupted data, the partitioned training and validation subsets contain 1024 and 240 volumes, respectively. To demonstrate the potential utility of this dataset, we trained deep learning models for image denoising and parallel imaging tasks and compared their performance with traditional reconstruction methods. This M4Raw dataset will be valuable for the development of advanced data-driven methods specifically for low-field MRI. It can also serve as a benchmark dataset for general MRI reconstruction algorithms.
| S-EPMC10172399 | biostudies-literature