MITT: Medical Image Tracking Toolbox

High-Resolution Maps of Left Atrial Displacements and Strains Estimated With 3D Cine MRI Using Online Learning Neural Networks

The functional analysis of the left atrium (LA) is important for evaluating cardiac health and understanding diseases like atrial fibrillation. Cine MRI is ideally placed for the detailed 3D characterization of LA motion and deformation but is lacking appropriate acquisition and analysis tools. Here, we propose tools for the Analysis of Left Atrial Displacements and DeformatIons using online learning neural Networks (Aladdin) and present a technical feasibility study on how Aladdin can characterize 3D LA function globally and regionally. Aladdin includes an online segmentation and image registration network, and a strain calculation pipeline tailored to the LA. We create maps of LA Displacement Vector Field (DVF) magnitude and LA principal strain values from images of 10 healthy volunteers and 8 patients with cardiovascular disease (CVD), of which 2 had large left ventricular ejection fraction (LVEF) impairment. We additionally create an atlas of these biomarkers using the data from the healthy volunteers. Results showed that Aladdin can accurately track the LA wall across the cardiac cycle and characterize its motion and deformation. Global LA function markers assessed with Aladdin agree well with estimates from 2D Cine MRI. A more marked active contraction phase was observed in the healthy cohort, while the CVD $\text {LVEF}_{\downarrow } $ group showed overall reduced LA function. Aladdin is uniquely able to identify LA regions with abnormal deformation metrics that may indicate focal pathology. We expect Aladdin to have important clinical applications as it can non-invasively characterize atrial pathophysiology. All source code and data are available at: https://github.com/cgalaz01/aladdin_cmr_la.

Robust unsupervised texture segmentation for motion analysis in ultrasound images

PURPOSE

Ultrasound imaging has emerged as a promising cost-effective and portable non-irradiant modality for the diagnosis and follow-up of diseases. Motion analysis can be performed by segmenting anatomical structures of interest before tracking them over time. However, doing so in a robust way is challenging as ultrasound images often display a low contrast and blurry boundaries.

METHODS

In this paper, a robust descriptor inspired from the fractal dimension is presented to locally characterize the gray-level variations of an image. This descriptor is an adaptive grid pattern whose scale locally varies as the gray-level variations of the image. Robust features are then located based on the gray-level variations, which are more likely to be consistently tracked over time despite the presence of noise.

RESULTS

The method was validated on three datasets: segmentation of the left ventricle on simulated echocardiography (Dice coefficient, DC), accuracy of diaphragm motion tracking for healthy subjects (mean sum of distances, MSD) and for a scoliosis patient (root mean square error, RMSE). Results show that the method segments the left ventricle accurately ( DC = 0.84 ) and robustly tracks the diaphragm motion for healthy subjects ( MSD = 1.10 mm) and for the scoliosis patient ( RMSE = 1.22 mm).

CONCLUSIONS

This method has the potential to segment structures of interest according to their texture in an unsupervised fashion, as well as to help analyze the deformation of tissues. Possible applications are not limited to US image. The same principle could also be applied to other medical imaging modalities such as MRI or CT scans.

Skeletal muscle symptoms and quantitative MRI in females with dystrophinopathy

INTRODUCTION/AIMS

The dystrophinopathies primarily affect males; however, female carriers of pathogenic dystrophin variants can develop skeletal muscle symptoms. This study aimed to evaluate muscle involvement and symptoms in females with dystrophinopathy using quantitative magnetic resonance imaging (MRI), functional assessments, and patient-reported outcomes.

METHODS

Controls and females with dystrophinopathy with muscle symptoms of pain, weakness, fatigue, or excessive tightness were enrolled in this cross-sectional study. Participants underwent lower extremity MRI to quantify muscle inflammation, replacement by fat, and disease asymmetry. Cardiac MRI, functional ability, muscle symptoms, and serum creatine kinase levels were also evaluated.

RESULTS

Six pediatric females with dystrophinopathy (mean age: 11.7 years), 11 adult females with dystrophinopathy (mean age: 41.3 years), and seven controls enrolled. The mean fat fraction was increased in females with dystrophinopathy compared to controls in the soleus (0.11 vs. 0.03, p = .0272) and vastus lateralis (0.16 vs. 0.03, p = .004). Magnetic resonance spectroscopy water T2, indicative of muscle inflammation, was elevated in the soleus and/or vastus lateralis in 11 of 17 individuals. North Star Ambulatory Assessment score was lower in the dystrophinopathy group compared to controls (29 vs. 34 points, p = .0428). From cardiac MRI, left ventricle T1 relaxation times were elevated in females with dystrophinopathy compared to controls (1311 ± 55 vs. 1263 ± 25 ms, p < .05), but ejection fraction and circumferential strain did not differ.

DISCUSSION

Symptomatic females with dystrophinopathy quantitatively demonstrate muscle replacement by fat and inflammation, along with impairments in functional ability and cardiac function. Additional research is needed to evaluate how symptoms and muscle involvement change longitudinally.

Mitral regurgitation increases systolic strains in remote zone and worsens left ventricular dyssynchrony in a swine model of ischemic cardiomyopathy

Background

Ischemic mitral regurgitation (IMR) imposes volume overload on the left ventricle (LV), accelerating adverse LV remodeling. In this study, we sought to investigate the impact of volume overload due to IMR on regional myocardial contractile mechanics.

Methods

Ten Yorkshire swine were induced with myocardial infarction (MI) by occluding the left circumflex coronary artery (LCx). Cardiac MRI was performed at baseline (BL) and 2.5 months (2.5M) post-MI. IMR was quantified with epicardial echocardiography 3 months post-MI. The animals were then assigned to 2 groups: no/mild MR (nmMR, n = 4) and moderate/severe MR (msMR, n = 6). MRI images were analyzed to assess infarction size, end-diastolic and end-systolic volume (EDV and ESV, respectively), ejection fraction (EF), longitudinal strain (LS), circumferential strain (CS), and systolic dyssynchrony index (SDI). The myocardial region was divided into infarction, border, and remote zones based on the LCx-supplied region.

Results

There was no difference in the infarction size. Group-wise comparison of LS and CS between BL and 2.5M demonstrated that LS and CS in the infarction zone and the border zone decreased at 2.5M in both groups. However, LS and CS in the remote zone were elevated only in the msMR group (LS: -9.81 ± 3.96 vs. -12.58 ± 5.07, p < 0.01; CS; -12.78 ± 3.81 vs. -16.09 ± 3.33, p < 0.01) at 2.5M compared to BL. The SDI of CS was significantly elevated in the msMR group (0.1255 vs. 0.0974, p = 0.015) at 2.5M compared to BL.

Conclusions

Elevated LS and CS in the remote zone were observed in moderate/severe MR and ventricular dyssynchrony. These elevated cardiac strains, coupled with ventricular dyssynchrony, may contribute to the progression of MR, thereby accelerating heart failure.

Long-short diffeomorphism memory network for weakly-supervised ultrasound landmark tracking

Ultrasound is a promising medical imaging modality benefiting from low-cost and real-time acquisition. Accurate tracking of an anatomical landmark has been of high interest for various clinical workflows such as minimally invasive surgery and ultrasound-guided radiation therapy. However, tracking an anatomical landmark accurately in ultrasound video is very challenging, due to landmark deformation, visual ambiguity and partial observation. In this paper, we propose a long-short diffeomorphism memory network (LSDM), which is a multi-task framework with an auxiliary learnable deformation prior to supporting accurate landmark tracking. Specifically, we design a novel diffeomorphic representation, which contains both long and short temporal information stored in separate memory banks for delineating motion margins and reducing cumulative errors. We further propose an expectation maximization memory alignment (EMMA) algorithm to iteratively optimize both the long and short deformation memory, updating the memory queue for mitigating local anatomical ambiguity. The proposed multi-task system can be trained in a weakly-supervised manner, which only requires few landmark annotations for tracking and zero annotation for deformation learning. We conduct extensive experiments on both public and private ultrasound landmark tracking datasets. Experimental results show that LSDM can achieve better or competitive landmark tracking performance with a strong generalization capability across different scanner types and different ultrasound modalities, compared with other state-of-the-art methods.

Atrial cardiopathy in young adults with embolic stroke of undetermined source: a myocardial deformation imaging analysis

BACKGROUND

Atrial cardiopathy (AC) has emerged as a potential pathological thrombogenic atrial substract of embolic stroke of undetermined source (ESUS), even in the absence of atrial fibrillation. Left atrium (LA) myocardial deformation analysis may be of value as a subclinical marker of AC and a predictor of ESUS.

AIMS

To compare LA mechanical function between ESUS cases and age and sex-matched controls.

METHODS

A single-center analytical study with case-control design was performed. Case group was composed by young patients admitted in the Neurology department from January 2017 to June 2021. Control group was composed by age and sex matched controls recruited from the community. All participants performed echocardiogram and a smaller sample underwent cardiac magnetic resonance.

RESULTS

We recruited 31 ESUS patients aged between 18 and 65 years and 31 age and sex matched controls. ESUS patients had a significantly higher prevalence of cardiovascular risk factors and patent foramen ovale (PFO). The prevalence of AC was not different between groups. Echocardiogram parameters, including strain analysis, were similar between groups, except for LA appendage (LAA) ostium variation which was significantly lower in ESUS patients (absolute: 6.5vs8.7mm, p<0.001; relative: 44.5%vs53.4%, p=0.002). After exclusion of patients with PFO, all the results were statistically similar. Regarding cardiac magnetic resonance analysis, there were no statistically significant differences between groups.

CONCLUSION

This study shows that in our population atria cardiopathy and atrial function was not associated with ESUS.LAA structural and functional abnormalities may play a major role. The role of LAA in ESUS warrants further studies.

Effects of spatial and temporal resolution on cardiovascular magnetic resonance feature tracking measurements using a simple realistic numerical phantom

OBJECTIVES

To develop a single-slice numerical phantom with known myocardial motion, at several temporal and in-plane spatial resolutions, for testing and comparison of Cardiovascular Magnetic Resonance (CMR) feature tracking (FT) software.

METHODS

The phantom was developed based on CMR acquisitions of one volunteer (acquired cine, tagging cine, T1 map, T2 map, proton density weighted image). The numerical MRI simulator JEMRIS was used, and the phantom was generated at several in-plane spatial resolutions (1.4 × 1.4 mm2 to 3.0 × 3.0 mm2) and temporal resolutions (20 to 40 cardiac phases). Two feature tracking software packages were tested: Medical Image Tracking Toolbox (MITT) and two versions of cvi42 (v5.3.8 and v5.13.7). The effect of resolution on strain results was investigated with reference to ground-truth radial and circumferential strain.

RESULTS

Peak radial strain was consistently undermeasured more for cvi42 v5.13.7 than for v5.3.8. Increased pixel size produced a trend of increased difference from ground-truth peak strain, with the largest changes for cvi42 obtained using v5.13.7 between 1.4 × 1.4 mm2 and 3.0 × 3.0 mm2, at 9.17 percentage points (radial) and 8.42 percentage points (circumferential).

CONCLUSIONS

The results corroborate the presence of intervendor differences in feature tracking results and show the magnitude of strain differences between software versions.

ADVANCES IN KNOWLEDGE

This study shows how temporal and in-plane spatial resolution can affect feature tracking with reference to the ground-truth strain of a numerical phantom. Results reaffirm the need for numerical phantom development for the validation and testing of FT software.

High Frame Rate Ultrasound Imaging by Means of Tensor Completion: Application to Echocardiography

High frame rate ultrasound (US) imaging enables the monitoring of fast-moving organs. In echocardiography, this is especially needed due to the existence of rapidly moving structures, such as the heart valves. In the last two decades, various methods have been proposed to improve the frame rate. Here, we propose a novel method, based on binary coding patterns (BCPs) and tensor completion (TC), to increase the temporal resolution (i.e., frame rate) in the preprocessing stage of conventional focused ultrasound imaging (CFUI). The rationale behind our proposal is to perform, at first, the beamforming of a fraction of the scan lines, randomly selected in each frame based on BCP. Then, we reconstruct the missing scan lines through TC. The latter is an effective technique for recovering missing information from a low-rank tensor, based on a small number of observations using rank minimization. Following our approach, reducing the transmissions events needed to generate an image, the frame rate is increased by the same proportion. We have applied the proposed technique to a pre-beamformed radio frequency (RF) echocardiographic dataset. Our results show that we can improve the frame rate by a factor from 3 to 4, while keeping the structural similarity (SSIM) of the reconstructed tensor and the original one at values higher than 0.98.

Model-Agnostic Temporal Regularizer for Object Localization Using Motion Fields

Video analysis often requires locating and tracking target objects. In some applications, the localization system has access to the full video, which allows fine-grain motion information to be estimated. This paper proposes capturing this information through motion fields and using it to improve the localization results. The learned motion fields act as a model-agnostic temporal regularizer that can be used with any localization system based on keypoints. Unlike optical flow-based strategies, our motion fields are estimated from the model domain, based on the trajectories described by the object keypoints. Therefore, they are not affected by poor imaging conditions. The benefits of the proposed strategy are shown on three applications: 1) segmentation of cardiac magnetic resonance; 2) facial model alignment; and 3) vehicle tracking. In each case, combining popular localization methods with the proposed regularizer leads to improvement in overall accuracies and reduces gross errors.

Assessment of LAA Strain and Thrombus Mobility and Its Impact on Thrombus Resolution-Added-Value of a Novel Echocardiographic Thrombus Tracking Method

PURPOSE

The mobility of left atrial appendage (LAA) thrombi and changes hereof under anticoagulation may serve as a marker of both risk of embolism and efficacy of treatment. In this study, we sought to evaluate thrombus mobility and hypothesized that LAA dynamics and thrombus mobility could serve as a baseline marker of thrombus dissolvability.

METHODS

Patients with two-dimensional transesophageal echocardiographic images of the LAA, and with evidence of LAA thrombus were included in this study. Using a speckle tracking algorithm, functional information from the LAA and thrombi of different patients was computed. While the LAA motion was quantified through the longitudinal strain, thrombus mobility was evaluated using a novel method by directly tracking the thrombus, isolated from the global cardiac motion. Baseline characteristics and echocardiographic parameters were compared between responders (thrombus resolution) and non-responders (thrombus persistence) to anticoagulation.

RESULTS

We included 35 patients with atrial fibrillation with evidence of LAA thrombi. Patients had a mean age of 72.9 ± 14.1 years, exhibited a high risk for thromboembolism (CHA2DS2-VASc-Score 4.1 ± 1.5) and had moderately reduced LVEF (41.7 ± 14.4%) and signs of diastolic dysfunction (E/E' = 19.7 ± 8.5). While anticoagulation was initiated in all patients, resolution was achieved in 51.4% of patients. Significantly higher LAA peak strain (- 3.0 ± 1.3 vs. - 1.6 ± 1.5%, p < 0.01) and thrombus mobility (0.33 ± 0.13 mm vs. 0.18 ± 0.08 mm, p < 0.01) were observed in patients in whom thrombi resolved (i.e. responders against non-responders). Receiver operating characteristic (ROC) analysis revealed a high discriminatory ability for thrombus mobility with regards to thrombus resolution (AUC 0.89).

CONCLUSION

Isolated tracking of thrombus mobility from echocardiographic images is feasible. In patients with LAA thrombus, higher thrombus mobility appeared to be associated with thrombus resolution. Future studies should be conducted to evaluate the role of the described technique to predict LAA thrombus resolution or persistence.

Speckle Tracking Accuracy Enhancement by Temporal Super-Resolution of Three-Dimensional Echocardiography Images

Background:

Speckle tracking has always been a challenging issue in echocardiography images due to the lowcontrast and noisy nature of ultrasonic imaging modality. While in ultrasound imaging, framerate is limited by image size and sound speed in tissue, speckle tracking results get worse inthree-dimensional imaging due to its lower frame rate. Therefore, numerous techniques have beenreported to overcome this limitation and enhance tracking accuracy.

Methods:

In this work, we have proposedto increase the frame rate temporally for a sequence of three-dimensional (3D) echocardiographyframes to make tracking more accurate. To increase the number of frames, cubic B-spline is usedto interpolate between intensity variation time curves extracted from every single voxel in theimage during the cardiac cycle. We have shown that the frame rate increase will result in trackingaccuracy improvement.

Results:

To prove the efficiency of the proposed method, numerical evaluation metricsfor tracking are reported to make a comparison between high temporal resolution sequences andlow temporal resolution sequences. Anatomical affine optical flow is selected as the state-of-the-artspeckle tracking method, and a 3D echocardiography dataset is used to evaluate the proposedmethod.

Conclusion:

Results show that it is beneficial for speckle tracking to perform on temporally condensedframes rather than ordinary clinical 3D echocardiography images. Normalized mean enhancementvalues for mean absolute error, Hausdorff distance, and Dice index for all cases and all frames are0.44 ± 0.09, 0.42± 0.09, and 0.36 ± 0.06, respectively.

Generative Adversarial Networks in Medical Image Processing

BACKGROUND

The emergence of generative adversarial networks (GANs) has provided new technology and framework for the application of medical images. Specifically, a GAN requires little to no labeled data to obtain high-quality data that can be generated through competition between the generator and discriminator networks. Therefore, GANs are rapidly proving to be a state-of-the-art foundation, achieving enhanced performances in various medical applications.

METHODS

In this article, we introduce the principles of GANs and their various variants, deep convolutional GAN, conditional GAN, Wasserstein GAN, Info-GAN, boundary equilibrium GAN, and cycle-GAN.

RESULTS

All various GANs have found success in medical imaging tasks, including medical image enhancement, segmentation, classification, reconstruction, and synthesis. Furthermore, we summarize the data processing methods and evaluation indicators. Finally, we note the limitations of existing methods and the existing challenges that need to be addressed in this field.

CONCLUSION

Although GANs are in the initial stage of development in medical image processing, it will have a great prospect in the future.

CardIAc: an open-source application for myocardial strain analysis

PURPOSE

This paper presents CardIAc, an open-source application designed as an alternative to commercial software for left ventricle myocardial strain quantification in short-axis cardiac magnetic resonance images. The aim is to provide a useful extension for myocardial strain analysis that can be easily adapted to incorporate different strategies of motion tracking to improve the strain accuracy. In this way, users with programming skills can easily modify the code and adjust the program's performance according to their own scientific or clinical requirements. The software is intended for research and clinical use is not advised.

METHODS

CardIAc was developed as a 3D Slicer extension for an easy installation and usability. The main contribution of this article is to provide a general workflow, going from data and segmentation loading, 3D heart modeling, analysis and several options for visualization of the myocardial strain.

RESULTS

CardIAc strain feature was evaluated on a public dataset (Cardiac Motion Analysis Challenge-STACOM 2011) of 15 volunteers, and a synthetic one generated from this real dataset. Results on the real dataset show that cardIAc achieves suitable accuracy for myocardial motion estimation with a median error of 3.66 mm. In particular, global strain curves show strong correlation with the bibliography for healthy patients and similar approaches. On the other hand, results on the synthetic dataset show a mean global error of 4.07%, 7.76% and 8.18% for circumferential, radial and longitudinal strain.

CONCLUSION

This paper introduces a new open-source application for strain analysis distributed under a BSD-style open-source license. Results demonstrate the capability and merits of the proposed application for strain analysis.

Strain maps of the left atrium imaged with a novel high-resolution CINE MRI protocol

To date, regional atrial strains have not been imaged in vivo, despite their potential to provide useful clinical information. To address this gap, we present a novel CINE MRI protocol capable of imaging the entire left atrium at an isotropic 2-mm resolution in one single breath-hold. As proof of principle, we acquired data in 10 healthy volunteers and 2 cardiovascular patients using this technique. We also demonstrated how regional atrial strains can be estimated from this data following a manual segmentation of the left atrium using automatic image tracking techniques. The estimated principal strains vary smoothly across the left atrium and have a similar magnitude to estimates reported in the literature.

Clinical outcomes and thrombus resolution in patients with solid left atrial appendage thrombi: results of a single-center real-world registry

BACKGROUND

Data on thrombus resolution and clinical outcome data after a therapy of LAA thrombus with novel oral anticoagulants (NOACs) are scarce.

METHODS

In this single-center study, we retrospectively analyzed 78 patients diagnosed with a solid LAA thrombus by transesophageal echocardiography (TEE). We assessed baseline clinical and echocardiographic characteristics, the anticoagulatory regimens and outcomes of patients with (responders) and without (non-responders) thrombus resolution.

RESULTS

Mean age was 76.1 ± 8.3 years, patients were male in 57.7% and presented with a high risk for thromboembolism (CHA₂DS₂-VASc: 4.3 ± 1.1). At thrombus diagnosis, 44.9% patients were treated with a NOAC, while 41.0% were under therapy with a VKA. Complete thrombus resolution was achieved after a mean of 116 ± 79 days in a total of 51.3% of patients, 35.9% showed a reduction of thrombus size, whereas 12.8% showed no changes in thrombus dimensions. There was no statistically significant difference in the rate of LAA thrombus resolution between VKA and NOACs (41.2 vs. 57.1%, p = 0.18). However, in cases in which only the therapy with a NOAC led to complete thrombus resolution, the time needed was significantly shorter than with VKA (81 ± 38 vs. 129 ± 46 days, p = 0.03). Regarding safety outcomes, no differences in bleeding or thromboembolism were observed between patients with and without thrombus resolution.

CONCLUSIONS

In this registry, approximately 85% of LAA thrombi were diagnosed in patients with ongoing OAC. Thrombus resolution was observed in nearly 50% of cases. Although there was no difference in the rate of LAA thrombus resolution between VKA and NOACs, the resolution time was shorter in patients prescribed a NOAC.