Respiratory organ motion in interventional MRI : tracking, guiding and modeling

Respiratory organ motion is one of the major challenges in interventional MRI, particularly in interventions with therapeutic ultrasound in the abdominal region. High-intensity focused ultrasound found an application in interventional MRI for noninvasive treatments of different abnormalities. In order to guide surgical and treatment interventions, organ motion imaging and modeling is commonly required before a treatment start. Accurate tracking of organ motion during various interventional MRI procedures is prerequisite for a successful outcome and safe therapy. In this thesis, an attempt has been made to develop approaches using focused ultrasound which could be used in future clinically for the treatment of abdominal organs, such as the liver and the kidney. Two distinct methods have been presented with its ex vivo and in vivo treatment results. In the first method, an MR-based pencil-beam navigator has been used to track organ motion and provide the motion information for acoustic focal point steering, while in the second approach a hybrid imaging using both ultrasound and magnetic resonance imaging was combined for advanced guiding capabilities. Organ motion modeling and four-dimensional imaging of organ motion is increasingly required before the surgical interventions. However, due to the current safety limitations and hardware restrictions, the MR acquisition of a time-resolved sequence of volumetric images is not possible with high temporal and spatial resolution. A novel multislice acquisition scheme that is based on a two-dimensional navigator, instead of a commonly used pencil-beam navigator, was devised to acquire the data slices and the corresponding navigator simultaneously using a CAIPIRINHA parallel imaging method. The acquisition duration for four-dimensional dataset sampling is reduced compared to the existing approaches, while the image contrast and quality are improved as well. Tracking respiratory organ motion is required in interventional procedures and during MR imaging of moving organs. An MR-based navigator is commonly used, however, it is usually associated with image artifacts, such as signal voids. Spectrally selective navigators can come in handy in cases where the imaging organ is surrounding with an adipose tissue, because it can provide an indirect measure of organ motion. A novel spectrally selective navigator based on a crossed-pair navigator has been developed. Experiments show the advantages of the application of this novel navigator for the volumetric imaging of the liver in vivo, where this navigator was used to gate the gradient-recalled echo sequence

UV Exposed Optical Fibers with Frequency Domain Reflectometry for Device Tracking in Intra-Arterial Procedures

Shape tracking of medical devices using strain sensing properties in optical fibers has seen increased attention in recent years. In this paper, we propose a novel guidance system for intra-arterial procedures using a distributed strain sensing device based on optical frequency domain reflectometry (OFDR) to track the shape of a catheter. Tracking enhancement is provided by exposing a fiber triplet to a focused ultraviolet beam, producing high scattering properties. Contrary to typical quasi-distributed strain sensors, we propose a truly distributed strain sensing approach, which allows to reconstruct a fiber triplet in real-time. A 3D roadmap of the hepatic anatomy integrated with a 4D MR imaging sequence allows to navigate the catheter within the pre-interventional anatomy, and map the blood flow velocities in the arterial tree. We employed Riemannian anisotropic heat kernels to map the sensed data to the pre-interventional model. Experiments in synthetic phantoms and an in vivo model are presented. Results show that the tracking accuracy is suitable for interventional tracking applications, with a mean 3D shape reconstruction errors of 1.6 +/- 0.3 mm. This study demonstrates the promising potential of MR-compatible UV-exposed OFDR optical fibers for non-ionizing device guidance in intra-arterial procedures

Towards in vivo g-ratio mapping using MRI: unifying myelin and diffusion imaging

The g-ratio, quantifying the comparative thickness of the myelin sheath encasing an axon, is a geometrical invariant that has high functional relevance because of its importance in determining neuronal conduction velocity. Advances in MRI data acquisition and signal modelling have put in vivo mapping of the g-ratio, across the entire white matter, within our reach. This capacity would greatly increase our knowledge of the nervous system: how it functions, and how it is impacted by disease. This is the second review on the topic of g-ratio mapping using MRI. As such, it summarizes the most recent developments in the field, while also providing methodological background pertinent to aggregate g-ratio weighted mapping, and discussing pitfalls associated with these approaches. Using simulations based on recently published data, this review demonstrates the relevance of the calibration step for three myelin-markers (macromolecular tissue volume, myelin water fraction, and bound pool fraction). It highlights the need to estimate both the slope and offset of the relationship between these MRI-based markers and the true myelin volume fraction if we are really to achieve the goal of precise, high sensitivity g-ratio mapping in vivo. Other challenges discussed in this review further evidence the need for gold standard measurements of human brain tissue from ex vivo histology. We conclude that the quest to find the most appropriate MRI biomarkers to enable in vivo g-ratio mapping is ongoing, with the potential of many novel techniques yet to be investigated.Comment: Will be published as a review article in Journal of Neuroscience Methods as parf of the Special Issue with Hu Cheng and Vince Calhoun as Guest Editor

Estimating Epipolar Geometry With The Use of a Camera Mounted Orientation Sensor

Context: Image processing and computer vision are rapidly becoming more and more commonplace, and the amount of information about a scene, such as 3D geometry, that can be obtained from an image, or multiple images of the scene is steadily increasing due to increasing resolutions and availability of imaging sensors, and an active research community. In parallel, advances in hardware design and manufacturing are allowing for devices such as gyroscopes, accelerometers and magnetometers and GPS receivers to be included alongside imaging devices at a consumer level. Aims: This work aims to investigate the use of orientation sensors in the field of computer vision as sources of data to aid with image processing and the determination of a scene’s geometry, in particular, the epipolar geometry of a pair of images - and devises a hybrid methodology from two sets of previous works in order to exploit the information available from orientation sensors alongside data gathered from image processing techniques. Method: A readily available consumer-level orientation sensor was used alongside a digital camera to capture images of a set of scenes and record the orientation of the camera. The fundamental matrix of these pairs of images was calculated using a variety of techniques - both incorporating data from the orientation sensor and excluding its use Results: Some methodologies could not produce an acceptable result for the Fundamental Matrix on certain image pairs, however, a method described in the literature that used an orientation sensor always produced a result - however in cases where the hybrid or purely computer vision methods also produced a result - this was found to be the least accurate. Conclusion: Results from this work show that the use of an orientation sensor to capture information alongside an imaging device can be used to improve both the accuracy and reliability of calculations of the scene’s geometry - however noise from the orientation sensor can limit this accuracy and further research would be needed to determine the magnitude of this problem and methods of mitigation

An open environment CT-US fusion for tissue segmentation during interventional guidance.

Therapeutic ultrasound (US) can be noninvasively focused to activate drugs, ablate tumors and deliver drugs beyond the blood brain barrier. However, well-controlled guidance of US therapy requires fusion with a navigational modality, such as magnetic resonance imaging (MRI) or X-ray computed tomography (CT). Here, we developed and validated tissue characterization using a fusion between US and CT. The performance of the CT/US fusion was quantified by the calibration error, target registration error and fiducial registration error. Met-1 tumors in the fat pads of 12 female FVB mice provided a model of developing breast cancer with which to evaluate CT-based tissue segmentation. Hounsfield units (HU) within the tumor and surrounding fat pad were quantified, validated with histology and segmented for parametric analysis (fat: -300 to 0 HU, protein-rich: 1 to 300 HU, and bone: HU>300). Our open source CT/US fusion system differentiated soft tissue, bone and fat with a spatial accuracy of ∼1 mm. Region of interest (ROI) analysis of the tumor and surrounding fat pad using a 1 mm(2) ROI resulted in mean HU of 68±44 within the tumor and -97±52 within the fat pad adjacent to the tumor (p<0.005). The tumor area measured by CT and histology was correlated (r(2) = 0.92), while the area designated as fat decreased with increasing tumor size (r(2) = 0.51). Analysis of CT and histology images of the tumor and surrounding fat pad revealed an average percentage of fat of 65.3% vs. 75.2%, 36.5% vs. 48.4%, and 31.6% vs. 38.5% for tumors <75 mm(3), 75-150 mm(3) and >150 mm(3), respectively. Further, CT mapped bone-soft tissue interfaces near the acoustic beam during real-time imaging. Combined CT/US is a feasible method for guiding interventions by tracking the acoustic focus within a pre-acquired CT image volume and characterizing tissues proximal to and surrounding the acoustic focus

Semiautomated Skeletonization of the Pulmonary Arterial Tree in Micro-CT Images

We present a simple and robust approach that utilizes planar images at different angular rotations combined with unfiltered back-projection to locate the central axes of the pulmonary arterial tree. Three-dimensional points are selected interactively by the user. The computer calculates a sub- volume unfiltered back-projection orthogonal to the vector connecting the two points and centered on the first point. Because more x-rays are absorbed at the thickest portion of the vessel, in the unfiltered back-projection, the darkest pixel is assumed to be the center of the vessel. The computer replaces this point with the newly computer-calculated point. A second back-projection is calculated around the original point orthogonal to a vector connecting the newly-calculated first point and user-determined second point. The darkest pixel within the reconstruction is determined. The computer then replaces the second point with the XYZ coordinates of the darkest pixel within this second reconstruction. Following a vector based on a moving average of previously determined 3- dimensional points along the vessel\u27s axis, the computer continues this skeletonization process until stopped by the user. The computer estimates the vessel diameter along the set of previously determined points using a method similar to the full width-half max algorithm. On all subsequent vessels, the process works the same way except that at each point, distances between the current point and all previously determined points along different vessels are determined. If the difference is less than the previously estimated diameter, the vessels are assumed to branch. This user/computer interaction continues until the vascular tree has been skeletonized

A framework for continuous target tracking during MR-guided high intensity focused ultrasound thermal ablations in the abdomen

Scatterplot showing percentage changes in stroke volume index (ΔSVI, %) and functional hemodynamic markers, Stroke Volume Variation (SVV, %) Pulse Pressure Variation (PPV, %), with the three tested tidal volumes (V T ), 6, 12 and 18 ml/kg during intra-abdominal hypertension. Solid line shows regression line between variables. (PDF 56 kb