bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of initial outlines on manual segmentation
Authors: Sensakovic William F. , Starkey Adam , Roberts Rachael , Straus Christopher , Caligiuri Philip , Kocherginsky Masha , Armato Samuel G. 
Published: April 2010

Purpose:Initial outlines are often presented as an aid to reduce the time‐cost associated with manual segmentation and measurement of structures in medical images. This study evaluated the influence of initial outlines on manual segmentation intraobserver and interobserver precision.Methods:Three observers independently outlined all pleural mesothelioma tumors present in five computed tomography (CT) sections in each of 30 patient scans. After a lapse of time, each observer was presented with the same series of CT sections with the outlines of each observer superimposed as initial outlines. Each observer created altered outlines by altering the initial outlines to reflect their perception of the tumor boundary. Altered outlines were compared to original outlines using the Jaccard similarity coefficient. Intraobserver and interobserver precision of observer outlines were calculated by applying linear mixed effects analysis of variance models to the values. The percent of minor alterations (alterations that resulted in only slight changes in the initial outline) was also recorded.Results:The average value between pairs of observer original outlines was 0.371. The average value between pairs of observer outlines when altered from an identical initial outline was 0.796, indicating increased interobserver precision. The average difference between values of an observer's segmentation created by altering their own initial outline and when altering a different observer's initial outline was 0.476, indicating initial outlines strongly influence intraobserver precision. Observers made minor alterations on 74.5% of initial outlines with which they were presented.Conclusions:Intraobserver and interobserver precision were strongly dependent on the initial outline. These effects are likely due to the tendency of observers to make only minor corrections to initial outlines. This finding could impact observer study design, tumor growth assessment, computer‐aided diagnosis system validation, and radiation therapy target volume definition when initial outlines are used as an observer aid.
Technical Note: Fiducial markers for correlation of whole‐specimen histopathology with MR imaging at 7 tesla
Authors: McGrath Deirdre M. , Vlad Roxana M. , Foltz Warren D. , Brock Kristy K. 
Published: April 2010

Purpose:There is increasing interest in the registration of 3‐D histopathology with 3‐Din vivo imaging, for example, to validate tumor boundary delineation for targeted radiation cancer therapy. However, accurate correlation is compromised by tissue distortion induced by histopathological processing. Reference landmarks that are visible in both data sets are required. In this study, two iridescent acrylic paints, “Bronze” (containing iron oxide coated mica particles) and “Stainless Steel” (containing iron, chromium, and nickel), were evaluated for creating MRI‐visible and histology‐visible fiducial markers at 7 T, where resolution is more similar to histology, but artifacts are accentuated. Furthermore, a straight‐line paint‐track fiducial method was developed to assist in registration and 3‐D histopathology reconstruction.Methods:First, the paints were injected intoex vivo porcine tissue samples, which were MR imaged prefixation and postfixation, and subsequently prepared for hematoxylin and eosin staining to verify stability through histopathological processing. Second, the severity of marker susceptibility artifacts produced was compared while using spin‐echo and gradient‐echo MRI pulse sequences. Finally, multiple paint tracks were injected prefixation through an ex vivo canine prostate sample to validate the potential for line‐based registration between MR images of prefixation and postfixation tissue and whole mount histology slides.Results:The Stainless Steel paint produced excessive susceptibility artifacts and image distortion, while the Bronze paint created stable and appropriate markers in MRI and histology. The Bronze paint produced artifacts approximately three times larger in gradient‐echo than in spin‐echo MR images. Finally, the paint‐track fiducials were visible in the prefixation and postfixation MRI and on whole mount histology.Conclusions:The Bronze iridescent acrylic paint is appropriate for fiducial marker creation in MRI at 7 T. The straight‐line paint‐track fiducials may assist 3‐D histopathology reconstruction and can provide important information on the deformation effects of fixation, and hence may improve registration accuracy.
Computer‐aided measurement of liver volumes in CT by means of geodesic active contour segmentation coupled with level‐set algorithms
Authors: Suzuki Kenji , Kohlbrenner Ryan , Epstein Mark L. , Obajuluwa Ademola M. , Xu Jianwu , Hori Masatoshi 
Published: April 2010

Purpose:Computerized liver extraction from hepatic CT images is challenging because the liver often abuts other organs of a similar density. The purpose of this study was to develop a computer‐aided measurement of liver volumes in hepatic CT.Methods:The authors developed a computerized liver extraction scheme based on geodesic active contour segmentation coupled with level‐set contour evolution. First, an anisotropic diffusion filter was applied to portal‐venous‐phase CT images for noise reduction while preserving the liver structure, followed by a scale‐specific gradient magnitude filter to enhance the liver boundaries. Then, a nonlinear grayscale converter enhanced the contrast of the liver parenchyma. By using the liver‐parenchyma‐enhanced image as a speed function, a fast‐marching level‐set algorithm generated an initial contour that roughly estimated the liver shape. A geodesic active contour segmentation algorithm coupled with level‐set contour evolution refined the initial contour to define the liver boundaries more precisely. The liver volume was then calculated using these refined boundaries. Hepatic CT scans of 15 prospective liver donors were obtained under a liver transplant protocol with a multidetector CT system. The liver volumes extracted by the computerized scheme were compared to those traced manually by a radiologist, used as “gold standard.”Results:The mean liver volume obtained with our scheme was 1504 cc, whereas the mean gold standard manual volume was 1457 cc, resulting in a mean absolute difference of 105 cc (7.2%). The computer‐estimated liver volumetrics agreed excellently with the gold‐standard manual volumetrics (intraclass correlation coefficient was 0.95) with no statistically significant difference . The average accuracy, sensitivity, specificity, and percent volume error were 98.4%, 91.1%, 99.1%, and 7.2%, respectively. Computerized CT liver volumetry would require substantially less completion time (compared to an average of 39 min per case by manual segmentation).Conclusions:The computerized liver extraction scheme provides an efficient and accurate way of measuring liver volumes in CT.
Dose mapping of the rectal wall during brachytherapy with an array of scintillation dosimeters
Authors: Cartwright L. E. , Suchowerska N. , Yin Y. , Lambert J. , Haque M. , McKenzie D. R. 
Published: April 2010

Purpose: In pelvic brachytherapy treatments, the rectum is an organ at risk. The authors have developed an array of scintillation dosimeters suitable for in vivo use that enables quality assurance of the treatment delivery and provides an alert to potential radiation accidents. Ultimately, this will provide evidence to direct treatment planning and dose escalation and correlate dose with the rectal response.Methods: An array of 16 scintillation dosimeters in an insertable applicator has been developed. The dosimeters were calibrated simultaneously in a custom designed circular jig before use. Each dosimeter is optically interfaced to a set of pixels on a CCD camera located outside the treatment bunker. A customized software converts pixel values into dose rate and accumulates dose for presentation during treatment delivery. The performance of the array is tested by simulating brachytherapy treatments in a water phantom. The treatment plans were designed to deliver a known dose distribution on the surface of the rectal applicator, assumed to represent the dose to the rectal wall.Results: The measured doses were compared to those predicted by the treatment plan and found to be in agreement to within the uncertainty in measurement, usually within 3%. The array was also used to track the progression of the source as it moved along the catheter. The measured position was found to agree with the position reported by the afterloader to within the measurement uncertainty, usually within 2 mm.Conclusions: This array is capable of measuring the actual dose received by each region of the rectal wall during brachytherapy treatments. It will provide real time monitoring of treatment delivery and raise an alert to a potential radiation accident. Real time dose mapping in the clinical environment will give the clinician additional confidence to carry out dose escalation to the tumor volume while avoiding rectal side effects.
An integrated 6 MV linear accelerator model from electron gun to dose in a water tank
Authors: St. Aubin J. , Steciw S. , Kirkby C. , Fallone B. G. 
Published: April 2010

Purpose: The details of a full simulation of an inline side‐coupled 6 MV linear accelerator (linac) from the electron gun to the target are presented. Commissioning of the above simulation was performed by using the derived electron phase space at the target as an input into Monte Carlo studies of dose distributions within a water tank and matching the simulation results to measurement data. This work is motivated by linac‐MR studies, where a validated full linac simulation is first required in order to perform future studies on linac performance in the presence of an external magnetic field.Methods: An electron gun was initially designed and optimized with a 2D finite difference program using Child's law. The electron gun simulation served as an input to a 6 MV linac waveguide simulation, which consisted of a 3D finite element radio‐frequency field solution within the waveguide and electron trajectories determined from particle dynamics modeling. The electron gun design was constrained to match the cathode potential and electron gun current of a Varian 600C, while the linac waveguide was optimized to match the measured target current. Commissioning of the full simulation was performed by matching the simulated Monte Carlo dose distributions in a water tank to measured distributions.Results: The full linac simulation matched all the electrical measurements taken from a Varian 600C and the commissioning process lead to excellent agreements in the dose profile measurements. Greater than 99% of all points met a 1%/1mm acceptance criterion for all field sizes analyzed, with the exception of the largest field for which 98% of all points met the 1%/1mm acceptance criterion and the depth dose curves matched measurement to within 1% deeper than 1.5 cm depth. The optimized energy and spatial intensity distributions, as given by the commissioning process, were determined to be non‐Gaussian in form for the inline side‐coupled 6 MV linac simulated.Conclusions: An integrated simulation of an inline side‐coupled 6 MV linac has been completed and benchmarked matching all electrical and dosimetric measurements to high accuracy. The results showed non‐Gaussian spatial intensity and energy distributions for the linac modeled.
Patient doses and projection angle in cone beam CT
Authors: He Wenjun , Huda Walter , Magill Dennise , Tavrides Emily , Yao Hai 
Published: April 2010

Purpose: To investigate how x‐ray tube projection angle affects organ and effective doses to patients undergoing a CT examination on a cone beam scanner.Methods: The authors investigated two cone beam CT systems that use a flat panel detector to capture the x‐ray pattern transmitted through patients. One system had the flat panel detector and x‐ray tube mounted on a conventional CT gantry (gantry CT), whereas the other CT scanner had the x‐ray tube and flat panel detector mounted on a C‐arm apparatus (C‐arm CT). PCXMC software package (version 2.0.1) was used to compute absorbed doses at a constant x‐ray beam output as a function of the x‐ray tube projection angle. This software uses a mathematical hermaphroditic phantom with a weight of 73.2 kg and a height of 178.6 cm. Average absorbed doses were generated and recorded for five radiosensitive organs (i.e., breast, colon, lung, red bone marrow, and stomach), as well as the corresponding effective dose. Doses for both CT gantries were obtained every 15° of the x‐ray tube projection angle, at each of six locations in 10 cm increments along the patient long axis. The authors also investigated the effect on patient dose of filtrations ranging from 2.5 to 9.5 mm Al, with x‐ray tube voltages ranging from 80 to 140 kV.Results: There were substantial differences in organ doses as a function of the projection angle, with higher organ doses for anteroposterior projection and lower doses for lateral projections. The maximum to minimum ratios of organ dose as a function of the x‐ray tube angle were for the lungs, for the colon, for the red bone marrow, for the breast, and for the stomach. At the same x‐ray tube voltage (kV) and intensity (mA s), the ratio of dose maxima for the two cone beam CT geometries for the five organs investigated was , which is mainly attributed to differences in source to isocenter distances. Effective doses varied with x‐ray tube angle by a factor of for chest CT examinations and by a factor of for abdomen/pelvis examinations. Changes in the x‐ray tube voltage and beam filtration showed the expected changes in absolute organ doses, but had little effect on relative doses.Conclusions: There are major differences in organ and effective dose as the x‐ray tube rotates around the patient. The results suggest that the use of x‐ray tube current modulation could produce substantial reductions in organ and effective dose for body imaging with cone beam CT.
Simultaneous segmentation and reconstruction: A level set method approach for limited view computed tomography
Authors: Yoon Sungwon , Pineda Angel R. , Fahrig Rebecca 
Published: April 2010

Purpose:An iterative tomographic reconstruction algorithm that simultaneously segments and reconstructs the reconstruction domain is proposed and applied to tomographic reconstructions from a sparse number of projection images.Methods:The proposed algorithm uses a two‐phase level set method segmentation in conjunction with an iterative tomographic reconstruction to achieve simultaneous segmentation and reconstruction. The simultaneous segmentation and reconstruction is achieved by alternating between level set function evolutions and per‐region intensity value updates. To deal with the limited number of projections,a prioriinformation about the reconstruction is enforced via penalized likelihood function. Specifically, smooth function within each region (piecewise smooth function) and bounded function intensity values for each region are assumed. Sucha prioriinformation is formulated into a quadratic objective function with linear bound constraints. The level set function evolutions are achieved by artificially time evolving the level set function in the negative gradient direction; the intensity value updates are achieved by using the gradient projection conjugate gradient algorithm.Results:The proposed simultaneous segmentation and reconstruction results were compared to “conventional” iterative reconstruction (with no segmentation), iterative reconstruction followed by segmentation, and filtered backprojection. Improvements of 6%–13% in the normalized root mean square error were observed when the proposed algorithm was applied to simulated projections of a numerical phantom and to real fan‐beam projections of the Catphan phantom, both of which did not satisfy thea prioriassumptions.Conclusions:The proposed simultaneous segmentation and reconstruction resulted in improved reconstruction image quality. The algorithm correctly segments the reconstruction space into regions, preserves sharp edges between different regions, and smoothes the noise within each region. The proposed algorithm framework has the flexibility to be adapted to differenta prioriconstraints while maintaining the benefits achieved by the simultaneous segmentation and reconstruction.
Uncertainty analysis of a Compton camera imaging system for radiation therapy dose reconstruction
Authors: Mundy Daniel W. , Herman Michael G. 
Published: April 2010

Purpose:Improved radiotherapy dose delivery techniques over the past decade have increased the necessity for accurate, independent verification of delivered dose. Compton camera imaging (CCI) systems may have the potential to quantitatively reconstruct three‐dimensional dose delivered to the patient with little or noa priori information.Methods:In this work, the adequacy of a Compton camera imaging system for application to radiotherapy dose reconstruction is explored using analytical models of system spatial and dosimetric resolution. The effects of scatter and absorption detector energy resolution, initial photon energy, and detector separation distance on system performance were calculated with the goal of determining whether current detector technology is adequate for such an application.Results:Results indicate that the energy and spatial resolutions associated with current Si and Ge double‐sided strip detectors in a planar configuration is sufficient to determine dose deposition to within an average of 1.9 mm and 2.5%. Minimum values of less than 0.5 mm and 1% are achievable under certain conditions. As the energy of the photon incident on the patient increases from 1.0 to 10 MeV, system performance improves at the expense of the range of patient and detector scattering angles over which the system is capable of reconstructing dose deposition to within the acceptable upper limits of 5 mm and 5%. System performance also improves with increasing distance between the scatter and absorption detectors, but is acceptable throughout the range of values likely to be associated with a gantry‐mounted system (2–20 cm).Conclusions:The results indicate that Compton camera imaging systems based on current solid‐state detector technology have the potential to provide independent verification of dose delivered to a patient during radiation therapy. Further consideration must be given to detector efficiency and image reconstruction algorithms for this application of CCI systems.
Image‐based modeling of tumor shrinkage in head and neck radiation therapya)
Authors: Chao Ming , Xie Yaoqin , Moros Eduardo G. , Le Quynh‐Thu , Xing Lei 
Published: April 2010

Purpose:Understanding the kinetics of tumor growth/shrinkage represents a critical step in quantitative assessment of therapeutics and realization of adaptive radiation therapy. This article presents a novel framework for image‐based modeling of tumor change and demonstrates its performance with synthetic images and clinical cases.Methods:Due to significant tumor tissue content changes, similarity‐based models are not suitable for describing the process of tumor volume changes. Under the hypothesis that tissue features in a tumor volume or at the boundary region are partially preserved, the kinetic change was modeled in two steps: (1) Autodetection of homologous tissue features shared by two input images using the scale invariance feature transformation (SIFT) method; and (2) establishment of a voxel‐to‐voxel correspondence between the images for the remaining spatial points by interpolation. The correctness of the tissue feature correspondence was assured by a bidirectional association procedure, where SIFT features were mapped from template to target images and reversely. A series of digital phantom experiments and five head and neck clinical cases were used to assess the performance of the proposed technique.Results:The proposed technique can faithfully identify the known changes introduced when constructing the digital phantoms. The subsequent feature‐guided thin plate spline calculation reproduced the “ground truth” with accuracy better than 1.5 mm. For the clinical cases, the new algorithm worked reliably for a volume change as large as 30%.Conclusions:An image‐based tumor kinetic algorithm was developed to model the tumor response to radiation therapy. The technique provides a practical framework for future application in adaptive radiation therapy.
Diaphragm motion quantification in megavoltage cone‐beam CT projection images
Authors: Chen Mingqing , Siochi R. Alfredo 
Published: April 2010

Purpose:To quantify diaphragm motion in megavoltage (MV) cone‐beam computed tomography (CBCT) projections.Methods:User identified ipsilateral hemidiaphragm apex (IHDA) positions in two full exhale and inhale frames were used to create bounding rectangles in all other frames of a CBCT scan. The bounding rectangle was enlarged to create a region of interest (ROI). ROI pixels were associated with a cost function: The product of image gradients and a gradient direction matching function for an ideal hemidiaphragm determined from 40 training sets. A dynamic Hough transform (DHT) models a hemidiaphragm as a contour made of two parabola segments with a common vertex (the IHDA). The images within the ROIs are transformed into Hough space where a contour's Hough value is the sum of the cost function over all contour pixels. Dynamic programming finds the optimal trajectory of the common vertex in Hough space subject to motion constraints between frames, and an active contour model further refines the result. Interpolated ray tracing converts the positions to room coordinates. Root‐mean‐square (RMS) distances between these positions and those resulting from an expert's identification of the IHDA were determined for 21 Siemens MV CBCT scans.Results:Computation time on a 2.66 GHz CPU was 30 s. The average craniocaudal RMS error was. While much larger errors occurred in a few near‐sagittal frames on one patient's scans, adjustments to algorithm constraints corrected them.Conclusions:The DHT based algorithm can compute IHDA trajectories immediately prior to radiation therapy on a daily basis using localization MVCBCT projection data. This has potential for calibrating external motion surrogates against diaphragm motion.
NON-GAUSSIAN NOISE-INDUCED FIRING TRANSITIONS AND ORDERED BURSTING IN A THERMO-SENSITIVE NEURON
Authors: GONG YUBING , LIN XIU , HAO YINGHANG , XIE YANHANG , MA XIAOGUANG 
Published: April 2010

In this letter, we investigate how a particular kind of non-Gaussian colored noise (NGN), especially the correlation time τ and the departure q from Gaussian noise, affects the chaotic firing behavior in a thermo-sensitive neuron. It is found that transitions between spiking and bursting occur with changing τ or q, and ordered bursting appears when τ is optimal. As τ is increased, the neuron alternately exhibits spiking and bursting when q < 1, but always bursts when q > 1, and chaotic bursts may become ordered at an optimal τ. As q is increased, the neuron also exhibits transitions between spiking and bursting. These findings provide a new mechanism for the firing transitions in the neuron and present the constructive role of the NGN in the firing activity in the neuron. This reveals that the NGN would play subtle roles in the communication and information processing in the neurons.