Registration of temporal sequences of coronal and sagittal MR images through respiratory patterns

This work discusses the determination of the breathing patterns in time sequence of images obtained from magnetic resonance (MR) and their use in the temporal registration of coronal and sagittal images. The registration is made without the use of any triggering information and any special gas to enhance the contrast. The temporal sequences of images are acquired in free breathing. The real movement of the lung has never been seen directly, as it is totally dependent on its surrounding muscles and collapses without them. The visualization of the lung in motion is an actual topic of research in medicine. The lung movement is not periodic and it is susceptible to variations in the degree of respiration. Compared to computerized tomography (CT), MR imaging involves longer acquisition times and it is preferable because it does not involve radiation. As coronal and sagittal sequences of images are orthogonal to each other, their intersection corresponds to a segment in the three-dimensional space. The registration is based on the analysis of this intersection segment. A time sequence of this intersection segment can be stacked, defining a two-dimension spatio-temporal (2DST) image. The algorithm proposed in this work can detect asynchronous movements of the internal lung structures and lung surrounding organs. It is assumed that the diaphragmatic movement is the principal movement and all the lung structures move almost synchronously. The synchronization is performed through a pattern named respiratory function. This pattern is obtained by processing a 2DST image. An interval Hough transform algorithm searches for synchronized movements with the respiratory function. A greedy active contour algorithm adjusts small discrepancies originated by asynchronous movements in the respiratory patterns. The output is a set of respiratory patterns. Finally, the composition of coronal and sagittal image pairs that are in the same breathing phase is realized by comparing of respiratory patterns originated from diaphragmatic and upper boundary surfaces. When available, the respiratory patterns associated to lung internal structures are also used. The results of the proposed method are compared with the pixel-by-pixel comparison method. The proposed method increases the number of registered pairs representing composed images and allows an easy check of the breathing phase. (C) 2010 Elsevier Ltd. All rights reserved.

Two dimensional computational fluid dynamic models for waste stabilisation ponds

Traditional waste stabilisation pond (WSP) models encounter problems predicting pond performance because they cannot account for the influence of pond features, such as inlet structure or pond geometry, on fluid hydrodynamics. In this study, two dimensional (2-D) computational fluid dynamics (CFD) models were compared to experimental residence time distributions (RTD) from literature. In one of the-three geometries simulated, the 2-D CFD model successfully predicted the experimental RTD. However, flow patterns in the other two geometries were not well described due to the difficulty of representing the three dimensional (3-D) experimental inlet in the 2-D CFD model, and the sensitivity of the model results to the assumptions used to characterise the inlet. Neither a velocity similarity nor geometric similarity approach to inlet representation in 2-D gave results correlating with experimental data. However. it was shown that 2-D CFD models were not affected by changes in values of model parameters which are difficult to predict, particularly the turbulent inlet conditions. This work suggests that 2-D CFD models cannot be used a priori to give an adequate description of the hydrodynamic patterns in WSP. (C) 1998 Elsevier Science Ltd. All rights reserved.

Dimensional Accuracy of Computer-Aided Design/Computer-Assisted Manufactured Orbital Prostheses

Purpose: The aim of this research was to assess the dimensional accuracy of orbital prostheses based on reversed images generated by computer-aided design/computer-assisted manufacturing (CAD/CAM) using computed tomography (CT) scans. Materials and Methods: CT scans of the faces of 15 adults, men and women older than 25 years of age not bearing any congenital or acquired craniofacial defects, were processed using CAD software to produce 30 reversed three-dimensional models of the orbital region. These models were then processed using the CAM system by means of selective laser sintering to generate surface prototypes of the volunteers` orbital regions. Two moulage impressions of the faces of each volunteer were taken to manufacture 15 pairs of casts. Orbital defects were created on the right or left side of each cast. The surface prototypes were adapted to the casts and then flasked to fabricate silicone prostheses. The establishment of anthropometric landmarks on the orbital region and facial midline allowed for the data collection of 31 linear measurements, used to assess the dimensional accuracy of the orbital prostheses and their location on the face. Results: The comparative analyses of the linear measurements taken from the orbital prostheses and the opposite sides that originated the surface prototypes demonstrated that the orbital prostheses presented similar vertical, transversal, and oblique dimensions, as well as similar depth. There was no transverse or oblique displacement of the prostheses. Conclusion: From a clinical perspective, the small differences observed after analyzing all 31 linear measurements did not indicate facial asymmetry. The dimensional accuracy of the orbital prostheses suggested that the CAD/CAM system assessed herein may be applicable for clinical purposes. Int J Prosthodont 2010;23:271-276.

Efeito da imobilização na radioterapia do cancro do pulmão

Mestrado em Radiações Aplicadas às Tecnologias da Saúde. Área de especialização: Terapia com Radiações.

Multi-dimensional scaling applied to histogram-based DNA analysis

This paper aims to study the relationships between chromosomal DNA sequences of twenty species. We propose a methodology combining DNA-based word frequency histograms, correlation methods, and an MDS technique to visualize structural information underlying chromosomes (CRs) and species. Four statistical measures are tested (Minkowski, Cosine, Pearson product-moment, and Kendall τ rank correlations) to analyze the information content of 421 nuclear CRs from twenty species. The proposed methodology is built on mathematical tools and allows the analysis and visualization of very large amounts of stream data, like DNA sequences, with almost no assumptions other than the predefined DNA “word length.” This methodology is able to produce comprehensible three-dimensional visualizations of CR clustering and related spatial and structural patterns. The results of the four test correlation scenarios show that the high-level information clusterings produced by the MDS tool are qualitatively similar, with small variations due to each correlation method characteristics, and that the clusterings are a consequence of the input data and not method’s artifacts.

Verificação dos desvios de setup e cálculo de margem de PTV em tumores de próstata com 3DCRT

Mestrado em Radioterapia

Effects of emotional valence and three-dimensionality of visual stimuli on brain activation: an fMRI study

BACKGROUND: Examining changes in brain activation linked with emotion-inducing stimuli is essential to the study of emotions. Due to the ecological potential of techniques such as virtual reality (VR), inspection of whether brain activation in response to emotional stimuli can be modulated by the three-dimensional (3D) properties of the images is important. OBJECTIVE: The current study sought to test whether the activation of brain areas involved in the emotional processing of scenarios of different valences can be modulated by 3D. Therefore, the focus was made on the interaction effect between emotion-inducing stimuli of different emotional valences (pleasant, unpleasant and neutral valences) and visualization types (2D, 3D). However, main effects were also analyzed.METHODS: The effect of emotional valence and visualization types and their interaction were analyzed through a 3x2 repeated measures ANOVA. Post-hoc t-tests were performed under a ROI-analysis approach. RESULTS: The results show increased brain activation for the 3D affective-inducing stimuli in comparison with the same stimuli in 2D scenarios, mostly in cortical and subcortical regions that are related to emotional processing, in addition to visual processing regions. CONCLUSIONS: This study has the potential of clarify brain mechanisms involved in the processing of emotional stimuli (scenarios’ valence) and their interaction with three-dimensionality.

Development of CBCT-based prostate setup correction strategies and impact of rectal distension.

BACKGROUND: Cone-beam computed tomography (CBCT) image-guided radiotherapy (IGRT) systems are widely used tools to verify and correct the target position before each fraction, allowing to maximize treatment accuracy and precision. In this study, we evaluate automatic three-dimensional intensity-based rigid registration (RR) methods for prostate setup correction using CBCT scans and study the impact of rectal distension on registration quality. METHODS: We retrospectively analyzed 115 CBCT scans of 10 prostate patients. CT-to-CBCT registration was performed using (a) global RR, (b) bony RR, or (c) bony RR refined by a local prostate RR using the CT clinical target volume (CTV) expanded with 1-to-20-mm varying margins. After propagation of the manual CT contours, automatic CBCT contours were generated. For evaluation, a radiation oncologist manually delineated the CTV on the CBCT scans. The propagated and manual CBCT contours were compared using the Dice similarity and a measure based on the bidirectional local distance (BLD). We also conducted a blind visual assessment of the quality of the propagated segmentations. Moreover, we automatically quantified rectal distension between the CT and CBCT scans without using the manual CBCT contours and we investigated its correlation with the registration failures. To improve the registration quality, the air in the rectum was replaced with soft tissue using a filter. The results with and without filtering were compared. RESULTS: The statistical analysis of the Dice coefficients and the BLD values resulted in highly significant differences (p<10(-6)) for the 5-mm and 8-mm local RRs vs the global, bony and 1-mm local RRs. The 8-mm local RR provided the best compromise between accuracy and robustness (Dice median of 0.814 and 97% of success with filtering the air in the rectum). We observed that all failures were due to high rectal distension. Moreover, the visual assessment confirmed the superiority of the 8-mm local RR over the bony RR. CONCLUSION: The most successful CT-to-CBCT RR method proved to be the 8-mm local RR. We have shown the correlation between its registration failures and rectal distension. Furthermore, we have provided a simple (easily applicable in routine) and automatic method to quantify rectal distension and to predict registration failure using only the manual CT contours.

Changes in patterns of practice for prostate cancer radiotherapy in Italy 1995-2003. A survey of the Prostate Cancer Study Group of the Italian Radiation Oncology Society.

Aims and background. In 2002, a survey including 1759 patients treated from 1980 to 1998 established a "benchmark" Italian data source for prostate cancer radiotherapy. This report updates the previous one. Methods. Data on clinical management and outcomes of 3001 patients treated in 15 centers from 1999 through 2003 were analyzed and compared with those of the previous survey. Results. Significant differences in clinical management (-10% had abdominal ma-gnetic resonance imaging; +26% received ≥70 Gy, +48% conformal radiotherapy, -20% pelvic radiotherapy) and in G3-4 toxicity rates (-3.8%) were recorded. Actuarial 5-year overall, disease-specific, clinical relapse-free, and biochemical relapse-free survival rates were 88%, 96%, 96% and 88%, respectively. At multivariate analysis, D'Amico risk categories significantly impacted on all the outcomes; higher radiotherapy doses were significantly related with better overall survival rates, and a similar trend was evident for disease-specific and biochemical relapse-free survival; cumulative probability of 5-year late G1-4 toxicity was 24.8% and was significantly related to higher radiotherapy doses (P <0.001). Conclusions. The changing patterns of practice described seem related to an improvement in efficacy and safety of radiotherapy for prostate cancer. However, the impact of the new radiotherapy techniques should be prospectively evaluated.

Concise reviews: in vitro-produced pancreas organogenesis models in three dimensions: self-organization from few stem cells or progenitors.

Three-dimensional models of organ biogenesis have recently flourished. They promote a balance between stem/progenitor cell expansion and differentiation without the constraints of flat tissue culture vessels, allowing for autonomous self-organization of cells. Such models allow the formation of miniature organs in a dish and are emerging for the pancreas, starting from embryonic progenitors and adult cells. This review focuses on the currently available systems and how these allow new types of questions to be addressed. We discuss the expected advancements including their potential to study human pancreas development and function as well as to develop diabetes models and therapeutic cells.

Atlas-based segmentation of pathological MR brain images using a model of lesion growth.

We propose a method for brain atlas deformation in the presence of large space-occupying tumors, based on an a priori model of lesion growth that assumes radial expansion of the lesion from its starting point. Our approach involves three steps. First, an affine registration brings the atlas and the patient into global correspondence. Then, the seeding of a synthetic tumor into the brain atlas provides a template for the lesion. The last step is the deformation of the seeded atlas, combining a method derived from optical flow principles and a model of lesion growth. Results show that a good registration is performed and that the method can be applied to automatic segmentation of structures and substructures in brains with gross deformation, with important medical applications in neurosurgery, radiosurgery, and radiotherapy.

From radiobiology to technology: what is changing in radiotherapy for prostate cancer.

In the last decades, new technologies have been introduced in the daily clinical practice of the radiation oncologist: 3D-Conformal radiotherapy (RT) became almost universally available, thereafter, intensity modulated RT (IMRT) gained large diffusion, due to its potential impact in improving the clinical outcomes, and more recently, helical and volumetric arc IMRT with image-guided RT are becoming more and more diffused and used for prostate cancer patients. The conventional dose-fractionation results to be the best compromise between the efficacy and the safety of the treatment, but combining new techniques, modern RT allows to overcame one of the major limits of the 'older' RT: the impossibility of delivering higher total doses and/or high dose/fraction. The evidences regarding radiobiology, clinical and technological evolution of RT in prostate cancer have been reported and discussed.

Long-term Outcome and Late Side Effects in Endometrial Cancer Patients Treated with Surgery and Postoperative Radiation Therapy.

BACKGROUND: We retrospectively reviewed the long-term outcome and late side effects of endometrial cancer (EC) patients treated with different techniques of postoperative radiotherapy (PORT). METHODS: Between 1999 and 2012, 237 patients with EC were treated with PORT. Two-dimensional external beam radiotherapy (2D-EBRT) was used in 69 patients (30 %), three-dimensional EBRT (3D-EBRT) in 51 (21 %), and intensity-modulated RT (IMRT) with helical Tomotherapy in 47 (20 %). All patients received a vaginal brachytherapy (VB) boost. Seventy patients (29 %) received VB alone. RESULTS: After a median of 68 months (range, 6-154) of follow-up, overall survival was 75 % [95 % confidence interval (CI), 69-81], disease-free survival was 72 % (95% CI, 66-78), cancer-specific survival was 85 % (95 % CI, 80-89), and locoregional control was 86 % (95 % CI, 81-91). The 5-year estimates of grade 3 or more toxicity and second cancer rates were 0 and 7 % (95 % CI, 1-13) for VB alone, 6 % (95 % CI, 1-11) and 0 % for IMRT + VB, 9 % (95 % CI, 1-17) and 5 % (95 % CI, 1-9) for 3D-EBRT + VB, and 22 % (95 % CI, 12-32) and 12 % (95 % CI, 4-20) for 2D-EBRT + VB (P = 0.002 and P = 0.01), respectively. CONCLUSIONS: Pelvic EBRT should be tailored to patients with high-risk EC because the severe late toxicity observed might outweigh the benefits. When EBRT is prescribed for EC, IMRT should be considered, because it was associated with a significant reduction of severe late side effects.

Large N phases, gravitational instantons and the nuts and bolts of AdS holography

Recent results in the literature concerning holography indicate that the thermodynamics of quantum gravity (at least with a negative cosmological constant) can be modeled by the large N thermodynamics of quantum field theory. We emphasize that this suggests a completely unitary evolution of processes in quantum gravity, including black hole formation and decay, and even more extreme examples involving topology change. As concrete examples which show that this correspondence holds even when the space-time is only locally asymptotically AdS, we compute the thermodynamical phase structure of the AdS-Taub-NUT and AdS-Taub-bolt spacetimes, and compare them to a (2+1)-dimensional conformal field theory (at large N) compactified on a squashed three-sphere and on the twisted plane.

Accuracy and predictability in use of AO three-dimensionally preformed titanium mesh plates for posttraumatic orbital reconstruction: a pilot study.

The aim of this study was to prospectively evaluate the accuracy and predictability of new three-dimensionally preformed AO titanium mesh plates for posttraumatic orbital wall reconstruction.We analyzed the preoperative and postoperative clinical and radiologic data of 10 patients with isolated blow-out orbital fractures. Fracture locations were as follows: floor (N = 7; 70%), medial wall (N = 1; 1%), and floor/medial wall (N = 2; 2%). The floor fractures were exposed by a standard transconjunctival approach, whereas a combined transcaruncular transconjunctival approach was used in patients with medial wall fractures. A three-dimensional preformed AO titanium mesh plate (0.4 mm in thickness) was selected according to the size of the defect previously measured on the preoperative computed tomographic (CT) scan examination and fixed at the inferior orbital rim with 1 or 2 screws. The accuracy of plate positioning of the reconstructed orbit was assessed on the postoperative CT scan. Coronal CT scan slices were used to measure bony orbital volume using OsiriX Medical Image software. Reconstructed versus uninjured orbital volume were statistically correlated.Nine patients (90%) had a successful treatment outcome without complications. One patient (10%) developed a mechanical limitation of upward gaze with a resulting handicapping diplopia requiring hardware removal. Postoperative orbital CT scan showed an anatomic three-dimensional placement of the orbital mesh plates in all of the patients. Volume data of the reconstructed orbit fitted that of the contralateral uninjured orbit with accuracy to within 2.5 cm(3). There was no significant difference in volume between the reconstructed and uninjured orbits.This preliminary study has demonstrated that three-dimensionally preformed AO titanium mesh plates for posttraumatic orbital wall reconstruction results in (1) a high rate of success with an acceptable rate of major clinical complications (10%) and (2) an anatomic restoration of the bony orbital contour and volume that closely approximates that of the contralateral uninjured orbit.