@article {1433797,
	title = {Accurate airway wall estimation using phase congruency},
	journal = {Med Image Comput Comput Assist Interv},
	volume = {9},
	number = {Pt 2},
	year = {2006},
	month = {2006},
	pages = {125-34},
	abstract = {Quantitative analysis of computed tomographic (CT) images of the lungs is becoming increasingly useful in the medical and surgical management of subjects with Chronic Obstructive Pulmonary Disease (COPD). Current methods for the assessment of airway wall work well in idealized models of the airway. We propose a new method for airway wall detection based on phase congruency. This method does not rely on either a specific model of the airway or the point spread function of the scanner. Our results show that our method gives a better localization of the airway wall than "full width at a half max" and is less sensitive to different reconstruction kernels and radiation doses.},
	keywords = {Algorithms, Artificial Intelligence, Humans, Imaging, Three-Dimensional, Lung, Pattern Recognition, Automated, Phantoms, Imaging, Radiographic Image Enhancement, Radiographic Image Interpretation, Computer-Assisted, Reproducibility of Results, Sensitivity and Specificity, Tomography, X-Ray Computed},
	author = {San Jos{\'e} Est{\'e}par, Ra{\'u}l and Washko, George G and Silverman, Edwin K and Reilly, John J and Kikinis, Ron and Westin, Carl-Fredrik}
}
@article {1433790,
	title = {Complementary aspects of diffusion imaging and fMRI; I: structure and function},
	journal = {Magn Reson Imaging},
	volume = {24},
	number = {4},
	year = {2006},
	month = {2006 May},
	pages = {463-74},
	abstract = {Studying the intersection of brain structure and function is an important aspect of modern neuroscience. The development of magnetic resonance imaging (MRI) over the last 25 years has provided new and powerful tools for the study of brain structure and function. Two tools in particular, diffusion imaging and functional MRI (fMRI), are playing increasingly important roles in elucidating the complementary aspects of brain structure and function. In this work, we review basic technical features of diffusion imaging and fMRI for studying the integrity of white matter structural components and for determining the location and extent of cortical activation in gray matter, respectively. We then review a growing body of literature in which the complementary aspects of diffusion imaging and fMRI, applied as separate examinations but analyzed in tandem, have been exploited to enhance our knowledge of brain structure and function.},
	keywords = {Brain Diseases, Diffusion, Diffusion Magnetic Resonance Imaging, Evoked Potentials, Visual, Humans, Magnetic Resonance Imaging, Memory, Short-Term, Motor Cortex, Oxygen, Visual Cortex},
	issn = {0730-725X},
	doi = {10.1016/j.mri.2006.01.007},
	author = {Mulkern, Robert V. and Davis, Peter E and Haker, Steven J and Estepar, Raul San Jose and Panych, Lawrence P. and Maier, Stephan E. and Rivkin, Michael J}
}
@article {1433792,
	title = {On diffusion tensor estimation},
	journal = {Conf Proc IEEE Eng Med Biol Soc},
	volume = {Suppl},
	year = {2006},
	month = {2006},
	pages = {6707-10},
	abstract = {In this paper we propose a formal formulation for the estimation of Diffusion Tensors in the space of symmetric positive semidefinite (PSD) tensors. Traditionally, diffusion tensor model estimation has been carried out imposing tensor symmetry without constraints for negative eigenvalues. When diffusion weighted data does not follow the diffusion model,due to noise or signal drop, negative eigenvalues may arise. An estimation method that accounts for the positive definiteness is desirable to respect the underlying principle of diffusion. This paper proposes such an estimation method and provides a theoretical interpretation of the result. A closed-form solution is derived that is the optimal data-fit in the matrix 2-norm sense,removing the need for optimization-based tensor estimation.},
	keywords = {Algorithms, Anisotropy, Brain, Diffusion, Humans, Pattern Recognition, Automated},
	issn = {1557-170X},
	doi = {10.1109/IEMBS.2006.260927},
	author = {Niethammer, Marc and Estepar, Raul San Jose and Bouix, Sylvain and Shenton, Martha and Westin, Carl-Fredrik}
}
@article {1433795,
	title = {On diffusion tensor estimation},
	journal = {Conf Proc IEEE Eng Med Biol Soc},
	volume = {1},
	year = {2006},
	month = {2006},
	pages = {2622-5},
	abstract = {In this paper we propose a formal formulation for the estimation of Diffusion Tensors in the space of symmetric positive semidefinite (PSD) tensors. Traditionally, diffusion tensor model estimation has been carried out imposing tensor symmetry without constraints for negative eigenvalues. When diffusion weighted data does not follow the diffusion model, due to noise or signal drop, negative eigenvalues may arise. An estimation method that accounts for the positive definiteness is desirable to respect the underlying principle of diffusion. This paper proposes such an estimation method and provides a theoretical interpretation of the result. A closed-form solution is derived that is the optimal data-fit in the matrix 2-norm sense, removing the need for optimization-based tensor estimation.},
	keywords = {Algorithms, Artificial Intelligence, Brain, Diffusion Magnetic Resonance Imaging, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated},
	issn = {1557-170X},
	doi = {10.1109/IEMBS.2006.259826},
	author = {Niethammer, Marc and Estepar, Raul San Jose and Bouix, Sylvain and Shenton, Martha and Westin, Carl-Fredrik}
}
@article {1433793,
	title = {Image quality assessment based on local variance},
	journal = {Conf Proc IEEE Eng Med Biol Soc},
	volume = {1},
	year = {2006},
	month = {2006},
	pages = {4815-8},
	abstract = {A new and complementary method to assess image quality is presented. It is based on the comparison of the local variance distribution of two images. This new quality index is better suited to assess the non-stationarity of images, therefore it explicitly focuses on the image structure. We show that this new index outperforms other methods for the assessment of image quality in medical images.},
	keywords = {Algorithms, Brain, Calibration, Diagnostic Imaging, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Models, Statistical, Pattern Recognition, Automated, Quality Control, Reproducibility of Results, Software},
	issn = {1557-170X},
	doi = {10.1109/IEMBS.2006.259516},
	author = {Aja-Fern{\'a}ndez, Santiago and San Jos{\'e} Est{\'e}par, Ra{\'u}l and Alberola-L{\'o}pez, Carlos and Westin, Carl-Fredrik}
}
@article {1433794,
	title = {A kernel-based approach for user-guided fiber bundling using diffusion tensor data},
	journal = {Conf Proc IEEE Eng Med Biol Soc},
	volume = {1},
	year = {2006},
	month = {2006},
	pages = {2626-9},
	abstract = {This paper describes a novel user-guided method for grouping fibers from diffusion tensor MRI tractography into bundles. The method finds fibers, that passing through user-defined ROIs, still fit to the underlying data model given by the diffusion tensor. This is achieved by filtering the data and the ROIs with a kernel derived from a geodesic metric between tensors. A standard approach using binary decisions defining tracts passing through ROIs is critically dependent on ROIs that includes all trace lines of interest. The method described in this paper uses a softer decision mechanism through a kernel which enables grouping of bundles driven less exact, or even single point, ROIs. The method analyzes the responses obtained from the convolution with a kernel function along the fiber with the ROI data. Results in real data shows the feasibility of the approach to fiber bundling.},
	keywords = {Algorithms, Artificial Intelligence, Diffusion Magnetic Resonance Imaging, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Nerve Fibers, Neural Pathways, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity},
	issn = {1557-170X},
	doi = {10.1109/IEMBS.2006.259829},
	author = {San Jos{\'e} Est{\'e}par, Ra{\'u}l and Kubicki, Marek and Shenton, Martha and Westin, Carl-Fredrik}
}
@article {1433796,
	title = {Towards scarless surgery: an endoscopic-ultrasound navigation system for transgastric access procedures},
	journal = {Med Image Comput Comput Assist Interv},
	volume = {9},
	number = {Pt 1},
	year = {2006},
	month = {2006},
	pages = {445-53},
	abstract = {Scarless surgery is a new and very promising technique that can mark a new era in surgical procedures. We have created and validated a navigation system for endoscopic and transgastric access interventions in in vivo pilot studies. The system provides augmented visual feedback and additional contextual information by establishing a correspondence between the real time endoscopic ultrasound image and a preoperative CT volume using rigid registration. The system enhances the operator{\textquoteright}s ability to interpret the ultrasound image reducing the mental burden used in probe placement. Our analysis shows that rigid registration is accurate enough to help physicians in endoscopic abdominal surgery where, by using preoperative data for context and real-time imaging for targeting, distortions that limit the use of only preoperative data can be overcome.},
	keywords = {Cicatrix, Endoscopy, Gastrointestinal, Humans, Image Interpretation, Computer-Assisted, Radiography, Reproducibility of Results, Sensitivity and Specificity, Stomach, Subtraction Technique, Surgery, Computer-Assisted, Ultrasonography, Interventional},
	author = {San Jos{\'e} Est{\'e}par, Ra{\'u}l and Stylopoulos, Nicholas and Ellis, Randy E and Samset, Eigil and Westin, Carl-Fredrik and Thompson, Christopher and Vosburgh, Kirby}
}
@article {1433791,
	title = {Volume-related and volume-independent effects of posture on esophageal and transpulmonary pressures in healthy subjects},
	journal = {J Appl Physiol (1985)},
	volume = {100},
	number = {3},
	year = {2006},
	month = {2006 Mar},
	pages = {753-8},
	abstract = {Ventilator management decisions in acute lung injury could be better informed with knowledge of the patient{\textquoteright}s transpulmonary pressure, which can be estimated using measurements of esophageal pressure. Esophageal manometry is seldom used for this, however, in part because of a presumed postural artifact in the supine position. Here, we characterize the magnitude and variability of postural effects on esophageal pressure in healthy subjects to better assess its significance in patients with acute lung injury. We measured the posture-related changes in relaxation volume and total lung capacity in 10 healthy subjects in four postures: upright, supine, prone, and left lateral decubitus. Then, in the same subjects, we measured static pressure-volume characteristics of the lung over a wide range of lung volumes in each posture by using an esophageal balloon catheter. Transpulmonary pressure during relaxation (PLrel) averaged 3.7 (SD 2.0) cmH2O upright and -3.3 (SD 3.2) cmH2O supine. Approximately 58\% of the decrease in PLrel between the upright and supine postures was due to a corresponding decrease in relaxation volume. The remaining 2.9-cmH2O difference is consistent with reported values of a presumed postural artifact. Relaxation volumes and pressures in prone and lateral postures were intermediate. To correct estimated transpulmonary pressure for the effect of lying supine, we suggest adding 3 cmH2O (95\% confidence interval: -1 to +7 cmH2O). We conclude that postural differences in estimated transpulmonary pressure at a given lung volume are small compared with the substantial range of PLrel in patients with acute lung injury.},
	keywords = {Adult, Catheterization, Esophagus, Exhalation, Female, Humans, Lung, Lung Volume Measurements, Male, Manometry, Middle Aged, Posture, Respiratory Function Tests, Respiratory Mechanics},
	issn = {8750-7587},
	doi = {10.1152/japplphysiol.00697.2005},
	author = {Washko, George R and O{\textquoteright}Donnell, Carl R and Loring, Stephen H}
}
@article {473461,
	title = {2006 International Conference of the IEEE Engineering in Medicine and Biology Society},
	journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. ConferenceConference proceedings : ... Annual International Conference of the IEEE Engi},
	volume = {1},
	year = {2006},
	month = {Aug 30},
	pages = {4815-4818},
	abstract = {A new and complementary method to assess image quality is presented. It is based on the comparison of the local variance distribution of two images. This new quality index is better suited to assess the non-stationarity of images, therefore it explicitly focuses on the image structure. We show that this new index outperforms other methods for the assessment of image quality in medical images.},
	author = {Aja-Fernandez, Santiago and San Jose Est{\'e}par, Ra{\'u}l and Alberola-Lopez, Carlos and Westin, Carl-Fredrik}
}
@conference {473456,
	title = {2006 International Conference of the IEEE Engineering in Medicine and Biology Society},
	booktitle = {2006 International Conference of the IEEE Engineering in Medicine and Biology Society2006 International Conference of the IEEE Engineering in Medicine and Biology Society},
	year = {2006},
	month = {Aug 30},
	pages = {2622-2625},
	publisher = {IEEE},
	organization = {IEEE},
	author = {Niethammer, Marc and San Jose Est{\'e}par, Ra{\'u}l and Bouix, Sylvain and Shenton, Martha and Westin, Carl-Fredrik}
}
@article {473451,
	title = {2006 International Conference of the IEEE Engineering in Medicine and Biology Society},
	journal = {Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. ConferenceConference proceedings : ... Annual International Conference of the IEEE Engi},
	volume = {Suppl},
	year = {2006},
	month = {Aug 30},
	pages = {6707-6710},
	address = {New York City},
	abstract = {In this paper we propose a formal formulation for the estimation of Diffusion Tensors in the space of symmetric positive semidefinite (PSD) tensors. Traditionally, diffusion tensor model estimation has been carried out imposing tensor symmetry without constraints for negative eigenvalues. When diffusion weighted data does not follow the diffusion model,due to noise or signal drop, negative eigenvalues may arise. An estimation method that accounts for the positive definiteness is desirable to respect the underlying principle of diffusion. This paper proposes such an estimation method and provides a theoretical interpretation of the result. A closed-form solution is derived that is the optimal data-fit in the matrix 2-norm sense,removing the need for optimization-based tensor estimation.},
	author = {Niethammer, Marc and San Jose Est{\'e}par, Ra{\'u}l and Bouix, Sylvain and Shenton, Martha and Westin, Carl-Fredrik}
}
@article {473471,
	title = {Towards scarless surgery: an endoscopic-ultrasound navigation system for transgastric access procedures.},
	journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted InterventionMedical image computing and computer-assisted intervention : MICCAI ... International Conference },
	volume = {9},
	year = {2006},
	pages = {445-453},
	type = {Evaluation Study},
	abstract = {Scarless surgery is a new and very promising technique that can mark a new era in surgical procedures. We have created and validated a navigation system for endoscopic and transgastric access interventions in in vivo pilot studies. The system provides augmented visual feedback and additional contextual information by establishing a correspondence between the real time endoscopic ultrasound image and a preoperative CT volume using rigid registration. The system enhances the operator\'s ability to interpret the ultrasound image reducing the mental burden used in probe placement. Our analysis shows that rigid registration is accurate enough to help physicians in endoscopic abdominal surgery where, by using preoperative data for context and real-time imaging for targeting, distortions that limit the use of only preoperative data can be overcome.},
	author = {San Jose Est{\'e}par, Ra{\'u}l and Stylopoulos, Nicholas and Ellis, Randy E and Samset, Eigil and Westin, Carl-Fredrik and Thompson, Christopher and Vosburgh, Kirby}
}
@conference {473446,
	title = {2006 International Conference of the IEEE Engineering in Medicine and Biology Society},
	booktitle = {2006 International Conference of the IEEE Engineering in Medicine and Biology Society},
	year = {2006},
	month = {Aug 30},
	pages = {2626-2629},
	publisher = {IEEE},
	organization = {IEEE},
	author = {San Jose Est{\'e}par, Ra{\'u}l and Kubicki, Marek and Shenton, Martha and Westin, Carl-Fredrik}
}
@article {473476,
	title = {Accurate airway wall estimation using phase congruency.},
	journal = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted InterventionMedical image computing and computer-assisted intervention : MICCAI ... International Conference },
	volume = {9},
	year = {2006},
	pages = {125-134},
	type = {Evaluation Study},
	abstract = {Quantitative analysis of computed tomographic (CT) images of the lungs is becoming increasingly useful in the medical and surgical management of subjects with Chronic Obstructive Pulmonary Disease (COPD). Current methods for the assessment of airway wall work well in idealized models of the airway. We propose a new method for airway wall detection based on phase congruency. This method does not rely on either a specific model of the airway or the point spread function of the scanner. Our results show that our method gives a better localization of the airway wall than "full width at a half max" and is less sensitive to different reconstruction kernels and radiation doses.},
	author = {San Jose Est{\'e}par, Ra{\'u}l and Washko, George G and Silverman, Edwin K and Reilly, John J and Kikinis, Ron and Westin, Carl-Fredrik}
}
@article {473466,
	title = {Complementary aspects of diffusion imaging and fMRI; I: structure and function.},
	journal = {Magnetic resonance imagingMagnetic resonance imaging},
	volume = {24},
	year = {2006},
	month = {Jun},
	pages = {463-474},
	abstract = {Studying the intersection of brain structure and function is an important aspect of modern neuroscience. The development of magnetic resonance imaging (MRI) over the last 25 years has provided new and powerful tools for the study of brain structure and function. Two tools in particular, diffusion imaging and functional MRI (fMRI), are playing increasingly important roles in elucidating the complementary aspects of brain structure and function. In this work, we review basic technical features of diffusion imaging and fMRI for studying the integrity of white matter structural components and for determining the location and extent of cortical activation in gray matter, respectively. We then review a growing body of literature in which the complementary aspects of diffusion imaging and fMRI, applied as separate examinations but analyzed in tandem, have been exploited to enhance our knowledge of brain structure and function.},
	author = {Mulkern, Robert V. and Davis, Peter E and Haker, Steven J and San Jose Est{\'e}par, Ra{\'u}l and Panych, Lawrence P. and Maier, Stephan E. and Rivkin, Michael J}
}