Publications

2006
San José Estépar R, Kubicki M, Shenton M, Westin C-F. A kernel-based approach for user-guided fiber bundling using diffusion tensor data. Conf Proc IEEE Eng Med Biol Soc 2006;1:2626-9.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.
San José Estépar R, Stylopoulos N, Ellis RE, Samset E, Westin C-F, Thompson C, Vosburgh K. Towards scarless surgery: an endoscopic-ultrasound navigation system for transgastric access procedures. Med Image Comput Comput Assist Interv 2006;9(Pt 1):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'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.
Washko GR, O'Donnell CR, Loring SH. Volume-related and volume-independent effects of posture on esophageal and transpulmonary pressures in healthy subjects. J Appl Physiol (1985) 2006;100(3):753-8.Abstract
Ventilator management decisions in acute lung injury could be better informed with knowledge of the patient'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.
Aja-Fernandez S, San Jose Estépar R, Alberola-Lopez C, Westin C-F. 2006 International Conference of the IEEE Engineering in Medicine and Biology Society. 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 2006;1:4815-4818.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.
Niethammer M, San Jose Estépar R, Bouix S, Shenton M, Westin C-F. 2006 International Conference of the IEEE Engineering in Medicine and Biology Society. In: 2006 International Conference of the IEEE Engineering in Medicine and Biology Society2006 International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE; 2006 p. 2622-2625.
Niethammer M, San Jose Estépar R, Bouix S, Shenton M, Westin C-F. 2006 International Conference of the IEEE Engineering in Medicine and Biology Society. 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 2006;Suppl:6707-6710.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.
San Jose Estépar R, Stylopoulos N, Ellis RE, Samset E, Westin C-F, Thompson C, Vosburgh K. Towards scarless surgery: an endoscopic-ultrasound navigation system for transgastric access procedures. 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 2006;9:445-453.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.
San Jose Estépar R, Kubicki M, Shenton M, Westin C-F. 2006 International Conference of the IEEE Engineering in Medicine and Biology Society. In: 2006 International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE; 2006 p. 2626-2629.
San Jose Estépar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin C-F. Accurate airway wall estimation using phase congruency. 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 2006;9:125-134.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.

med_image_comput_comput_assist_interv_2006_san_jose_estepar.pdf
Mulkern RV, Davis PE, Haker SJ, San Jose Estépar R, Panych LP, Maier SE, Rivkin MJ. Complementary aspects of diffusion imaging and fMRI; I: structure and function. Magnetic resonance imagingMagnetic resonance imaging 2006;24:463-474.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.

magn_reson_imaging_2006_mulkern.pdf
2004
Kubicki M, Maier SE, Westin C-F, Mamata H, Ersner-Hershfield H, Estepar R, Kikinis R, Jolesz FA, McCarley RW, Shenton ME. Comparison of single-shot echo-planar and line scan protocols for diffusion tensor imaging. Acad Radiol 2004;11(2):224-32.Abstract
RATIONALE AND OBJECTIVES: Both single-shot diffusion-weighted echo-planar imaging (EPI) and line scan diffusion imaging (LSDI) can be used to obtain magnetic resonance diffusion tensor data and to calculate directionally invariant diffusion anisotropy indices, ie, indirect measures of the organization and coherence of white matter fibers in the brain. To date, there has been no comparison of EPI and LSDI. Because EPI is the most commonly used technique for acquiring diffusion tensor data, it is important to understand the limitations and advantages of LSDI relative to EPI. MATERIALS AND METHODS: Five healthy volunteers underwent EPI and LSDI diffusion on a 1.5 Tesla magnet (General Electric Medical Systems, Milwaukee, WI). Four-mm thick coronal sections, covering the entire brain, were obtained. In addition, one subject was tested with both sequences over four sessions. For each image voxel, eigenvectors and eigenvalues of the diffusion tensor were calculated, and fractional anisotropy (FA) was derived. Several regions of interest were delineated, and for each, mean FA and estimated mean standard deviation were calculated and compared. RESULTS: Results showed no significant differences between EPI and LSDI for mean FA for the five subjects. When intersession reproducibility for one subject was evaluated, there was a significant difference between EPI and LSDI in FA for the corpus callosum and the right uncinate fasciculus. Moreover, errors associated with each FA measure were larger for EPI than for LSDI. CONCLUSION: Results indicate that both EPI- and LSDI-derived FA measures are sufficiently robust. However, when higher accuracy is needed, LSDI provides smaller error and smaller inter-subject and inter-session variability than EPI.
Levitt JJ, Westin CF, Nestor PG, Estepar RSJ, Dickey CC, Voglmaier MM, Seidman LJ, Kikinis R, Jolesz FA, McCarley RW, Shenton ME. Shape of caudate nucleus and its cognitive correlates in neuroleptic-naive schizotypal personality disorder. Biol Psychiatry 2004;55(2):177-84.Abstract
BACKGROUND: We measured the shape of the head of the caudate nucleus with a new approach based on magnetic resonance imaging (MRI) in schizotypal personality disorder (SPD) subjects in whom we previously reported decreased caudate nucleus volume. We believe MRI shape analysis complements traditional MRI volume measurements. METHODS: Magnetic resonance imaging scans were used to measure the shape of the caudate nucleus in 15 right-handed male subjects with SPD, who had no prior neuroleptic exposure, and in 14 matched normal comparison subjects. With MRI processing tools, we measured the head of the caudate nucleus using a shape index, which measured how much a given shape deviates from a sphere. RESULTS: In relation to comparison subjects, neuroleptic never-medicated SPD subjects had significantly higher (more "edgy") head of the caudate shape index scores, lateralized to the right side. Additionally, for SPD subjects, higher right and left head of the caudate SI scores correlated significantly with poorer neuropsychological performance on tasks of visuospatial memory and auditory/verbal working memory, respectively. CONCLUSIONS: These data confirm the value of measuring shape, as well as volume, of brain regions of interest and support the association of intrinsic pathology in the caudate nucleus, unrelated to neuroleptic medication, with cognitive abnormalities in the schizophrenia spectrum.
Levitt JJ, Westin C-F, Nestor PG, San Jose Estépar R, Dickey CC, Voglmaier MM, Seidman LJ, Kikinis R, Jolesz FA, McCarley RW, Shenton ME. Shape of caudate nucleus and its cognitive correlates in neuroleptic-naive schizotypal personality disorder. Biological psychiatryBiological psychiatry 2004;55:177-184.Abstract

BACKGROUND: We measured the shape of the head of the caudate nucleus with a new approach based on magnetic resonance imaging (MRI) in schizotypal personality disorder (SPD) subjects in whom we previously reported decreased caudate nucleus volume. We believe MRI shape analysis complements traditional MRI volume measurements. METHODS: Magnetic resonance imaging scans were used to measure the shape of the caudate nucleus in 15 right-handed male subjects with SPD, who had no prior neuroleptic exposure, and in 14 matched normal comparison subjects. With MRI processing tools, we measured the head of the caudate nucleus using a shape index, which measured how much a given shape deviates from a sphere. RESULTS: In relation to comparison subjects, neuroleptic never-medicated SPD subjects had significantly higher (more "edgy") head of the caudate shape index scores, lateralized to the right side. Additionally, for SPD subjects, higher right and left head of the caudate SI scores correlated significantly with poorer neuropsychological performance on tasks of visuospatial memory and auditory/verbal working memory, respectively. CONCLUSIONS: These data confirm the value of measuring shape, as well as volume, of brain regions of interest and support the association of intrinsic pathology in the caudate nucleus, unrelated to neuroleptic medication, with cognitive abnormalities in the schizophrenia spectrum.

biol._psychiatry_2004_levitt.pdf
2003
San José-Estépar R, Martín-Fernández M, Caballero-Martínez PP, Alberola-López C, Ruiz-Alzola J. A theoretical framework to three-dimensional ultrasound reconstruction from irregularly sampled data. Ultrasound Med Biol 2003;29(2):255-69.Abstract
Several techniques have been described in the literature in recent years for the reconstruction of a regular volume out of a series of ultrasound (US) slices with arbitrary orientations, typically scanned by means of US freehand systems. However, a systematic approach to such a problem is still missing. This paper focuses on proposing a theoretical framework for the 3-D US volume reconstruction problem. We introduce a statistical method for the construction and trimming of the sampling grid where the reconstruction will be carried out. The results using in vivo US data demonstrate that the computed reconstruction grid that encloses the region-of-interest (ROI) is smaller than those obtained from other reconstruction methods in those cases where the scanning trajectory deviates from a pure straight line. In addition, an adaptive Gaussian interpolation technique is studied and compared with well-known interpolation methods that have been applied to the reconstruction problem in the past. We find that the proposed method numerically outperforms former proposals in several control studies; subjective visual results also support this conclusion and highlight some potential deficiencies of methods previously proposed.
San Jose Estépar R, Martín Fernández M, Caballero-Martínez PP, Alberola-Lopez C, Ruiz-Alzola J. A theoretical framework to three-dimensional ultrasound reconstruction from irregularly sampled data. Ultrasound in medicine & biologyUltrasound in medicine & biology 2003;29:255-269.Abstract

Several techniques have been described in the literature in recent years for the reconstruction of a regular volume out of a series of ultrasound (US) slices with arbitrary orientations, typically scanned by means of US freehand systems. However, a systematic approach to such a problem is still missing. This paper focuses on proposing a theoretical framework for the 3-D US volume reconstruction problem. We introduce a statistical method for the construction and trimming of the sampling grid where the reconstruction will be carried out. The results using in vivo US data demonstrate that the computed reconstruction grid that encloses the region-of-interest (ROI) is smaller than those obtained from other reconstruction methods in those cases where the scanning trajectory deviates from a pure straight line. In addition, an adaptive Gaussian interpolation technique is studied and compared with well-known interpolation methods that have been applied to the reconstruction problem in the past. We find that the proposed method numerically outperforms former proposals in several control studies; subjective visual results also support this conclusion and highlight some potential deficiencies of methods previously proposed.

ultrasound_med_biol_2003_san_jose_estepar.pdf
1986
Christiani DC, Eisen EA, Wegman DH, Ye TT, Lu PL, Gong ZC, Dai HL. Respiratory disease in cotton textile workers in the People's Republic of China. I. Respiratory symptoms. Scand J Work Environ Health 1986;12(1):40-5.Abstract

The prevalence of byssinosis and nonspecific respiratory symptoms was studied in 887 textile workers with at least two years of employment in two cotton mills and one silk mill in Shanghai, the People's Republic of China. A standardized respiratory questionnaire was used, and environmental sampling was performed with vertical elutriators and colorimeter grading. Eight percent of the cotton textile workers complained of byssinosis. The reports of byssinosis were mostly mild (grade 1/2), more prevalent among women, and unrelated to duration of employment or elutriator dust levels. Nonspecific respiratory symptoms were significantly more prevalent among cotton textile workers than silk workers. After adjustment for age, gender, and smoking in logistic regression models, the odds ratios for the effect of working in cotton textile mills on chronic bronchitis, chronic cough, and frequent chest illness were 3.3, 2.9 and 4.7, respectively. Although none of the symptoms were related to current dust levels, the range of exposures was narrow, and information was only available on current levels of cotton dust. This study represents the first respiratory survey of the textile industry in China using diagnostic criteria similar to that used in the United States and England; it defines a cohort for prospective investigation.

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