Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.

The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision.

The National Alliance for Medical Image Computing, a roadmap initiative to build a free and open source software infrastructure for translational research in medical image analysis.

The National Alliance for Medical Image Computing (NA-MIC), is a multi-institutional, interdisciplinary community of researchers, who share the recognition that modern health care demands improved technologies to ease suffering and prolong productive life. Organized under the National Centers for Biomedical Computing 7 years ago, the mission of NA-MIC is to implement a robust and flexible open-source infrastructure for developing and applying advanced imaging technologies across a range of important biomedical research disciplines. A measure of its success, NA-MIC is now applying this technology to diseases that have immense impact on the duration and quality of life: cancer, heart disease, trauma, and degenerative genetic diseases. The targets of this technology range from group comparisons to subject-specific analysis.

Racial differences in pelvic morphology among asymptomatic nulliparous women as seen on three-dimensional magnetic resonance images.

OBJECTIVE: Compare pelvic morphology between asymptomatic African-American and white nulliparous women. STUDY DESIGN: Resting supine T2-weighted magnetic resonance (MR) images were obtained in 12 African-American (AA) and 10 white American (WA) women without pelvic floor dysfunction. Three-dimensional models were reconstructed from the MR images by a masked investigator, and predefined bony and soft tissue pelvic floor parameters were measured and compared. Nonparametric statistics were used, with significance considered at P < .05. RESULTS: Subjects were similar in age and body mass index. Levator ani volume was significantly greater in the AA versus the WA group (mean = 26.8 vs 19.8 cm3, P = .002). The levator-symphysis gap was smaller in the AA (left-18.2, right-18.8 mm) versus the WA group (22.4, 22.6 mm, P = .003, .048) on the left and right. Significant differences were seen in bladder neck position, urethral angle, and the pubic arch angle. CONCLUSION: The increased muscle bulk and closer puborectalis attachment seen among the African-American nulliparous women may impact the development of pelvic floor dysfunction. These findings need further study.

Deficits of motion integration and segregation in patients with unilateral extrastriate lesions.

Functional neuroimaging in human subjects and single cell recordings in monkeys show that several extra-striate visual areas are activated by visual motion. However, the extent to which different types of motion are processed in different regions remains unclear, although neuropsychological studies of patients with circumscribed lesions hint at regional specialization. We, therefore, studied four patients with unilateral damage to different regions of extrastriate visual cortex on a series of visual discrimination tasks that required them, to a different extent, to integrate local motion signals in order to correctly perceive the direction of global motion. Performance was assessed psychophysically and compared with that of control subjects and with the patients' performance with stimuli presented in the visual field ipsilateral to the lesion. The results indicate considerable regional specialization in extra-striate regions for different aspects of motion processing, namely the largest displacement from frame to frame (D-max) that can sustain perception of coherent motion; perception of relative speed; the amount of coherent motion needed to sustain a percept of global motion in a particular direction; the detection of discontinuities within a moving display; the extraction of form from motion. It was also clear that a defect in local motion, i.e. D-max, can be overcome by integrating local motion signals over a longer period of time. Although no patient suffered from only one defect, the overall pattern of results strongly supports the notion of regional specialization for different aspects of motion processing.

Levator ani thickness variations in symptomatic and asymptomatic women using magnetic resonance-based 3-dimensional color mapping.

OBJECTIVE: This study was undertaken to develop and test a 3-dimensional (3D) color thickness mapping technique on levator ani imaged with magnetic resonance imaging (MRI). METHODS: Supine MRI datasets from 30 women were studied: 10 asymptomatic, 10 with urodynamic stress incontinence, and 10 with pelvic organ prolapse. Levators were manually outlined, and thickness mapping applied. Three-dimensional models were colored topographically, reflecting levator thickness. Thickness and occurrences of absent levator substance (gaps) were compared across the 3 groups, using nonparametric statistical tests. RESULTS: Color thickness mapping was successful in all subjects. There were statistically significant differences in thickness and gap percentages among the 3 groups of women, with thicker, bulkier levators in asymptomatic women, compared with women with prolapse or urodynamic stress incontinence. CONCLUSION: Color thickness mapping is feasible. It may be used to compare levators in symptomatic and asymptomatic women, to study relationships between levator thickness and pelvic floor dysfunction. This technique can be used in larger studies for hypothesis testing.

Anatomic and physiologic predictors of apnea severity in morbidly obese subjects.

STUDY OBJECTIVES: While obesity is the most common risk factor for the development of obstructive sleep apnea, the correlation between measures of obesity and apnea severity is only moderate. We thus attempted to identify anatomic and physiologic predictors of apnea severity. DESIGN: We combined a careful assessment of upper airway anatomy, upper airway physiology, and ventilatory control in a group of obese individuals to identify predictors of apnea severity. SETTING: Tertiary care academic medical center. PATIENTS: 14 morbidly obese subjects being evaluated for weight-reduction surgery. INTERVENTIONS: N/A MEASUREMENT AND RESULTS: We found no relationship between obesity (weight or body mass index) and apnea severity (respiratory disturbance index, RDI). However, those with severe apnea (RDI > 30) were found to have higher peak genioglossus EMG (GGEMG) (23.5 +/- 1.9 vs. 14.1 +/- 3.7 %max, p = 0.05) and greater airway collapsibility during pulses of negative pressure (7.6 +/- 0.9 vs. 4.4 -/+/-0.7 cmH2O, p =0.02). Airway collapsibility was significantly associated with RDI (r = 0.62, p < 0.01) as was peak GGEMG (r = 0.55, p < 0.05). Of the anatomic variables airway shape (A-P/lateral ratio) and volume change of the pharyngeal airway between total lung capacity and residual volume were different between those with and without severe apnea. Both correlated with RDI (A-P/lateral ratio: r = 0.70, p < 0.01 and volume change: r = 0.77, p < 0.01). CONCLUSIONS: We believe these findings suggest that specific anatomic and physiologic properties of the airway interact with obesity to predispose to the development of airway collapse during sleep.

Three-dimensional magnetic resonance imaging assessment of levator ani morphologic features in different grades of prolapse.

OBJECTIVE: The study was undertaken to identify the morphologic changes in the levator ani in different grades of prolapse by using reconstructed three-dimensional models of magnetic resonance images (MRI) and to subclassify prolapse into different categories on the basis of their levator ani morphologic characteristics. STUDY DESIGN: Sixty-one women were studied, 8 women in stage I, 15 women in stage II, 22 women in stage III, 7 women in stage IV prolapse, and 9 asymptomatic volunteers with stage 0 prolapse. Axial, sagittal, and coronal T2-weighted pelvic magnetic resonance scans were obtained with the patient in the supine position. The three-dimensional models were reconstructed from the source images by using manual segmentation and surface modeling. The morphologic characteristics of the puborectalis were assessed on these reconstructed models by measuring (1). the levator symphysis gap, (2). the width of the levator hiatus, and (3). the length of the levator hiatus. To assess the iliococcygeus, we measured (1). the maximum width of the iliococcygeus, (2). the direction of its fibers that was assessed by measuring the iliococcygeal angle, and (3) the levator plate angle. Nine nulliparous asymptomatic women were studied as controls. RESULTS: Alterations in levator ani morphologic features are not dependent on the grade of the prolapse, and not all women with pelvic floor prolapse have abnormal morphologic features. In healthy control subjects, the iliococcygeal width measured less than 40 mm and the iliococcygeal angle measured less than 20 degrees. On the basis of the MRI findings, four patterns of changes in the levator ani have been identified. Both the levator symphysis gap and the levator hiatus, which is dependent on the puborectalis function, widen with increasing grade of prolapse. CONCLUSION: It is possible to subclassify prolapse on the basis of morphologic changes in the levator ani by using MRI. This may be a very useful predictor as to which patients have recurrent prolapse develop after surgery.

An MRI study of temporal lobe abnormalities and negative symptoms in chronic schizophrenia.

Previous magnetic resonance imaging (MRI) studies have reported various subtle brain abnormalities in schizophrenic patients, including temporal lobe abnormalities, which are of particular interest given the role of this brain region in auditory and language processing, and the characteristic deficits in these processes in schizophrenia. Subjects in this study were 16 male patients diagnosed with chronic schizophrenia and 15 healthy male comparison subjects. These patients were characterized by negative symptoms. High spatial resolution coronal MRI 1.5-mm-thick slices were used to measure the gray matter volume of the superior temporal gyrus, anterior and posterior amygdala/hippocampal complex, and parahippocampal gyrus. Patients, relative to normal comparison subjects, evinced a reduction of gray matter volume in bilateral superior temporal gyri and anterior amygdala/hippocampal complex. The reduction in gray matter of the superior temporal gyrus in patients with schizophrenia is consistent with previous findings, and is noteworthy in that it was found in this group of patients with predominantly negative symptoms. The reduction in the anterior amygdala/hippocampal complex was an additional temporal lobe finding. These results underscore the role of temporal lobe structures in the pathophysiology of schizophrenia.