# Publications

## 2014

Revanth Reddy Garlapati, Aditi Roy, Grand Roman Joldes, Adam Wittek, Ahmed Mostayed, Barry Doyle, Simon Keith Warfield, Ron Kikinis, Neville Knuckey, Stuart Bunt, and Karol Miller. 2014. . J Neurosurg, 120, 6, Pp. 1477-83.
It is possible to improve neuronavigation during image-guided surgery by warping the high-quality preoperative brain images so that they correspond with the current intraoperative configuration of the brain. In this paper, the accuracy of registration results obtained using comprehensive biomechanical models is compared with the accuracy of rigid registration, the technology currently available to patients. This comparison allows investigation into whether biomechanical modeling provides good-quality image data for neuronavigation for a larger proportion of patients than rigid registration. Preoperative images for 33 neurosurgery cases were warped onto their respective intraoperative configurations using both the biomechanics-based method and rigid registration. The Hausdorff distance-based evaluation process, which measures the difference between images, was used to quantify the performance of both registration methods. A statistical test for difference in proportions was conducted to evaluate the null hypothesis that the proportion of patients for whom improved neuronavigation can be achieved is the same for rigid and biomechanics-based registration. The null hypothesis was confidently rejected (p
Takeshi Sasaki, Ofer Pasternak, Michael Mayinger, Marc Muehlmann, Peter Savadjiev, Sylvain Bouix, Marek Kubicki, Eli Fredman, Brian Dahlben, Karl G Helmer, Andrew M Johnson, Jeffrey D Holmes, Lorie A Forwell, Elaine N Skopelja, Martha E Shenton, Paul S Echlin, and Inga K Koerte. 2014. . J Neurosurg, 120, 4, Pp. 882-90.
OBJECT: The aim of this study was to examine the brain’s white matter microstructure by using MR diffusion tensor imaging (DTI) in ice hockey players with a history of clinically symptomatic concussion compared with players without a history of concussion. METHODS: Sixteen players with a history of concussion (concussed group; mean age 21.7 ± 1.5 years; 6 female) and 18 players without a history of concussion (nonconcussed group; mean age 21.3 ± 1.8 years, 10 female) underwent 3-T DTI at the end of the 2011-2012 Canadian Interuniversity Sports ice hockey season. Tract-based spatial statistics (TBSS) was used to test for group differences in fractional anisotropy (FA), axial diffusivity (AD), radial diffusivity (RD), and the measure "trace," or mean diffusivity. Cognitive evaluation was performed using the Immediate Postconcussion Assessment and Cognitive Test (ImPACT) and the Sport Concussion Assessment Tool-2 (SCAT2). RESULTS: TBSS revealed a significant increase in FA and AD, and a significant decrease in RD and trace in several brain regions in the concussed group, compared with the nonconcussed group (p
Karl G Helmer, Ofer Pasternak, Eli Fredman, Ronny I Preciado, Inga K Koerte, Takeshi Sasaki, Michael Mayinger, Andrew M Johnson, Jeffrey D Holmes, Lorie A Forwell, Elaine N Skopelja, Martha E Shenton, and Paul S Echlin. 2014. . J Neurosurg, 120, 4, Pp. 864-72.
OBJECT: Concussion, or mild traumatic brain injury (mTBI), is a commonly occurring sports-related injury, especially in contact sports such as hockey. Cerebral microbleeds (CMBs), which appear as small, hypointense lesions on T$_2$*-weighted images, can result from TBI. The authors use susceptibility-weighted imaging (SWI) to automatically detect small hypointensities that may be subtle signs of chronic and acute damage due to both subconcussive and concussive injury. The goal was to investigate how the burden of these hypointensities changes over time, over a playing season, and postconcussion, in comparison with subjects who did not suffer a medically observed and diagnosed concussion. METHODS: Images were obtained in 45 university-level adult male and female ice hockey players before and after a single Canadian Interuniversity Sports season. In addition, 11 subjects (5 men and 6 women) underwent imaging at 72 hours, 2 weeks, and 2 months after concussion. To identify subtle changes in brain tissue and potential CMBs, nonvessel clusters of hypointensities on SWI were automatically identified, and a hypointensity burden index was calculated for all subjects at the beginning of the season (BOS), the end of the season (EOS), and at postconcussion time points (where applicable). RESULTS: A statistically significant increase in the hypointensity burden, relative to the BOS, was observed for male subjects with concussions at the 2-week postconcussion time point. A smaller, nonsignificant rise in the burden for female subjects with concussions was also observed within the same time period. There were no significant changes in burden for nonconcussed subjects of either sex between the BOS and EOS time points. However, there was a statistically significant difference in the burden between male and female subjects in the nonconcussed group at both the BOS and EOS time points, with males having a higher burden. CONCLUSIONS: This method extends the utility of SWI from the enhancement and detection of larger (> 5 mm) CMBs, which are often observed in more severe cases of TBI, to cases involving smaller lesions in which visual detection of injury is difficult. The hypointensity burden metric proposed here shows statistically significant changes over time in the male subjects. A smaller, nonsignificant increase in the burden metric was observed in the female subjects.
Ofer Pasternak, Inga K Koerte, Sylvain Bouix, Eli Fredman, Takeshi Sasaki, Michael Mayinger, Karl G Helmer, Andrew M Johnson, Jeffrey D Holmes, Lorie A Forwell, Elaine N Skopelja, Martha E Shenton, and Paul S Echlin. 2014. . J Neurosurg, 120, 4, Pp. 873-81.
OBJECT: Concussion is a common injury in ice hockey and a health problem for the general population. Traumatic axonal injury has been associated with concussions (also referred to as mild traumatic brain injuries), yet the pathological course that leads from injury to recovery or to long-term sequelae is still not known. This study investigated the longitudinal course of concussion by comparing diffusion MRI (dMRI) scans of the brains of ice hockey players before and after a concussion. METHODS: The 2011-2012 Hockey Concussion Education Project followed 45 university-level ice hockey players (both male and female) during a single Canadian Interuniversity Sports season. Of these, 38 players had usable dMRI scans obtained in the preseason. During the season, 11 players suffered a concussion, and 7 of these 11 players had usable dMRI scans that were taken within 72 hours of injury. To analyze the data, the authors performed free-water imaging, which reflects an increase in specificity over other dMRI analysis methods by identifying alterations that occur in the extracellular space compared with those that occur in proximity to cellular tissue in the white matter. They used an individualized approach to identify alterations that are spatially heterogeneous, as is expected in concussions. RESULTS: Paired comparison of the concussed players before and after injury revealed a statistically significant (p
Tung Nguyen, Lucia Cevidanes, Beatriz Paniagua, Hongtu Zhu, Leonardo Koerich, and Hugo De Clerck. 2014. . Angle Orthod, 84, 2, Pp. 329-36.
OBJECTIVE: To evaluate the three-dimensional (3D) skeletal changes in the mandibles of Class III patients treated with bone-anchored maxillary protraction using shape correspondence analysis. MATERIAL AND METHOD: Twenty-five consecutive patients with skeletal Class III who were between the ages of 9 and 13 years (mean age, 11.10 ± 1.1 years) were treated using Class III intermaxillary elastics and bilateral miniplates (two in the infrazygomatic crests of the maxilla and two in the anterior mandible). Cone-beam computed tomography (CBCT) was performed for each patient before initial loading (T1) and at 1 year out (T2). From the CBCT scans, 3D models were generated, registered on the anterior cranial base, and analyzed using 3D linear distances and vectors between corresponding point-based surfaces. RESULTS: Bone-anchored traction produced anteroposterior and vertical skeletal changes in the mandible. The novel application of Shape correspondence analysis showed vectors of mean (± standard deviation) distal displacement of the posterior ramus of 3.6 ± 1.4 mm, while the chin displaced backward by 0.5 ± 3.92 mm. The lower border of the mandible at the menton region was displaced downward by 2.6 ± 1.2 mm, and the lower border at the gonial region moved downward by 3.6 ± 1.4 mm. There was a downward and backward displacement around the gonial region with a mean closure of the gonial angle by 2.1°. The condyles were displaced distally by a mean of 2.6 ± 1.5 mm, and there were three distinct patterns for displacement: 44% backward, 40% backward and downward, and 16% backward and upward. CONCLUSION: This treatment approach induces favorable control of the mandibular growth pattern and can be used to treat patients with components of mandibular prognathism.
Harini Veeraraghavan and James Miller. 2014. . Neuroinformatics, 12, 2, Pp. 245-59.
In this work, we present a faceted-search based approach for visualization of anatomy by combining a three dimensional digital atlas with an anatomy ontology. Specifically, our approach provides a drill-down search interface that exposes the relevant pieces of information (obtained by searching the ontology) for a user query. Hence, the user can produce visualizations starting with minimally specified queries. Furthermore, by automatically translating the user queries into the controlled terminology our approach eliminates the need for the user to use controlled terminology. We demonstrate the scalability of our approach using an abdominal atlas and the same ontology. We implemented our visualization tool on the opensource 3D Slicer software. We present results of our visualization approach by combining a modified Foundational Model of Anatomy (FMA) ontology with the Surgical Planning Laboratory (SPL) Brain 3D digital atlas, and geometric models specific to patients computed using the SPL brain tumor dataset.
Thomas L Chenevert, Dariya I Malyarenko, David Newitt, Xin Li, Mohan Jayatilake, Alina Tudorica, Andriy Fedorov, Ron Kikinis, Tiffany Ting Liu, Mark Muzi, Matthew J Oborski, Charles M Laymon, Xia Li, Yankeelov Thomas, Kalpathy-Cramer Jayashree, James M Mountz, Paul E Kinahan, Daniel L Rubin, Fiona Fennessy, Wei Huang, Nola Hylton, and Brian D Ross. 2014. . Transl Oncol, 7, 1, Pp. 65-71.
PURPOSE: To evaluate the ability of various software (SW) tools used for quantitative image analysis to properly account for source-specific image scaling employed by magnetic resonance imaging manufacturers. METHODS: A series of gadoteridol-doped distilled water solutions (0%, 0.5%, 1%, and 2% volume concentrations) was prepared for manual substitution into one (of three) phantom compartments to create "variable signal," whereas the other two compartments (containing mineral oil and 0.25% gadoteriol) were held unchanged. Pseudodynamic images were acquired over multiple series using four scanners such that the histogram of pixel intensities varied enough to provoke variable image scaling from series to series. Additional diffusion-weighted images were acquired of an ice-water phantom to generate scanner-specific apparent diffusion coefficient (ADC) maps. The resulting pseudodynamic images and ADC maps were analyzed by eight centers of the Quantitative Imaging Network using 16 different SW tools to measure compartment-specific region-of-interest intensity. RESULTS: Images generated by one of the scanners appeared to have additional intensity scaling that was not accounted for by the majority of tested quantitative image analysis SW tools. Incorrect image scaling leads to intensity measurement bias near 100%, compared to nonscaled images. CONCLUSION: Corrective actions for image scaling are suggested for manufacturers and quantitative imaging community.
Thomas Kahn, Ferenc A Jolesz, and Jonathan S Lewin. 2014. . 10th Interventional MRI Symposium, 10, Pp. 1-85.
Tina Kapur, Clare M. Tempany, and Ferenc A. Jolesz. 2014. . Image Guided Therapy Workshop, 7, Pp. 1-60.
Liangija Zhu, Ivan Kolesov, Yi Gao, Ron Kikinis, and Allen Tannenbaum. 2014. . Int Conf Med Image Comput Comput Assist Interv. Workshop on Interactive Methods., 17, WS.
Segmentation of anatomical structures in medical imagery is a key step in a variety of clinical applications. Designing a generic, automated method that works for various structures and imaging modalities is a daunting task. In this paper, we present an effective interactive segmentation method that reformulates the GrowCut algorithm as a clustering problem and computes a fast, approximate solution. The method is further improved by using an efficient updating scheme requiring only local computations when new user input becomes available, making it applicable to high resolution images. The algorithm may easily be included as a user-oriented software module in any number of available medical imaging/image processing platforms such as 3D Slicer. The efficiency and effectiveness of the algorithm are demonstrated through tests on several challenging data sets where it is also compared to standard GrowCut.