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Ron Kikinis, MD
Associate Professor of Radiology
Harvard Medical School/Brigham & Women's Hospital






MRRC Project(s)

Neuroimaging Analysis Center

Research Description

Major Results

The Neuroimaging Analysis Center (NAC) is a computer science-based, application oriented image processing laboratory that is solidly established in a rich clinical environment. The Center represents a continuation and expansion of our ongoing efforts in the algorithmic domain, in basic and clinical applications. It has expanded our high performance computing facility, focusing on neuroimaging applications in the form of collaborative projects as well as providing training and educational support for the local, national and internal scientific community. We are disseminating the scientific and clinical tools developed within the NAC, making them available for a wide range of applications within and outside of the field of clinical neurosciences and neurosurgery. The main focus of the NAC is to develop post-processing methods for digital medical imaging data and to use these algorithms for clinical applications. The ultimate goal of the work conducted in the NAC is to have fully automated identification of relevant structures from the images for quantitative morphologic analysis of the brain and for visualization of these structures to be applied to: (1) interactive visualization during neurosurgery; (2) the identification and follow-up of white matter lesions in multiple sclerosis (MS); (3) the identification, quantification, visualization and follow-up of morphometric anomalies in Alzheimer's disease, (4) the identification, quantification, visualization and follow- up of morphometric anomalies in Schizophrenia. Three basic algorithmic approaches (segmentation, registration and visualization) are the Core Technologies which are advanced by the scientists of the Resource. The continuously expanding and improving interactive digital brain atlas serves as a basis for many of the algorithms and applications, as well as for teaching purposes. These Core Technologies are utilized for all Collaborative and Service Projects. The existing and continuously upgraded High Performance Computing (HPC) facilities of the Center are equally important as in infrastructure hardware resource. Algorithms that are used extensively in the day-to-day operation of the NAC are ported into state of the art cluster facilities. This significantly speeds up the execution of algorithms and improves availability and utilization of the resources. In the context of this proposal the presented primary applications of the technology to schizophrenia, multiple sclerosis, Alzheimer's disease and image guidance in neurosurgery are the major foci for three basic approaches to the extraction of information from images: quantitative manual, quantitative automated, and qualitative. These fundamental methods are also utilized in the planning and simulation of neurosurgical procedures, many of which ultimately take place in the operating room or within an open-MRI system. These major efforts along with and other, smaller, projects represent the foundation of the NAC. The NAC provides a vehicle to the dissemination of the results of our research to a larger user community.

Publications

Benson RR, Guttmann CR, Wei X, Warfield SK, Hall C, Schmidt JA, Kikinis R, Wolfson LI. Older people with impaired mobility have specific loci of periventricular abnormality on MRI. Neurology 2002;58:48-55.

Ferrant M, Nabavi A, Macq B, Black PM, Jolesz FA, Kikinis R, Warfield SK. Serial registration of intraoperative MR images of the brain. Med Image Anal 2002;6:337-359.

Fielding JR, Hoyte LX, Okon SA, Schreyer A, Lee J, Zou KH, Warfield S, Richie JP, O'Leary MP, Doyle CJ, Kikinis R. Tumor detection by virtual cystoscopy with color mapping of bladder wall thickness. J Urol 2002;167:559-562.

Fogel RB, Malhotra A, Dalagiorgou G, Robinson MK, Jakab M, Kikinis R, Pittman SD, White DP. Anatomic and physiologic predictors of apnea severity in morbidly obese subjects. Sleep 2003;26(2):150-5.

Frumin M, Golland P, Kikinis R, Hirayasu Y, Salisbury DF, Hennen J, Dickey CC, Anderson M, Jolesz FA, Grimson WE, McCarley RW, Shenton ME. Shape differences in the corpus callosum in first-episode schizophrenia and first-episode psychotic affective disorder. Am J Psychiatry 2002;159:866-868.

Hirose M, Bharatha A, Hata N, Zou KH, Warfield SK, Cormack RA, D'Amico A, Kikinis R, Jolesz FA, Tempany CM. Quantitative MR imaging assessment of prostate gland deformation before and during MR imaging-guided brachytherapy. Acad Radiol 2002;9:906-912.

Jaume S, Ferrant M, Macq B, Hoyte L, Fielding JR, Schreyer A, Kikinis R, Warfield SK. Tumor detection in the bladder wall with a measurement of abnormal thickness in CT scans. IEEE Trans Biomed Engr 2003;50:383-390.

Kasai K, Shenton ME, Salisbury DF, Hirayasu Y, Lee CU, Ciszewski AA, Yurgelun-Todd D, Kikinis R, Jolesz FA, McCarley RW. Progressive decrease of left superior temporal gyrus gray matter volume in patients with first-episode schizophrenia. Am J Psychiatry 2003;160:156-164.

Kasai K, Shenton ME, Salisbury DF, Hirayasu Y, Onitsuka T, Spencer MH, Yurgelun-Todd DA, Kikinis R, Jolesz FA, McCarley RW. Progressive decrease of left Heschl gyrus and planum temporale gray matter volume in first-episode schizophrenia: a longitudinal magnetic resonance imaging study. Arch Gen Psychiatry 2003;60(8):766-75.

Kasai K, Shenton ME, Salisbury DF, Onitsuka T, Toner SK, Yurgelun-Todd D, Kikinis R, Jolesz FA, McCarley RW. Differences and similarities in insular and temporal pole MRI gray matter volume abnormalities in first-episode schizophrenia and affective psychosis. Arch Gen Psychiatry 2003;60(11):1069-77.

Killiany RJ, Hyman BT, Gomez-Isla T, Moss MB, Kikinis R, Jolesz F, Tanzi R, Jones K, Albert MS. MRI measures of entorhinal cortex vs hippocampus in preclinical AD. Neurology 2002;58:1188-1196.

Kubicki M, Maier SE, Westin CF, 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.

Kubicki M, McCarley RW, Nestor PG, Huh T, Kikinis R, Shenton ME, Wible CG. An fMRI study of semantic processing in men with schizophrenia. Neuroimage 2003;20(4):1923-33.

Kubicki M, Shenton ME, Salisbury DF, Hirayasu Y, Kasai K, Kikinis R, Jolesz FA, McCarley RW. Voxel-based morphometric analysis of gray matter in first episode schizophrenia. Neuroimage 2002;17:1711-1719.

Kubicki M, Westin CF, Maier SE, Frumin M, Nestor PG, Salisbury DF, Kikinis R, Jolesz FA, McCarley RW, Shenton ME. Uncinate fasciculus findings in schizophrenia: a magnetic resonance diffusion tensor imaging study. Am J Psychiatry 2002;159:813-820.

Kubicki M, Westin CF, Maier SE, Mamata H, Frumin M, Ersner-Hershfield H, Kikinis R, Jolesz FA, McCarley R, Shenton ME. Diffusion tensor imaging and its application to neuropsychiatric disorders. Harv Rev Psychiatry 2002;10:324-336.

Kubicki M, Westin CF, Nestor PG, Wible CG, Frumin M, Maier SE, Kikinis R, Jolesz FA, McCarley RW, Shenton ME. Cingulate fasciculus integrity disruption in schizophrenia: a magnetic resonance diffusion tensor imaging study. Biol Psychiatry 2003;54(11):1171-80.

Lee CU, Shenton ME, Salisbury DF, Kasai K, Onitsuka T, Dickey CC, Yurgelun-Todd D, Kikinis R, Jolesz FA, McCarley RW. Fusiform gyrus volume reduction in first-episode schizophrenia: a magnetic resonance imaging study. Arch Gen Psychiatry 2002;59:755-781.

Levitt JJ, McCarley RW, Dickey CC, Voglmaier MM, Niznikiewicz MA, Seidman LJ, Hirayasu Y, Ciszewski AA, Kikinis R, Jolesz FA, Shenton ME. MRI study of caudate nucleus volume and its cognitive correlates in neuroleptic-naive patients with schizotypal personality disorder. Am J Psychiatry 2002;159:1190-1197.

Levitt JJ, Westin CF, Nestor PG, Estepar RS, 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.

Malhotra A, Huang Y, Fogel RB, Pillar G, Edwards JK, Kikinis R, Loring SH, White DP. The male predisposition to pharyngeal collapse: importance of airway length. Am J Respir Crit Care Med 2002;166(10):1388-95.

Mamata H, Mamata Y, Westin CF, Shenton ME, Kikinis R, Jolesz FA, Maier SE. High-resolution line scan diffusion tensor MR imaging of white matter fiber tract anatomy. AJNR 2002;23:67-75.

McCarley RW, Salisbury DF, Hirayasu Y, Yurgelun-Todd DA, Tohen M, Zarate C, Kikinis R, Jolesz FA, Shenton ME. Association between smaller left posterior superior temporal gyrus volume on magnetic resonance imaging and smaller left temporal P300 amplitude in first-episode schizophrenia. Arch Gen Psychiatry 2002;59:321-331.

Nabavi A, Gering DT, Kacher DF, Talos IF, Wells WM, Kikinis R, Black PM, Jolesz FA. Surgical navigation in the open MRI. Acta Neurochir 2003;85:121-125.

Onitsuka T, Shenton ME, Kasai K, Nestor PG, Toner SK, Kikinis R, Jolesz FA, McCarley RW. Fusiform gyrus volume reduction and facial recognition in chronic schizophrenia. Arch Gen Psychiatry 2003;60(4):349-55.

Park HJ, Kubicki M, Shenton ME, Guimond A, McCarley RW, Maier SE, Kikinis R, Jolesz FA, Westin CF. Spatial normalization of diffusion tensor MRI using multiple channels. Neuroimage 2003;20(4):1995-2009.

Rodt T, Ratiu P, Becker H, Bartling S, Kacher DF, Anderson M, Jolesz FA, Kikinis R. 3D visualisation of the middle ear and adjacent structures using reconstructed multi-slice CT datasets, correlating 3D images and virtual endoscopy to the 2D cross-sectional images. Neuroradiology 2003;44:783-790.

Ruiz-Alzola J, Westin CF, Warfield SK, Alberola C, Maier S, Kikinis R. Nonrigid registration of 3D tensor medical data. Med Image Anal 2002;6:143-161.

San Jose Estepar R, Alberola C, Ruiz J, Kikinis R, Westin CF. CF. Shape alignment based on phase spectrum and ICA. Eurocast 2003:63-66.

Schreyer AG, Herfarth H, Kikinis R, Seitz J, Scholmerich J, Geissler A, Feuerbach S. 3D modeling and virtual endoscopy of the small bowel based on magnetic resonance imaging in patients with inflammatory bowel disease. Invest Radiol 2002;37(9):528-33.

Shenton ME, Gerig G, McCarley RW, Szekely G, Kikinis R. Amygdala-hippocampal shape differences in schizophrenia: the application of 3D shape models to volumetric MR data. Psychiatry Res 2002;115(1-2):15-35.

Troulis MJ, Everett P, Seldin EB, Kikinis R, Kaban LB. Development of a three-dimensional treatment planning system based on computed tomographic data. Int J Oral Maxillofac Surg 2002;31(4):349-57.

Vaina LM, Cowey A, LeMay M, Bienfang DC, Kikinis R. Visual deficits in a patient with 'kaleidoscopic disintegration of the visual world'. Eur J Neurol 2002;9(5):463-77.

Warfield SK, Guimond A, Roche A, Bharatha A, Tei A, Talos F, Rexilius J, Ruiz-Alzola J, Westin C-F, Haker S, Angenent S, Tannenbaum A, Jolesz FA, Kikinis R. Advanced nonrigid registration algorithms for image fusion. In: Toga AW, Mazziotta JC, editors. Brain Mapping: The Methods. San Diego: Academic Press; 2002, 661-690.

Warfield SK, Talos F, Tei A, Bharatha A, Nabavi A, Ferrant M, Black PM, Jolesz FA, Kikinis R. Real-time registration of volumetric brain MRI by biomechanical simulation of deformation during image guided neurosurgery. Comput Visual Sci 2002;5:3-11.

Watanabe M, Kikinis R, Westin CF. Level set-based integration of segmentation and computational fluid dynamics for flow correction in phase contrast angiography. Acad Radiol 2003;10(12):1416-23.

Westin CF, Maier SE, Mamata H, Nabavi A, Jolesz FA, Kikinis R. Processing and visualization for diffusion tensor MRI. Med Image Anal 2002;6:93-108.

Wiegand LC, Warfield SK, Levitt JJ, Hirayasu Y, Salisbury DF, Heckers S, Dickey CC, Kikinis R, Jolesz FA, McCarley RW, Shenton ME. Prefrontal cortical thickness in first-episode psychosis: a magnetic resonance imaging study. Biol Psychiatry 2004;55(2):131-40.

Zou KH, Warfield SK, Bharatha A, Tempany CM, Kaus MR, Haker SJ, Wells WM, 3rd, Jolesz FA, Kikinis R. Statistical validation of image segmentation quality based on a spatial overlap index. Acad Radiol 2004;11(2):178-89.

Zou KH, Warfield SK, Fielding JR, Tempany CM, William MW, 3rd, Kaus MR, Jolesz FA, Kikinis R. Statistical validation based on parametric receiver operating characteristic analysis of continuous classification data. Acad Radiol 2003;10(12):1359-68.

Zou KH, Wells WM, 3rd, Kikinis R, Warfield SK. Three validation metrics for automated probabilistic image segmentation of brain tumours. Stat Med 2004;23(8):1259-82.

See Dr. Kikinis' publications via PubMed

Contact Information

Email: Ron Kikinis, MD
Associate Professor of Radiology
Harvard Medical School/Brigham & Women's Hospital