title: Sodium 3D COncentration MApping (COMA 3D) using (23)Na and proton MRI.
abstract: Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/h concentration maps were generated on a personal computer (ca. 2012) using 21.1T 3D sodium MRI brain images of live rats with spatial resolution of 0.8×0.8×0.8 mm(3) and imaging matrices of 60×60×60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/.
authors.affiliation: Department of Radiology, Vanderbilt University Institute of Imaging Science (VUIIS), Nashville, TN 37232, USA. Electronic address: milton.truong@vanderbilt.edu.
authors.forename: Milton L
authors.initials: ML
authors.lastname: Truong
authors.affiliation: Huntington Medical Research Institutes, 99 North El Molino Ave, Pasadena, CA 91101, USA.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Harrington
authors.affiliation: National High Magnetic Field Laboratory (NHMFL), Florida State University, 1800 E Paul Dirac Drive, Tallahassee, FL 32310, USA.
authors.forename: Victor D
authors.initials: VD
authors.lastname: Schepkin
authors.affiliation: Department of Radiology, Vanderbilt University Institute of Imaging Science (VUIIS), Nashville, TN 37232, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232, USA. Electronic address: eduard.chekmenev@vanderbilt.edu.
authors.forename: Eduard Y
authors.initials: EY
authors.lastname: Chekmenev
mesh_terms: D000465:Algorithms; D000818:Animals; D001921:Brain / Q000473:pathology; D001923:Brain Chemistry; D001932:Brain Neoplasms / Q000378:metabolism / Q000473:pathology; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male; D008881:Migraine Disorders / Q000378:metabolism / Q000473:pathology; D011522:Protons; D051381:Rats; D017207:Rats, Sprague-Dawley; D012964:Sodium / Q000032:analysis* / Q000378:metabolism; D012975:Sodium Isotopes / Q000032:analysis*; D012984:Software
chemical_list: D011522:Protons; D012975:Sodium Isotopes; D012964:Sodium
keywords: (23)Na; 21.1T; 3D MRI; Concentration; Imaging; MATLAB; NMR; Sodium