title: Quantitative comparison of cortical surface reconstructions from MP2RAGE and multi-echo MPRAGE data at 3 and 7 T.
abstract: The Magnetization-Prepared 2 Rapid Acquisition Gradient Echo (MP2RAGE) method achieves spatially uniform contrast across the entire brain between gray matter and surrounding white matter tissue and cerebrospinal fluid by rapidly acquiring data at two points during an inversion recovery, and then combining the two volumes so as to cancel out sources of intensity and contrast bias, making it useful for neuroimaging studies at ultrahigh field strengths (≥7T). To quantify the effectiveness of the MP2RAGE method for quantitative morphometric neuroimaging, we performed tissue segmentation and cerebral cortical surface reconstruction of the MP2RAGE data and compared the results with those generated from conventional multi-echo MPRAGE (MEMPRAGE) data across a group of healthy subjects. To do so, we developed a preprocessing scheme for the MP2RAGE image data to allow for automatic cortical segmentation and surface reconstruction using FreeSurfer and analysis methods to compare the positioning of the surface meshes. Using image volumes with 1mm isotropic voxels we found a scan-rescan reproducibility of cortical thickness estimates to be 0.15 mm (or 6%) for the MEMPRAGE data and a slightly lower reproducibility of 0.19 mm (or 8%) for the MP2RAGE data. We also found that the thickness estimates were systematically smaller in the MP2RAGE data, and that both the interior and exterior cortical boundaries estimated from the MP2RAGE data were consistently positioned within the corresponding boundaries estimated from the MEMPRAGE data. Therefore several measureable differences exist in the appearance of cortical gray matter and its effect on automatic segmentation methods that must be considered when choosing an acquisition or segmentation method for studies requiring cortical surface reconstructions. We propose potential extensions to the MP2RAGE method that may help to reduce or eliminate these discrepancies.
authors.affiliation: Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street, Suite 2301, Charlestown, MA 02129, USA.
authors.forename: Kyoko
authors.initials: K
authors.lastname: Fujimoto
authors.affiliation: Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street, Suite 2301, Charlestown, MA 02129, USA; Department of Radiology, Harvard Medical School, 55 Fruit St, Boston, MA 02114, USA. Electronic address: jonp@nmr.mgh.harvard.edu.
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Polimeni
authors.affiliation: Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street, Suite 2301, Charlestown, MA 02129, USA; Department of Radiology, Harvard Medical School, 55 Fruit St, Boston, MA 02114, USA.
authors.forename: André J W
authors.initials: AJ
authors.lastname: van der Kouwe
authors.affiliation: Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street, Suite 2301, Charlestown, MA 02129, USA; Department of Neurology, Massachusetts General Hospital, 15 Parkman Street, Boston, MA 02114, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Reuter
authors.affiliation: Laboratory for Functional and Metabolic Imaging, Ecole Polytechnique Fédérale de Lausanne, EPFL-SB-IPSB-LIFMET, Station 6, CH-1015 Lausanne, Switzerland; Advanced Clinical Imaging Technology, Siemens Suisse SA -CIBM, Lausanne, Switzerland.
authors.forename: Tobias
authors.initials: T
authors.lastname: Kober
authors.affiliation: Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street, Suite 2301, Charlestown, MA 02129, USA; Department of Radiology, Harvard Medical School, 55 Fruit St, Boston, MA 02114, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Benner
authors.affiliation: Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street, Suite 2301, Charlestown, MA 02129, USA; Department of Radiology, Harvard Medical School, 55 Fruit St, Boston, MA 02114, USA; Computer Science and AI Lab (CSAIL), Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA.
authors.forename: Bruce
authors.initials: B
authors.lastname: Fischl
authors.affiliation: Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 149 13th Street, Suite 2301, Charlestown, MA 02129, USA; Department of Radiology, Harvard Medical School, 55 Fruit St, Boston, MA 02114, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 45 Carleton Street, Cambridge, MA 02142, USA.
authors.forename: Lawrence L
authors.initials: LL
authors.lastname: Wald
mesh_terms: D001921:Brain / Q000033:anatomy & histology*; D001931:Brain Mapping / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging
keywords: Brain segmentation; Cortical thickness; FreeSurfer; Quantitative morphometry; Ultra high-field MRI