title: An improved FSL-FIRST pipeline for subcortical gray matter segmentation to study abnormal brain anatomy using quantitative susceptibility mapping (QSM).
abstract: Accurate and robust segmentation of subcortical gray matter (SGM) nuclei is required in many neuroimaging applications. FMRIB's Integrated Registration and Segmentation Tool (FIRST) is one of the most popular software tools for automated subcortical segmentation based on T1-weighted (T1w) images. In this work, we demonstrate that FIRST tends to produce inaccurate SGM segmentation results in the case of abnormal brain anatomy, such as present in atrophied brains, due to a poor spatial match of the subcortical structures with the training data in the MNI space as well as due to insufficient contrast of SGM structures on T1w images. Consequently, such deviations from the average brain anatomy may introduce analysis bias in clinical studies, which may not always be obvious and potentially remain unidentified. To improve the segmentation of subcortical nuclei, we propose to use FIRST in combination with a special Hybrid image Contrast (HC) and Non-Linear (nl) registration module (HC-nlFIRST), where the hybrid image contrast is derived from T1w images and magnetic susceptibility maps to create subcortical contrast that is similar to that in the Montreal Neurological Institute (MNI) template. In our approach, a nonlinear registration replaces FIRST's default linear registration, yielding a more accurate alignment of the input data to the MNI template. We evaluated our method on 82 subjects with particularly abnormal brain anatomy, selected from a database of >2000 clinical cases. Qualitative and quantitative analyses revealed that HC-nlFIRST provides improved segmentation compared to the default FIRST method.
authors.affiliation: Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany. Electronic address: xiang.feng@med.uni-jena.de.
authors.forename: Xiang
authors.initials: X
authors.lastname: Feng
authors.affiliation: Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany; Section of Experimental Neurology, Department of Neurology, Essen University Hospital, Essen, Germany; Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, Essen, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Deistung
authors.affiliation: Buffalo Neuroimaging Analysis Center, Dept. of Neurology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Dwyer
authors.affiliation: Buffalo Neuroimaging Analysis Center, Dept. of Neurology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States.
authors.forename: Jesper
authors.initials: J
authors.lastname: Hagemeier
authors.affiliation: Buffalo Neuroimaging Analysis Center, Dept. of Neurology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States.
authors.forename: Paul
authors.initials: P
authors.lastname: Polak
authors.affiliation: UNATI, CEA DRF/I2BM, INSERM, Université Paris-Sud, Université Paris-Saclay, NeuroSpin Center, Gif/Yvette, France.
authors.forename: Jessica
authors.initials: J
authors.lastname: Lebenberg
authors.affiliation: Inserm/CEA/Université Paris Sud/CNRS, CEA/I2BM/SHFJ, Laboratoire IMIV, Orsay, France.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Frouin
authors.affiliation: Buffalo Neuroimaging Analysis Center, Dept. of Neurology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States; MRI Molecular and Translational Imaging Center, Buffalo CTRC, State University of New York at Buffalo, Buffalo, NY, United States.
authors.forename: Robert
authors.initials: R
authors.lastname: Zivadinov
authors.affiliation: Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital - Friedrich Schiller University Jena, Jena, Germany; Center of Medical Optics and Photonics, Friedrich Schiller University Jena, Germany; Michael Stifel Center for Data-driven and Simulation Science Jena, Friedrich Schiller University Jena, Germany.
authors.forename: Jürgen R
authors.initials: JR
authors.lastname: Reichenbach
authors.affiliation: Buffalo Neuroimaging Analysis Center, Dept. of Neurology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States; MRI Molecular and Translational Imaging Center, Buffalo CTRC, State University of New York at Buffalo, Buffalo, NY, United States.
authors.forename: Ferdinand
authors.initials: F
authors.lastname: Schweser
mesh_terms: D000293:Adolescent; D000328:Adult; D001284:Atrophy / Q000473:pathology; D001921:Brain / Q000000981:diagnostic imaging* / Q000473:pathology; D001931:Brain Mapping / Q000379:methods*; D005260:Female; D066128:Gray Matter / Q000033:anatomy & histology / Q000000981:diagnostic imaging*; D064368:Healthy Volunteers; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male; D064847:Multimodal Imaging; D059906:Neuroimaging; D019047:Phantoms, Imaging; D015203:Reproducibility of Results; D012189:Retrospective Studies; D012680:Sensitivity and Specificity; D012984:Software; D055815:Young Adult
keywords: Brain; FIRST; MRI; Quantitative susceptibility mapping; Segmentation; Subcortical gray matter