Improved segmentation of deep brain grey matter structures using magnetization transfer (MT) parameter maps

Basal ganglia and brain stem nuclei are involved in the pathophysiology of various neurological and neuropsychiatric disorders. Currently available structural T1-weighted (T1w) magnetic resonance images do not provide sufficient contrast for reliable automated segmentation of various subcortical grey matter structures. We use a novel, semi-quantitative magnetization transfer (MT) imaging protocol that overcomes limitations in T1w images, which are mainly due to their sensitivity to the high iron content in subcortical grey matter. We demonstrate improved automated segmentation of putamen, pallidum, pulvinar and substantia nigra using MT images. A comparison with segmentation of high-quality T1w images was performed in 49 healthy subjects. Our results show that MT maps are highly suitable for automated segmentation, and so for multi-subject morphometric studies with a focus on subcortical structures.

[1]  Line Garnero,et al.  Dystonia: Lessons from Brain Mapping , 2003, The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry.

[2]  P. Dechent,et al.  Quantitative FLASH MRI at 3T using a rational approximation of the Ernst equation , 2008, Magnetic resonance in medicine.

[3]  Karl J. Friston,et al.  Voxel-Based Morphometry—The Methods , 2000, NeuroImage.

[4]  P. Strick,et al.  Basal Ganglia Output and Cognition: Evidence from Anatomical, Behavioral, and Clinical Studies , 2000, Brain and Cognition.

[5]  Nick C Fox,et al.  Computer-assisted imaging to assess brain structure in healthy and diseased brains , 2003, The Lancet Neurology.

[6]  John Ashburner,et al.  A fast diffeomorphic image registration algorithm , 2007, NeuroImage.

[7]  Daniela Berg,et al.  Role of Iron in Neurodegenerative Disorders , 2006, Topics in magnetic resonance imaging : TMRI.

[8]  C D Frith,et al.  Functional Anatomy of Obsessive–Compulsive Phenomena , 1994, British Journal of Psychiatry.

[9]  P. Strick,et al.  The Organization of Cerebellar and Basal Ganglia Outputs to Primary Motor Cortex as Revealed by Retrograde Transneuronal Transport of Herpes Simplex Virus Type 1 , 1999, The Journal of Neuroscience.

[10]  A. Parent,et al.  Functional anatomy of the basal ganglia. I. The cortico-basal ganglia-thalamo-cortical loop , 1995, Brain Research Reviews.

[11]  Karl J. Friston,et al.  Computing average shaped tissue probability templates , 2009, NeuroImage.

[12]  Karl J. Friston,et al.  Unified segmentation , 2005, NeuroImage.

[13]  E. Haacke,et al.  Imaging iron stores in the brain using magnetic resonance imaging. , 2005, Magnetic resonance imaging.

[14]  P. Dechent,et al.  High‐resolution maps of magnetization transfer with inherent correction for RF inhomogeneity and T1 relaxation obtained from 3D FLASH MRI , 2008, Magnetic resonance in medicine.

[15]  S. Haber.  The primate basal ganglia: parallel and integrative networks , 2003, Journal of Chemical Neuroanatomy.

[16]  G Helms,et al.  Multi-parameter mapping of the human brain at 1mm resolution in less than 20 minutes , 2008 .

[17]  G. Percheron,et al.  The Basal Ganglia Related System of Primates: Definition, Description and Informational Analysis , 1994 .

[18]  Christian Gaser,et al.  Magnetic resonance-based morphometry: a window into structural plasticity of the brain , 2006, Current opinion in neurology.

[19]  P. Dechent,et al.  Increased SNR and reduced distortions by averaging multiple gradient echo signals in 3D FLASH imaging of the human brain at 3T , 2009, Journal of magnetic resonance imaging : JMRI.

[20]  Reeti Tandon,et al.  High-field Magnetic Resonance Imaging of Brain Iron in Alzheimer Disease , 2006, Topics in magnetic resonance imaging : TMRI.

[21]  P. Strick,et al.  Anatomical evidence for cerebellar and basal ganglia involvement in higher cognitive function. , 1994, Science.

[22]  A. Graybiel.  The basal ganglia , 1995, Trends in Neurosciences.

[23]  P. Strick,et al.  New concepts about the organization of basal ganglia output. , 1997, Advances in neurology.

[24]  R I Grossman,et al.  Experimental allergic encephalomyelitis and multiple sclerosis: lesion characterization with magnetization transfer imaging. , 1992, Radiology.

[25]  André J. W. van der Kouwe,et al.  Reliability of MRI-derived cortical and subcortical morphometric measures: Effects of pulse sequence, voxel geometry, and parallel imaging , 2009, NeuroImage.

[26]  P. Strick,et al.  Basal-ganglia 'projections' to the prefrontal cortex of the primate. , 2002, Cerebral cortex.

[27]  Bostjan Likar,et al.  A Review of Methods for Correction of Intensity Inhomogeneity in MRI , 2007, IEEE Transactions on Medical Imaging.

[28]  R Turner,et al.  Optimisation of the 3D MDEFT sequence for anatomical brain imaging: technical implications at 1.5 and 3 T , 2004, NeuroImage.

[29]  Martin Lévesque,et al.  Organization of the basal ganglia: the importance of axonal collateralization , 2000, Trends in Neurosciences.

[30]  Peter Dechent,et al.  Erratum to Helms, Dathe, and Dechent. Quantitative FLASH MRI at 3 tesla using a rational approximation of the ernst equation. Magn Reson Med 2008;59:667–672. , 2010 .

[31]  M. A. Basso,et al.  The basal ganglia: An overview of circuits and function , 2008, Neuroscience & Biobehavioral Reviews.

[32]  E. G. Jones,et al.  A new parcellation of the human thalamus on the basis of histochemical staining , 1989, Brain Research Reviews.

[33]  Anders M. Dale,et al.  An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest , 2006, NeuroImage.

[34]  R G Steen,et al.  Age‐related changes in Brain T1 are correlated with iron concentration , 1998, Magnetic resonance in medicine.