Patch-based label fusion segmentation of brainstem structures with dual-contrast MRI for Parkinson’s disease

  • Yiming XiaoEmail author
  • Vladimir S. Fonov
  • Silvain Beriault
  • Ian Gerard
  • Abbas F. Sadikot
  • G. Bruce Pike
  • D. Louis Collins
Original Article



Parkinson’s disease (PD) is a neurodegenerative disorder that impairs the motor functions. Both surgical treatment and study of PD require delineation of basal ganglia nuclei morphology. While many automatic volumetric segmentation methods have been proposed for the lentiform nucleus, few have attempted to identify the key brainstem substructures including the subthalamic nucleus (STN), substantia nigra (SN), and red nucleus (RN) due to their small size and poor contrast in conventional T1W MRI.


A dual-contrast patch-based label fusion method was developed to segment the SN, STN, and RN using multivariate cross-correlation. Two different MRI contrasts (T2*w and phase) are produced from a multi-contrast multi-echo FLASH MRI sequence, enabling visualization of these nuclei. T1–T2* fusion MRI was used to resolve the issue of poor nuclei (i.e., the STN, SN, and RN) contrast on T1w MRI, and to mitigate susceptibility artifacts that may hinder accurate nonlinear registration on T2*w MRI. Unbiased group-wise registration was used for anatomical normalization between the atlas library and the target subject. The performance of the proposed method was compared with a state-of-the-art single-contrast label fusion technique.


The proposed method outperformed a state-of-the-art single-contrast patch-based method in segmenting the STN, RN and SN, and the results were better than those reported in previous literature.


Our dual-contrast patch-based label fusion method was superior to a single-contrast method for segmenting brainstem nuclei using a multi-contrast multi-echo FLASH MRI sequence. The method is promising for the treatment and research of Parkinson’s disease. This method can be extended for multiple alternative image contrasts and other fields of applications.


Patch-based label-fusion Subthalamic nucleus Substantia nigra Red nucleus  Susceptibility-weighted imaging Parkinson’s disease 


Conflict of interest

Yiming Xiao, Vladimir Fonov, Silvain Bériault, Ian Gerard, Abbas F. Sadikot, G. Bruce Pike, and D. Louis Collins declare that they have no conflict of interest. All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration of 1975, as revised in 2008 (5). Informed consent was obtained from all patients for being included in the study.


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Copyright information

© CARS 2014

Authors and Affiliations

  • Yiming Xiao
    • 1
    Email author
  • Vladimir S. Fonov
    • 1
  • Silvain Beriault
    • 1
  • Ian Gerard
    • 1
  • Abbas F. Sadikot
    • 2
  • G. Bruce Pike
    • 3
  • D. Louis Collins
    • 1
  1. 1.McConnell Brain Imaging CenterMontreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
  2. 2.Division of NeurosurgeryMontreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
  3. 3.Department of Radiology and Clinical Neurosciences, Hotchkiss Brain InstituteUniversity of CalgaryCalgaryCanada

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