Customized FreeSurfer-based brain atlas for diffeomorphic anatomical registration through exponentiated lie algebra tool



Digital brain template and atlas designed for a specific group provide advantages for the analysis and interpretation of neuroimaging data, but require a significant workload for development. We developed a simple method to create customized brain atlas for diffeomorphic anatomical registration through exponentiated lie algebra (DARTEL) tool using FreeSurfer-generated volume-of-interest (FSVOI) images and validated.


18F-florbetaben positron emission tomography (PET) and magnetic resonance (MR) imaging data were obtained from 248 participants of Alzheimer’s disease spectrum (from cognitively normal to Alzheimer’s disease dementia). To create a customized atlas, MR images of 84 amyloid-negative controls were first processed with FreeSurfer to obtain individual FSVOI and with DARTEL tool to create DARTEL template. Individual FSVOI images were spatially normalized, and each voxel was then labelled with a VOI label with maximum probability. Using these template and atlas, all images were normalized, and the regional standardized uptake value ratios (SUVR) were measured.


18F-florbetaben SUVR values measured with customized atlas showed excellent one-to-one correlation with SUVR measured with individual FSVOI in all regions, and thereby showed almost identical between-group comparison results and outperformed the classic methods.


Customized FreeSurfer-based brain atlas for DARTEL tool is easy to create and useful for the analysis of PET and MR images with high adaptability and reliability for broad research purposes.

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This research was supported by a grant from Korean Neurological Association (KNA-19-MI-12), faculty research Grant of Yonsei University College of Medicine for (6-2018-0068), Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning (NRF-2017R1A2B2006694) and the Ministry of Education (NRF-2018R1D1A1B07049386), and a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI) funded by the Ministry of Health & Welfare, Republic of Korea (Grant Number: HI18C1159).

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Correspondence to Young Hoon Ryu or Chul Hyoung Lyoo.

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Baek, M., Cho, H., Ryu, Y. et al. Customized FreeSurfer-based brain atlas for diffeomorphic anatomical registration through exponentiated lie algebra tool. Ann Nucl Med 34, 280–288 (2020).

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  • Atlas
  • Template
  • FreeSurfer
  • Magnetic resonance imaging
  • Positron emission tomography