Paper submitted to Scientific Data - Nature

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"In-vivo probabilistic atlas of human thalamic nuclei based on diffusion weighted magnetic resonance imaging"
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E. Najdenovska*, Y. Aléman-Gómez*, G. Battistella, M. Descoteaux, P. Hagmann, S. Jacquemont, P. Maeder, J.-P. Thiran, E. Fornari and M. Bach Cuadra

*Equally contributed authors


Copyright (c) - All rights reserved. University of Lausanne. 2018.



We provide NifTI-1 files representing a digital atlas of seven thalamic subparts per hemisphere. More precisely, the files include the spatial probabilistic atlas maps for each thalamic subpart (Thalamus_Nuclei-HCP-4DSPAMs.nii.gz) and the maximum likelihood atlas (Thalamus_Nuclei-HCP-MaxProb.nii.gz) in MNI space. The region corresponding to each labeled thalamic part respectively is given in the look-up table Thalamic_Nuclei-ColorLUT.txt.
The NIFTI files can be visualised with the main available tools such as tkmedit, freeview or 3D-Slicer.

We also provide a step by step pseudo code for creating the atlas.


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The atlas was build from a subset of the Human Connectome Project (HCP) database (https://db.humanconnectome.org). The IDs, age and gender of the HCP subjects whose images were used for the atlas construction are given in Description_HCPdata.txt.
The used HCP data is provided by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657) funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University.

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The atlas is provided in the MNI space corresponding to ICBM 2009a Nonlinear Symmetric – 1×1x1mm template (http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09a_nifti.zip).
Related references: 
[1] VS Fonov, AC Evans, K Botteron, CR Almli, RC McKinstry, DL Collins and BDCG, Unbiased average age-appropriate atlases for pediatric studies, NeuroImage,Volume 54, Issue 1, January 2011, ISSN 1053–8119, DOI: 10.1016/j.neuroimage.2010.07.033
[2] VS Fonov, AC Evans, RC McKinstry, CR Almli and DL Collins, Unbiased nonlinear average age-appropriate brain templates from birth to adulthood, NeuroImage, Volume 47, Supplement 1, July 2009, Page S102 Organization for Human Brain Mapping 2009 Annual Meeting, DOI: http://dx.doi.org/10.1016/S1053-8119(09)70884-5