Data for In vivo structural MRI-based atlas of human thalamic nuclei

  • Manojkumar Saranathan (Contributor)
  • Charles Iglehart (Contributor)
  • Martin M. Monti (Contributor)
  • Thomas Tourdias (Contributor)
  • Brian K. Rutt (Contributor)



This version uses only control data (as opposed to a mix of control and MS data) in Version 2.0 to create the atlas. It also packages the files in a single zip file with BIDS format nomenclature in this version compared to Version 3.0. Details are in README.txt and also reproduced here. Data for the above titled paper being submitted to Scientific Data. Paper accepted Oct 2021. Link: IMPORTANT NOTE: This atlas is mostly for doing fMRI or DTI analysis in MNI space. For native segmentation of thalamic nuclei in individual subject space, please use the THOMAS segmentation scheme directly. THOMAS be found at and this version can handle both T1 data and WMn (FGATIR) data. MNI space (152 asymmetric 09b) We provide digital atlases in MNI space for maximum probability maps for left and right sides- Atlas-Thalamus_space-MNI_hemi-left_label-AllNuclei_desc-MaxProb.nii.gz Atlas-Thalamus_space-MNI_hemi-right_label-AllNuclei_desc-MaxProb.nii.gz We also provide the maximum probability maps for the left and right VIM in the same MNI space- Atlas-Thalamus_space-MNI_hemi-left_label-VIM_desc-MaxProb.nii.gz Atlas-Thalamus_space-MNI_hemi-right_label-VIM_desc-MaxProb.nii.gz These MNI atlases are at 0.5x0.5x0.5 mm resolution with 394x466x378 matrix. Custom template space We provide these atlases in custom WMn MPRAGE template space for maximum probability maps for left and right sides- Atlas-Thalamus_space-customWMN_hemi-left_label-AllNuclei_desc-MaxProb.nii.gz Atlas-Thalamus_space-customWMN_hemi-right_label-AllNuclei_desc-MaxProb.nii.gz We also provide the maximum probability map for the left and right VIM in the custom WMn template space- Atlas-Thalamus_space-customWMN_hemi-left_label-VIM_desc-MaxProb.nii.gz Atlas-Thalamus_space-customWMN_hemi-right_label-VIM_desc-MaxProb.nii.gz The custom WMn template atlases are at 0.7x0.7x0.5 mm resolution with 256x256x440 matrix. Lastly, we also provide a spatial probability map in custom WMn template space Atlas-Thalamus_space-customWMN_label-AllNuclei_desc-SpatialProb4D.nii.gz The description of this file is in SpatialProbMap4D_descr.txt CustomAtlas.ctbl is a color table file that can be used to standardize colors (read by 3D-Slicer, freeview etc). It also maps the labels to nuclei names (e.g. 2-AV 4-VA.... 14-MTT). For this atlas, only 2-14 are used. Code is provided as a courtesy that will enable segmentation of user specified T1 data from the custom WMn template. This can be found under the code subdirectory (script name atlasseg, see atlasseg_README.txt for usage details) testcases.tgz is a set of 5 test cases (subset of what was used for testing the atlas). Details inside in the README file in testcases folder. For each case, the standard T1 and WMn MPRAGE are provided as csfn.nii.gz and wmn.nii.gz and manualsegs directory contains the left side thalamic segmentation performed manually on the WMn MPRAGE data by a neuroradiologist. Copyright Manojkumar Saranathan 2020, 2021, 2022, 2023 Note that this atlas has not been tested or validated for clinical use.
Date made availableNov 15 2021

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