If you are here for the "THOMAS atlas in MNI space", just use these two files for the left and right sides- Atlas-Thalamus_space-MNI_hemi-left_label-AllNuclei_desc-MaxProb.nii.gzAtlas-Thalamus_space-MNI_hemi-right_label-AllNuclei_desc-MaxProb.nii.gz 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: https://www.nature.com/articles/s41597-021-01062-y?proof=t%2Btarget%253D 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 https://github.com/thalamicseg/hipsthomasdocker 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.gzAtlas-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.gzAtlas-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.gzAtlas-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.gzAtlas-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 spaceAtlas-Thalamus_space-customWMN_label-AllNuclei_desc-SpatialProb4D.nii.gzThe 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.

Usage of atlasseg script (if you are using custom template instead of MNI for segmentation, the preferred method) 1. Download all of the above files in your favourite location e.g. ~/thalamicatlas 2. Set the environment variable ATLASPATH to that location. e.g. setenv ATLASPATH ~/thalamicatlas/code 3. You can copy the atlasseg script from ~/thalamicatlas to ~/bin if you like 4. Then invoke atlasseg with T1file as argument. e.g. atlasseg mprage.nii.gz thout If the second argument is omitted, it will put the output files in the current directory. To run a batch of T1 files, simply write a script to cd to each directory with the T1 file and run atlasseg T1filename Outputs: FusedLeft.nii.gz and FusedRight.nii.gz are the left and right nuclei segmentation. See CustomAtlas.ctbl file for label details. In addition 1l.nii.gz and 1r.nii.gz are the whole left and right thalami segmentation (label value 1) The nonlinear registration of custom template to input is ntemp2t1.nii.gz. Use this to check for registration accuracy. See atlasseg_README.txt also. A set of 5 testcases is also provided with WMn MPRAGE, MPRAGE and manual segmentation (see README inside the testcases.tgz for details)