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

This version uses only control data (as opposed to a mix of control and MS data) in Version 2.0 to create the atlas. Data for the above titled paper being submitted to Scientific Data. MNI space (152 asymmetric 09b) MNI_MaxProb_Left.nii.gz and MNI_MaxProb_Right.nii.gz are the maximum probability (deterministic) thalamic nuclei atlas in MNI space. MNI_VIM_Left and MNI_VIM_Right are VIM nuclei (ventral part of VLP in Morel notation) in MNI space Note crop_mni_t1.nii.gz is the thalamus cropped MNI atlas provided to users for reference Custom template space Customtemplate.nii.gz - full size WMn MPRAGE custom (mean brain) template of 20 subjects (11 MS 9 healthy) CustomWMN_MaxProb_Left.nii.gz and CustomWMN_MaxProb_Right.nii.gz are the maximum probability (deterministic) thalamic nuclei atlas in custom template space for left and right thalamus CustomWMN_SpatialProbMap4D.nii.gz is the spatial probability map in custom template space for each of the 11 left and 11 right nuclei (4th dimension). See SpatialProbMap_descr.txt for the order and names of the nuclei CustomWMN_VIM_Left and CustomWMN_VIM_Right are VIM nuclei (ventral part of VLP in Morel notation) in custom template space CustomAtlas.ctbl is a color table file that can be used to standardize colors (read by Slicer,fsleyes 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. atlasseg is a tcsh script that can be used to segment your T1 data (see Notes below or atlas_README.txt for usage) Remaining files are used for atlas based segmentation (cropped custom template, mask used to crop the template etc) and uncrop.py is to changed the script output to full size testdata.tgz is a set of 5 test cases (subset of what was used for testing the atlas). Details inside in the README file. Copyright Manojkumar Saranathan 2020, 2021 For research use only and not 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 3. You can move the atlasseg script from ~/thalamicatlas to ~/bin if you like 4. Then invoke atlasseg T1file 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