Software Closed Access
Saranathan, Manojkumar; Iglehart, Charles; Monti, Martin; Tourdias, Thomas; Rutt, Brian
This version fixes a bug in the atlasseg script in Version 1.0. Please use this.
Data for the above titled paper being submitted to Scientific Data.
MNI space (152 asymmetric 09b)
MNIMaxProb_left.nii.gz and MNIMaxProb_right.nii.gz are the maximum probability (deterministic) thalamic nuclei atlas in MNI space
Note crop_mni_t1.nii.gz is the thalamus cropped MNI atlas provided for users for reference
Custom template space
Customtemplate.nii.gz - full size WMn MPRAGE custom (mean brain) template of 20 subjects (11 MS 9 healthy)
CustomAtlasMaxProb_left.nii.gz and CustomAtlasMaxProb_right.nii.gz are the maximum probability (deterministic) thalamic nuclei atlas in custom template space for left and righ tthalamus
CustomAtlasSpatialProbMap4D.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
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).
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
For research use only.
Files are not publicly accessible.