Revisiting the Role of Structural Connectivity-Based Parcellation in Thalamic Nuclei Segmentation: Benchmarking Against Recent State-of-the-Art Methods.

Dataset Description This repository contains scripts, atlas label definitions, subject identifiers, and MNI-space neuroimaging atlas files used for connectivity-based parcellation (CBP) analyses that are associated with the paper titled " Revisiting the Role of Structural Connectivity-Based Parcellation in Thalamic Nuclei Segmentation: Benchmarking Against Recent State-of-the-Art Methods" that is in press with PlosOne. The MRI data used is from Human Connectome Project Young Adult (HCP-YA) 1200 Subjects database which users have to get permission on their own to download. We just provide the subject IDs used in our analyses. For the Glasser, we used a volumetric rather than surface version and simplified to 8/11/23 regions. The 23-region atlas is essentially the 22-region atlas but splitting motor and somatosensory cortices. We further combined regions to create a simple 8-region made up of frontal, prefrontal, premotor, motor, sensory, occipital, temporal, parietal. The 11-region is a compromise between 8 and 23. The exact regions and the constituent Glasser nuclei can be found in the medrxiv preprint. We provide the 3 atlases in ICBM 2009a Nonlinear Asymmetric MNI space and also scripts that can be used to warp this into native T1 space. Contents Subject and Label Information subjectid.csvContains the 'Human Connectome Project Young Adult (HCP-YA) 1200 Subjects' subject identifiers used in the analyses. labelid.csvMaps numerical label values to their corresponding anatomical or parcellation labels for the 8-, 11-, and 23-Label Glasser Volumetric Atlas. Parcellation Scripts The following shell scripts perform connectivity-based parcellation analyses using different labeling schemes: 8parcellation.shGenerates an 8-region Glasser parcellation.. 11parcellation.shGenerates an 11-region Glasser parcellation. 23parcellation.shGenerates a 23-region Glasser parcellation. These scripts are provided as reference implementations and may require modification depending on local software installations, file paths, and computing environments. Atlas Files 8-Label Atlas glassvolume_8label_mni.nii.gz Volumetric Glasser atlas in ICBM 2009a Nonlinear Asymmetric MNI space containing 8 labels. The file is provided in NIfTI format and can be viewed using common neuroimaging software such as 3D Slicer. 11-Label Atlas glassvolume_11label_mni.nii.gz Volumetric Glasser atlas in ICBM 2009a Nonlinear Asymmetric MNI space containing 11 labels. The file is provided in NIfTI format and can be viewed using common neuroimaging software such as 3D Slicer. 23-Label Atlas glassvolume_23label_mni.nii.gz Volumetric Glasser atlas in ICBM 2009a Nonlinear Asymmetric MNI space containing 23 labels. The file is provided in NIfTI format and can be viewed using common neuroimaging software such as 3D Slicer. Users should consult the accompanying publication and analysis scripts for methodological details regarding atlas generation and validation.