Processing Pipeline Details¶
Workflow¶
The Multi-Scale Brain Parcellator
pipelines uses a combination of tools from the well-known software packages FSL, FreeSurfer, ANTs as well as in-house tools from the Connectome Mapping ToolKit (CMTK).
Segmentation¶
Surfaces are extracted using Freesurfer.
T1 is segmented using Freesurfer.
Brainstem sub-structures are segmented using Freesurfer.
Hippocampal subfields are segmented using Freesurfer.
Thalamic nuclei are segmented using an in-house tool of CMTK which implement the probabilistic atlas-based thalamic segmentation method with the help of ANTs (See Najdenovska 2018 in Citing Section).
Parcellation¶
Desikan-Killiany brain parcellation is performed using Freesurfer.
5-Scale Brain parcellation is created according to Cammoun et al. 2012 (See Citing
) at 5 different scales.
All structures are then combined to create the final brain parcellation at each scale.