Processing Pipeline Details


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).



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).



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.