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).

_images/multiscalebrainparcellator.png

Segmentation

Surfaces are extracted using Freesurfer.

_images/ex_segmentation1.png

T1 is segmented using Freesurfer.

_images/ex_segmentation2.png

Brainstem sub-structures are segmented using Freesurfer.

_images/sag_brainstemSS.png

Hippocampal subfields are segmented using Freesurfer.

_images/sag_hippsub.png

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).

_images/ax_thalamus.png

Parcellation

Desikan-Killiany brain parcellation is performed using Freesurfer.

_images/aparcaseg.png

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.

_images/multiscaleparcellation.png