FreeSurfer 6.0 with Brainstem Substructures

Full morphological processing of a T1 anatomical image using FreeSurfer's recon-all script [Dale et al. 1999], including integration of the additional Brainstem Substructures module. This module uses a Bayesian segmentation algorithm to segment four further brainstem regions in addition to the volumetric processing undergone in the standard FreeSurfer pipeline. More information can be found here.

The workflow includes:

  • Image pre-processing: bias field correction, skull-stripping.
  • Automated whole-brain tissue segmentation into CSF, cortical grey matter, subcortical grey matter, white matter, brainstem and cerebellum.
  • Atlas-based full cortex parcellation and labeling using DKT40 scheme.
  • Subcortical volumetry
  • Cortical thickness computation for cortical regions.
  • Optional full-head T2 or T2 FLAIR input to improve pial surface estimation.
  • Automated segmentation of four additional brainstem structures: medulla oblongata, pons, midbrain and superior cerebellar peduncle.
  • Comprehensive volumetric report including brainstem substructures.

Volumetric report output examples

Figure 1 - Freesurfer recon-all segmentation

Figure 2 - Brainstem substructures segmentation

Figure 3 - Volumetric information of brainstem substructures

Required inputs:

  • T1
    • Anatomical 3D image
    • Isotropic resolution recommended
    • Must be labeled as 'T1' modality

Optional inputs:

  • T2
    • Anatomical 3D image
    • Isotropic resolution recommended
    • Must be labeled as 'T2' modality
  • T2 FLAIR
    • Anatomical 3D image
    • Isotropic resolution recommended
    • Must be labeled as 'T2' modality and have a ‘flair’ tag

Minimum input requirements:

  • Image must contain full skull (not brain extracted).
  • For optimal results reliability, isotropic resolution is recommended.
    • Recommended resolution: 1 mm isotropic.
    • Minimum reliable resolution: 2 mm isotropic.

Outputs:

  • Workflow main output:
    • report.pdf: report file with results summary.
    • Aseg_stats CSV files: Freesurfer volumetry and thickness complete results.
    • Volumetric.csv: CSV file with gray matter parcellated regions volume and cortical thickness information
  • Images in RECONALL step:
    • T1.nii.gz: the input T1 image used in the tool.
    • T1brain.nii.gz: preprocessed T1 image acpc-aligned.
    • labeled.nii.gz: preprocessed and skull-stripped T1 image.
    • tissueSegmentation.nii.gz: 5-tissue (csf, gm, wm, brainstem, cerebellum) tissue segmentation image.
    • Folders:
  • Brainstem Substructures output:
    • T1.nii.gz
    • brainstemSs_voxelspace.nii.gz
    • brainstem_substructures_volume.csv
    • FREESURFER output folder

Typical execution time:

  • 8 hours.

References:

License Information:

  • Users of this tool should be in possession of a FreeSurfer license. Obtaining a license is free and comes in the form of a license.txt file.
  • More information on the FreeSurfer license can be found here.
  • Follow this link to obtain a license key.