Freesurfer 6.0 Hippocampal Stream

Full morphology processing of a T1 anatomical image using FreeSurfer recon-all script [Dale et al. 1999] . Includes:

  • Image pre-processing: intensity normalization, skull-stripping.
  • Tissue segmentation into CSF, cortical grey matter, subcortical grey matter, white matter, brainstem and cerebellum.
  • Atlas-based parcellation and labelling using DKT40 scheme.
  • Cortical thickness computation for cortical regions.
  • Hippocampal Subfields Segmentation.

Volumetric report output samples


Fig 1 - Volumetric information


Fig 2 - Freesurfer recon-all segmentation

 

Platform results visualization:

 

  

Required inputs:

  • T1: anatomical 3D image
    • Isotropic resolution recommended
    • Must be labelled as 'T1' modality

Optional inputs:

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

Minimum input requirements:

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

Outputs:

  • Workflow main output:
    • T1.nii.gz: the input T1 image used in the tool.
    • Hippocampal_subfield_lh.nii.gz / hippocampal_subfield_rh.nii.gz: Hippocampal subfields segmentation files.
    • Hippocampal_subfields_volumes.csv: Volumetric information about hippocampal region volumes.
  • PostRECONALL step:
    • 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:

The tool will write the total left and right hippocampal volume in the session’s metadata.

Typical execution time:

  • 9 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.

 

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