FreeSurfer 5.3

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.
    • A sub-selection of 85 relevant gray matter regions over the labels provided by the selected atlas is used for the final volumetry and cortical thickness table provided, in order to assure sensible outputs and comparability of analysis.
  • Volumetry (for each tissue type and parcellated regions).
  • Cortical thickness computation for cortical regions.

An additional step is taken after the script finishes and relevant outputs are acpc-aligned.

FreeSurfer output examples

Grey Matter Labels

Analysis Report

Required inputs:

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

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.


  • Report:
    • report.pdf: report file with results summary.
  • Images:
    • T1_original.nii.gz: the input T1 image used in the tool.
    • T1_acpc.nii.gz: preprocessed T1 image acpc-aligned.
    • T1strip.nii.gz: preprocessed and skull-stripped T1 image.
    • T1strip_bin.nii.gz: binary brain-extraction mask for the T1 image.
    • tissueSegmentation.nii.gz: 5-tissue (csf, gm, wm, brainstem, cerebellum) tissue segmentation image.
    • full_labeled.nii.gz: parcellated labels image, using all labels provided by the selected atlas.
    • labeled.nii.gz: label image with a selection of labels from of 85 relevant gray matter regions.
  •  Datasheets:
  •  Folders:

Typical execution time:

  • 7 hours.


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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