ANTs Morphology (2.1.0)

Full morphology processing of a T1 anatomical image using the ANTs Cortical Thickness script [Tustison et al. 2014]. Includes:

  • Image pre-processing: bias field correction, skull-stripping.
  • acpc-alignment.
  • Tissue segmentation into CSF, cortical grey matter, subcortical grey matter, white matter, brainstem, and cerebellum.
  • Atlas-based parcellation and labeling: AAL Tzourio-Mazoyer et al., 2002 ; Rolls et al. 2015 .
    • A sub-selection of 85 relevant gray matter regions over the labels provided by the selected atlas is used for the volumetry and cortical thickness analysis, in order to assure sensible outputs and comparability of analysis.
  • Volumetry (for each tissue type and parcellated regions).
  • Cortical thickness computation for cortical regions.

ANTs output examples

Grey Matter Labels

Cortical Thickness

Analysis Report


Required inputs:

  • T1: anatomical 3D image
    Isotropic resolution recommended
    Must be labelled 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.


  • Preferred DICOM to Nifti conversion tool.
    The selected tool will be tried first to convert DICOM to nifti. If the conversion fails, the other options will be tried sequentially until a successful conversion.
    • Mrtrix (Default)
    • DCM2nii
    • diffunpack

  • Brain Atlas for parcellation.
    Template and labeled atlas used to parcellate grey matter regions.
    • AAL
  • Skip thickness computation.
    • If checked does not compute cortical thickness measures. Significantly reduces computation time.


  • 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.
    • T1mask.nii.gz: binary brain-extraction mask for the T1 image.
    • GM.nii.gz: gray matter tissue mask.
    • WM.nii.gz: white matter tissue mask.
    • CSF.nii.gz: cerebrospinal fluid tissue mask.
    • 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.
    • thickness.nii.gz: cortical thickness values image (not present if thickness computation is de-selected).
  •  Datasheets:
  •  Folders:
    • ANTS: Folder with full outputs of the ANTs script.

Typical execution time:

  • 3 hours (with cortical thickness computation).
  • 25 minutes (without cortical thickness computation).

Additional details:

  • Cortical thickness computation is the most time-consuming step of this tool, if not required, select to skip this step and the tool will be completed in a fraction of the time.



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