Custom morphology

Full morphology processing of a T1 anatomical image using an array of tools where the user can customize the preferred tool for each step of the pipeline.
This tool can use age-matched templates for tissue and region parcellation priors – using the information from the Age-at-scan field – for subjects between 3 months and 17 years-old, making it especially suited for children and young adult data.
The morphology pipeline Includes the following steps:

  • Skull-stripping
  • Bias-field correction
  • AC-PC alignment to template.
  • Tissue segmentation into CSF, gray matter and white matter.
  • Atlas-based parcellation and labeling using LPBA40 56-region parcellation scheme Shattuck et al. 2008 .
  • Volumetry (for each tissue type and parcellated regions).
  • Cortical thickness computation for cortical regions.

    Custom Morphology output examples

Grey Matter Labels

Cortical Thickness

Analysis Report

Required inputs:

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

Minimum input requirements:

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


  • NIfTI converter
    • Preferred DICOM to NIfTI conversion tool (drop-down selection)
      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)
      • bru2nii
      • DCM2nii
      • mcverter
      • diffunpack
  • Resampling
    • Isotropic resolution (mm) (decimal) (Default: 1)
      Choose the desired output isotropic resolution in mm. A 0 value will resample to the highest resolution dimension of the input data.
  • Registration
    • Select tool for image registrations (drop-down selection)
      • ANTs (Default) 
      • FSL
    • AC-PC alignment (checkbox)
      If checked the image is AC-PC aligned (Default checked).
  • Skull-Stripping
    • T1 Skull-stripping tool (drop-down selection)
      • ROBEX (Default) 
      • optiBET
      • ROptibeX (the addition of both ROBEX and Optibet masks)
      • AFNI
      • BET
      • Brainsuite
    • Additional skull-stripping parameters (string)
      String with additional command parameters for the skull stripping tool. Optional (Default empty).
  • Tissue Segmentation
    • Select tool for segmentation (drop-down selection)
      • ANTs (Default) 
      • FreeSurfer v5.3.0
    • Atropos (ANTs) segmentation parameters (string)
      String with additional command parameters for the skull stripping tool. Optional (Default "-m 2 -n 20 -w 0.25 ").
  • Cortical Thickness
    • Cortical thickness (checkbox)
      If checked computes cortical thickness measures. Significantly increases computation time (Default checked).


  • Report:
    • report.pdf: report file with results summary.
  • Images:
    • 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.
    • T1_act.nii.gz: image containing the different segmented tissues as separate volumes.
    • tissueSegmentation.nii.gz: 5-tissue (csf, gm, wm, brainstem, cerebellum) tissue segmentation image.
    • atlas_registered.nii.gz: template atlas labels registered into subject space.<
    • 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:

Typical execution time:

  • 4 hours (with cortical thickness computation).
  • 1 hour (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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