ANTs Workflow (2.3)

The ANTs workflow does a tissue segmentation and a cortical thickness analysis. Another step of this workflow performs an atlas-based cortical parcellation and derives the volume of each region, followed by the computation of the average and standard deviation of each region's thickness.

Captura de pantalla 2023-05-29 122927

The automated, volume-based Advanced Normalization Tools (ANTs) cortical thickness pipeline comprising well-vetted components such as:

  • SyGN (multivariate template construction)
  • SyN (image registration)
  • N4 (bias correction)
  • Atropos (n-tissue segmentation) 
  • DiReCT (cortical thickness estimation)

Click here to access the reference paper.

Captura de pantalla 2023-05-29 123219

The full workflow includes:

  • DICOM files to NIfTI conversion and reorientation to standard template images (MNI152).
  • ANTs cortical volumetry over the structural T1w image to extract the tissue segmentation file. Cortical thickness is optional.
  • Applies an atlas to the segmented mask of the cortex (gray matter + subcortical gray matter + brainstem + cerebellum).

Required inputs:

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

Minimum input requirements:

  • For optimal result reliability, an isotropic resolution is highly recommended
  • T1 recommended resolution: 1 mm isotropic.
    • T1 minimum reliable resolution: 2mm isotropic.



  • Check when data is skull stripped (checkbox): Enable this if the input data is skull stripped (default unchecked)
  • Change image resolution (checkbox): Changes the voxel size to isotropic resolution, defined in the next setting (default checked)
  • Isotropic voxel final size (mm) (integer): Define new isotropic resolution for the T1 image (default: 1)
  • ACPC alignment and remove subject face (checkbox): enable defacing step
  • Output transformation mat (checkbox): get the transformation matrix in the output container.


  • 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.
    • DCM2niix (Default)
    • Mrtrix
    • DCM2nii
    • diffunpack
    • MRIConvert (mcverter)
  • Reorient images to standard space (checkbox)


  • Compute thickness map (checkbox): Perform additional cortical thickness on T1 (default unchecked)


  • Brain atlas for parcellation (drop-down selection):
  • DKT40 (Mindboggle-101) (default)

Metadata results

This workflow is not adding results as metadata.

This tool provides the volume of 89 brain regions. 


  1. Avants BB, Epstein CL, Grossman M, Gee JC. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med Image Anal. 2008 Feb;12(1):26-41. Epub 2007 Jun 23.
  2. Avants BB, Tustison NJ, Song G, Cook PA, Klein A, Gee JC., A reproducible evaluation of ANTs similarity metric performance in brain image registration. Neuroimage. 2011 Feb 1;54(3):2033-44. doi: 10.1016/j.neuroimage.2010.09.025. Epub 2010 Sep 17.
  3. Avants B, Duda JT, Kim J, Zhang H, Pluta J, Gee JC, Whyte J. Multivariate analysis of structural and diffusion imaging in traumatic brain injury. Acad Radiol. 2008 Nov;15(11):1360-75. doi: 10.1016/j.acra.2008.07.007.
  4. Tustison NJ, Avants BB, Cook PA, Kim J, Whyte J, Gee JC, Stone JR. Logical circularity in voxel-based analysis: normalization strategy may induce statistical bias. Hum Brain Mapp. 2014 Mar;35(3):745-59. doi: 10.1002/hbm.22211. Epub 2012 Nov 14.


Create free account now!

Sign Up