Anatomy pre-processing

Performs basic pre-processing of a T1 anatomical image, including bias-field correction (to compensate for magnetic field inhomogeneities), acpc-alignment and resampling to isotropic resolution if required.
It also performs de-facing: anonymization fo the image by removing the voxels around the face.
A T2 image can be additionally selected as optional input, the image will be co-registered with the T1, and defaced.

Pre-processed and anonymized T1 and T2 outputs


Required inputs:

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

Optional inputs:

  • T2: anatomical 3D image
    Isotropic resolution recommended
    Must be labeled as 'T2' modality

Minimum input requirements:

  • Images 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.


  • DICOM conversion
    • 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 (min: 0.5, max: 3)
  • Image correction
    • Bias field correction (checkbox)
      • If set will perform bias-field correction on the data to correct field homogeneities (Default: checked)
  •  Alignment
    • AC-PC alignment + de-facing (single choice)
      • AC-PCP + de-face (Default)
      • AC-PC only
      • None
    • Alignment tool (drop-down selection)
      • ANTs (Default)
      • FLIRT/FSL
    • Skull-stripped data (checkbox)
      • If set the tool will take into account the data has been brain-extracted: otherwise the AC-PC alignment might fail for skull-stripped datasets (Default: unchecked)


  • Images:
    • T1_acpc_defaced.nii.gz: the pre-processed output T1
    • T2_acpc_defaced.nii.gz: the pre-processed output T2 (if optional T2 input was given).

Typical execution time:

  • 7 minutes



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