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      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.

      Settings:

      • 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)

      Outputs:

      • 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

      References:

       

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