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      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.

      Settings:

      • 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).

      Outputs:

      • 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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      References: