GRP-43 ANTs DBM Cross Sectional

A Flywheel gear wrapping ANTs antsCorticalThickness.sh script. Within the antsCorticalThickness.sh pipeline, it performs bias correction using the N4 algorithm, segmentation using ANTs Atropos algorithm and cortical thickness calculation using these segmentations as input.

Usage

This gear should be run on Session level.

Inputs

• anatomical_image: Structural intensity image, typically T1 that will be used as anatomical image in antsCorticalThickness
• registered_predefined_template (zip archive file): (Optional) A zip archive that contains brain segmentation template, brain extraction probability mask, extraction registration mask, T1 registration template and brain segmentation priors. This file should be a zip archive that contains the following hierarchy:

  <working_dir_name>
  └── <template_folder_name>
      ├── Priors2
      │   ├── <nifti-file-name>
      │   ├── <nifti-file-name>
      │   ├── <nifti-file-name>
      │   ├── <nifti-file-name>
      │   ├── <nifti-file-name>
      │   └── <nifti-file-name>
      ├── brain_extraction_probability_mask
      │   └── <nifti-file-name>
      ├── brain_segmentation_template
      │   └── <nifti-file-name>
      ├── extraction_registration_mask
      │   └── <nifti-file-name>
      └── t1_registration_template
          └── <nifti-file-name>
  

As shown above, each directory should be labeled with one of the following names:

• Priors2
• brain_extraction_probability_mask
• brain_segmentation_template
• extraction_registration_mask
• t1_registration_template

Within each directory, it should contain only ONE template/mask image, except for the Priors2 directory.

Note: If registered predefined template is not provided, the gear will use the default atlases template which can be configured in the gear config (Default: OASIS-30_Atropos_template).

Configuration

• debug (boolean, default: False): Include debug statements in output.
• dimension (int, default: 3): 2 or 3 (for 2- or 3-dimensional image)
• denoise_anatomical_images (int, default: 1): Denoise anatomical images.
• max_iterations (str, default: "100x100x70x20"): ANTS registration max iterations
• prior_segmentation_weight (float, default: 0.25): Atropos spatial prior probability weight for the segmentation
• segmentation_iterations (int, default: 3): N4 -> Atropos -> N4 iterations during segmentation
• use_floatingpoint_precision (float, default: 0): Use single float precision in registrations
• b_spline_smoothing (boolean, default: True): Use B-spline SyN for registrations and B-spline exponential mapping in DiReCT
• atropos_iteration (int, default: 5): Number of iterations within Atropos
• atlases_template (string, default: OASIS-30_Atropos_template): If registered predefined template are not provided as an input, the gear will use this as the default predefined template.
• args: (string, default: None) Additional arguments

Contributing

For more information about how to get started contributing to that gear, checkout CONTRIBUTING.md.