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BetSurfacesExtraction brick

Surfaces (skull, inskull, outskull, outskin) extraction using BET (FSL)

Both bet2 and betsurf programs are used in order to get skull and scalp surfaces created by betsurf (fsl BET -A option) This involves registering to standard space in order to allow betsurf to find the standard space masks it needs.

The mask and mesh files (.vtk) are generated.

Mandatory inputs parameters:

  • in_file (a string representing an existing file)

    Input file to skull strip. An existing file (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/T1w.nii'

Optional inputs with default value parameters:

  • output_type (‘NIFTI’ or ‘NIFTI_GZ’, optional, default value is NIFTI)
    Format of the output image (one of NIFTI, NIFTI_GZ).
    - NIFTI: *.nii
    - NIFTI_GZ: *.nii.gz
    ex. NIFTI

Outputs parameters:

  • inskull_mask_file (a pathlike object or string representing a file)

    Inskull mask (extensions: [.nii, .nii.gz])

    ex. '/home/username/data/derived_data/T1w_brain_inskull_mask.nii'
  • inskull_mesh_vtk_file (a pathlike object or string representing a file)

    Inskull mesh (extensions [.nii, .nii.gz])

    ex. '/home/username/data/derived_data/T1w_brain_inskull_mesh.nii'
  • inskull_mesh_vtk_file (a pathlike object or string representing a file)

    Inskull mesh (extensions [.vtk])

    ex. '/home/username/data/derived_data/T1w_brain_inskull_mesh.vtk'
  • out_file (a pathlike object or string representing a file)

    Skullstripped file (extensions: [.nii, .nii.gz])

    ex. '/home/username/data/derived_data/T1w_brain.nii'
  • outskin_mask_file (a pathlike object or string representing a file)

    Outskin mask (extensions: [.nii, .nii.gz])

    ex. '/home/username/data/derived_data/T1w_brain_outskin_mask.nii'
  • outskin_mesh_file (a pathlike object or string representing a file)

    Outskin mesh (extensions [.nii, .nii.gz])

    ex. '/home/username/data/derived_data/T1w_brain_outskin_mesh.vtk'
  • outskin_mesh_vtk_file (a pathlike object or string representing a file)

    Outskin mesh (extensions [.vtk])

    ex. '/home/username/data/derived_data/T1w_brain_outskin_mesh.vtk'
  • outskull_mask_file (a pathlike object or string representing a file)

    Outskull mask (extensions: [.nii, .nii.gz])

    ex. '/home/username/data/derived_data/T1w_brain_outskull_mask.nii'
  • outskull_mesh_vtk_file (a pathlike object or string representing a file)

    Outskull mesh (extensions [.vtk])

    ex. /home/username/data/derived_data/T1w_brain_outskull_mesh.vtk
  • outskull_mesh_file (a pathlike object or string representing a file)

    Outskull mesh (extensions [.nii, .nii.gz])

    ex. /home/username/data/derived_data/T1w_brain_outskull_mesh.vtk
  • skull_mask_file (a pathlike object or string representing a file)

    Skull mask (extensions: [.nii, .nii.gz])

    ex. '/home/username/data/derived_data/T1w_brain_skull_mask.nii'

Useful links:

FSL BET

FSL BET - nipype