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Anat_skullstrip pipeline

Bias correction and skull stripping of a structural image

Pipeline insight

Anat_skullstrip pipeline combines the following pipelines and processes:
- Bias field correction (using ANTs N4BiasFieldCorrection)
(default: dimension = 3)
- Skull Stripping (using AFNI SkullStrip)
(default expr = ‘a*step(b)’)
Anat SkullStrip pipeline

Mandatory inputs parameters

  • in_file (a string representing an existing file)

    Anatomical image (T1w or T2w) (valid extensions: [.nii, .nii.gz]).

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

Outputs parameters:

  • bias_corrected

    Bias corrected image.

    ex. '/home/username/data/derived_data/n4c_T1w.nii'
    
  • bias_image

    Bias image.

    ex. '/home/username/data/derived_data/n4c_T1w_bias.nii'
    
  • out_file

    Skull stripped image.

    ex. '/home/username/data/derived_data/ss_orig_T1w.nii'
    
  • out_mask

    Head mask.

    ex. '/home/username/data/derived_data/ss_orig_T1w_bin.nii'