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)
- Calc
(default expr = ‘a*step(b)’)
- Binarize
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'