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Anat_skullstrip_synthstrip pipeline

Create a brain-extraction workflow using SynthStrip (Freesurfer)

Adapted from mriqc v22.06 synthstrip workflow


Pipeline insight

Anat_skullstrip_synthstrip pipeline combines the following pipelines and processes:
- Bias field correction (using ANTs N4BiasFieldCorrection)
(default for first correction: dimension = 3, rescale_intensities = True,
default for second correction: dimension = 3, n_iterations = [50] * 4)
- Skull Stripping (using Freesurfer Synthstrip)
Anat SkullStrip synthstrip 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_image

    Bias image.

    ex. '/home/username/data/derived_data/n4c_T1w_clipped_bias.nii'
    
  • out_corrected

    Bias corrected image.

    ex. '/home/username/data/derived_data/n4c_T1w_clipped.nii'
    
  • out_brain

    Skull stripped image.

    ex. '/home/username/data/derived_data/ss_n4c_T1w_clipped.nii'
    
  • out_mask

    Head mask from SynthStrip.

    ex. '/home/username/data/derived_data/pre_n4c_T1w_clipped_desc_brain_mask.nii'
    

Useful links:

SynthStrip

mriqc synthstrip workflow