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)
- Mask
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'
Usefull links: