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SynthStripMriqc brick

Skull-stripping using SynthStrip tool (mri_synthstrip in FreeSurfer) as done in mriqc v22.06

Adapted from mriqc_1, mriqc_2 and FreeSurfer

If you use this bricks in your analysis, please cite: SynthStrip: Skull-Stripping for Any Brain Image..


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:

  • border_mm (an integer, optional, default value is 1)

    Mask border threshold in mm. Controls the boundary distance from the brain.

    ex. 1
    
  • model (a string representing an existing file, optional, default value is /freeesurfer_path/models/synthstrip.1.pt)

    Alternative model weights.

    ex. '/freeesurfer_path/models/synthstrip.1.pt'
    
  • gpu (a boolean, optional, default value is False)

    Exclude CSF from brain border.

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

Outputs parameters:

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

    Brain-extracted image

    ex. '/home/username/data/raw_data/T1w_desc-brain.nii'
    
  • out_mask (a pathlike object or string representing a file)

    Binary brain mask

    ex. '/home/username/data/raw_data/T1w_desc-brain_mask.nii'
    

Useful links:

mriqc v22.06 - cli

mriqc v22.06 - model

Freesurfer SynthStrip