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'
Usefull links: