SkullStrip brick¶

Using AFNI 3dSkullStrip, from T1-weighted MRI images, extract the brain from surrounding tissue¶

Mandatory inputs parameters:

in_file (a string representing an existing file)
A 3D-T1 file to skull-strip (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/T1w.nii'

Optional inputs with default value parameters:

output_type (NIFTI or NIFTI_GZ, optional, default value is NIFTI)
Format of the output image (one of NIFTI, NIFTI_GZ).

- NIFTI: *.nii

- NIFTI_GZ: *.nii.gz
ex. NIFTI
out_prefix (a string, optional, default value is ‘ss’)
Prefix of the output image.
ex. 'ss_'

Outputs parameters:

out_file (a strings representing a file)
Out image (extensions: [.nii, .nii.gz]).
ex. '/home/username/data/derived_data/ss_T1w.nii'

Useful links: