Defacing with the FreeSurfer ‘mri_deface’ command.

pydcmio.deface.mri_deface.deface(input_files, outdir, reference_file=None, verbose=0, fs_config='/i2bm/local/freesurfer/SetUpFreeSurfer.sh')

Deface MRI head images using the FreeSurfer ‘mri_deface’ command.

Parameters:

input_files: list of str

Input MRI head images to be defaced.

outdir: str

The output folder.

reference_file: str (optional, default None)

The image that must be used as reference if more than one image have been supplied as input.

verbose: int (optional, default 0)

The verbosity level.

fs_config: str (optional, default DEFAULT_FREESURFER_PATH)

The FreeSurfer configuration file.

Returns:

deface_files: list of str

The defaced input MRI head images.

snap_files: list of str

The corresponding snaps that can be used to check the defacing result.