cmind.pipeline.cmind_rigid_coregister

Functions

cmind_rigid_coregister(output_nii, ...[, ...]) Rigid registration of moving_nii to fixed_nii
cmind.pipeline.cmind_rigid_coregister.cmind_rigid_coregister(output_nii, fixed_nii, moving_nii, flirt_args='-cost corratio -dof 6 -searchrx -60 60 -searchry -60 60 -searchrz -60 60 -interp sinc', generate_figures=True, ForceUpdate=True, verbose=False, logger=None)[source]

Rigid registration of moving_nii to fixed_nii

Parameters:

output_nii : str

filename for the registered volume output

fixed_nii : str

filename of fixed (reference) volume to register to

moving_nii : str

filename of moving volume to be registered

flirt_args : str, optional

additional command line arguments to FLIRT

generate_figures : bool, optional

if true, generate additional summary images

ForceUpdate : bool,optional

if True, rerun and overwrite any previously existing results

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

Returns:

output_nii : str

filename of the registered volume

output_affine : str

filename of the affine transformation used during registration