cmind.pipeline.cmind_baselineCBF_coregisterT1

Functions

cmind_baselineCBF_coregisterT1(output_dir, ...)

coregister T1map images to CBF

cmind.pipeline.cmind_baselineCBF_coregisterT1.cmind_baselineCBF_coregisterT1(output_dir, CBF_nii, T1concat_N4_brain_nii, T1_map_nii, I0_map_nii, T1_NRMSE_map_nii=None, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)

coregister T1map images to CBF

Parameters:

output_dir : str

directory in which to store the output

CBF_nii : str

filename of Baseline CBF volume to register to

T1concat_N4_brain_nii : str

filename containing the brain extracted 4D TI image series used during T1 fitting

T1_map_nii : str

filename containing the T1_map volume to register

I0_map_nii : str

filename containing the I0_map (M0) volume to register

T1_NRMSE_map_nii : str or None, optional

filename containing the T1 fit NRMSE_map volume to register

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:

T1map_reg2CBF : str

filename of the T1_map volume that has been registered to CBF_nii

I0map_reg2CBF : str

filename of the I0_map volume that has been registered to CBF_nii

T1_NRMSE_map_reg2CBF : str or None

filename of the NRMSE map that has been registered to CBF_nii

T1map2CBF_affine : str

affine transform of the T1_map to the BaselineCBF image

Notes

T1map image registered to the BaselineCBF volume