cmind_fieldmap_process(output_dir, ...[, ...]) coregister functional images to a structural image, optionally using a
cmind.pipeline.cmind_fieldmap_process.cmind_fieldmap_process(output_dir, fieldmap_nii_rads, fieldmap_nii_mag, T1_head_vol, T1_brain_vol, deltaTE=0.0023, unwarpdir='y', ForceUpdate=False, verbose=False, logger=None)[source]

coregister functional images to a structural image, optionally using a fieldmap to correct distortions along the phase encoding direction


output_dir : str

directory in which to store the output

fieldmap_nii_rads : str

fieldmap volume in rad/s

fieldmap_nii_mag : str

magnitude image corresponding to fieldmap_nii_rads

T1_head_vol : str

filename of the “fixed” head image (before brain extraction)

T1_brain_vol : str

filename of the “fixed” brain image

deltaTE : str, optional

echo time difference used to generate fieldmap_nii_rads

unwarpdir : {‘x’,’y’,’z’,’x-‘,’y-‘,’z-‘}, optional

phase encoding direction during the readout

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)


fieldmap_vol : str

processed fieldmap

fieldmap_unmasked : str

unmasked processed fieldmap

fieldmap2struct_affine : str

affine transform from fieldmap to structural space

See also



uses fugue and fslmaths to preprocess the fieldmap image


Processed fieldmap volume