cmind.pipeline.cmind_fieldmap_process¶
Functions
cmind_fieldmap_process (output_dir, ...[, ...]) |
coregister functional images to a structural image, optionally using a |
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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
Parameters: 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)
Returns: fieldmap_vol : str
processed fieldmap
fieldmap_unmasked : str
unmasked processed fieldmap
fieldmap2struct_affine : str
affine transform from fieldmap to structural space
See also
cmind_fieldmap_regBBR
Notes
uses fugue and fslmaths to preprocess the fieldmap image