cmind.pipeline.cmind_fieldmap_regBBR¶
Functions
cmind_fieldmap_regBBR (output_dir, ...[, ...]) |
coregister functional images to a structural image, optionally using a |
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cmind.pipeline.cmind_fieldmap_regBBR.
cmind_fieldmap_regBBR
(output_dir, lowres_vol, reg_struct_file, T1_vol, T1_brain_vol, WMseg_vol, use_bbr=True, bbr_schedule_file=None, Fieldmap_vol_processed=None, Fieldmap_vol_unmasked=None, fieldmap2struct_affine=None, unwarpdir=None, EPI_echo_spacing=None, SENSE_factor=None, generate_figures=True, 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
lowres_vol : str
image filename for the “moving” image
reg_struct_file : str
filename of the existing .csv registration structure
T1_vol : str
filename of the “fixed” head image (before brain extraction)
T1_brain_vol : str
filename of the “fixed” brain image
WMseg_vol : str
filename of the white matter partial volume estimate image
use_bbr : bool, optional
use BBR registration for FLIRT
bbr_schedule_file : str, optional
filename of flirt schedule to use (e.g. $FSLDIR/etc/flirtsch/bbr.sch)
Fieldmap_vol_processed : str or None, optional
filename of the fieldmap volume
Fieldmap_vol_unmasked : str or None, optional
filename of the unmasked fieldmap volume
fieldmap2struct_affine : str or None, optional
filename of the affine transform of the fieldmap to structural space
unwarpdir : {‘x’,’y’,’z’,’x-‘,’y-‘,’z-‘}, optional
phase encoding direction during the readout
EPI_echo_spacing : float, optional
EPI echo spacing (seconds)
SENSE_factor : float, optional
SENSE acceleration factor
generate_figures : bool,optional
if true, generate overlay images summarizing the registration
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: LRtoHR_Affine_fname : str or None
If no fieldmap is used, this is the transform from lowres->structural
HRtoLR_Affine_fname : str or None
If no fieldmap is used, this is the transform from structural->lowres
LRtoHR_Warp_fname : str or None
If a fieldmap is used, this is the warp from lowres->structural
HRtoLR_Warp_fname : str or None
If a fieldmap is used, this is the warp from structural->lowres
regBBR_dir : str
directory where the registration outputs were stored (= output_dir input)
See also
cmind_fieldmap_process
Notes