cmind.pipeline.cmind_fieldmap_regBBR

Functions

cmind_fieldmap_regBBR(output_dir, ...[, ...])

coregister functional images to a structural image, optionally using a

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)

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

quantitative CBF volume (top row) registered to MNI standard space (bottom row)

Example of a subject where the registration is substantial improved by fieldmap correction