cmind.pipeline.cmind_brain_extract

Functions

cmind_brain_extract(fname_bias[, ...])

Brain extraction using FSL’s BET

cmind.pipeline.cmind_brain_extract.cmind_brain_extract(fname_bias, bet_thresh=0.4, brain_vol=None, extra_AFNI_args='', oname_root='T1W', generate_figures=False, ForceUpdate=False, verbose=False, logger=None, use_AFNI=False)

Brain extraction using FSL’s BET

Parameters:

fname_bias : str

input head volume

bet_thresh : float, optional

bet brain extraction threshold

brain_vol : str, optional

output volume (default is to append _brain to the input volume name)

extra_AFNI_args : str, optional

string of extra arguments to pass on to AFNI (e.g. “-use_skull”)

oname_root : str, optional

output image filename prefix

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)

use_AFNI : bool, optional

if True use AFNI’s 3dSkullStrip instead of BET

Returns:

brain_vol : str

Bias corrected + brain extracted

brain_mask : str

brain mask

Notes

T1-weighted head prior to brain extraction

T1-weighted head after brain extraction

brain mask overlay