cmind.pipeline.cmind_brain_extract¶
Functions
cmind_brain_extract (fname_bias[, ...]) |
Brain extraction using FSL’s BET |
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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)[source]¶ 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