cmind.pipeline.cmind_segment

Functions

cmind_segment(fname_brain[, seg_name, ...]) Segmentation using FSL’s FAST
cmind.pipeline.cmind_segment.cmind_segment(fname_brain, seg_name=None, reg_struct=None, use_prior=False, use_alt_prior=False, use_prior_throughout=False, resegment_using_N4mask=False, ANTS_bias_cmd=None, generate_figures=False, ForceUpdate=False, verbose=False, logger=None)[source]

Segmentation using FSL’s FAST

Parameters:

fname_brain : str

input brain volume

seg_name : str

root name to use for the output filenames

reg_struct : str or dict, optional

registration structure

use_prior : bool, optional

prior image: see FSL Fast documentation

use_alt_prior : bool, optional

alternative prior images: see FSL Fast documentation

use_prior_throughout : bool, optional

use priors throughout: see FSL Fast documentation

resegment_using_N4mask : bool, optional

rerun N4 bias correction on a mask weighted toward white matter then resegment

ANTS_bias_cmd : str, optional

path to ANTs N4BiasFieldCorrection binary (used if resegment_using_N4mask=True)

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)

Returns:

WM_vol : str

WM partial volume estimate

GM_vol : str

GM partial volume estimate

CSF_vol : str

CSF partial volume estimate

Notes

../_images/Segmentation_Slices_squeezed.png

Examples of segmentation partial volume estimates (Top: CSF, Middle: GM, Bottom: WM)