cmind.pipeline.cmind_bias_correct¶
Functions
cmind_bias_correct(fname_crop, fname_bias[, ...]) |
N4 Bias Field correction |
gauss_bias_corr(im1[, sigma]) |
Divide gaussian smoothed version of image to correct severe bias fields |
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cmind.pipeline.cmind_bias_correct.cmind_bias_correct(fname_crop, fname_bias, ANTS_bias_cmd=None, oname_root='T1W', weight_mask=None, N4_shrinkFactor=3, use_gaussian_prefilt=False, gaussian_sigma=6.0, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)[source]¶ N4 Bias Field correction
Parameters: fname_crop : str
input volume
fname_bias : str
filename to use for output volume. if a directory name is given instead, a file named ${oname_root}_Structural_N4.nii.gz will be created in that folder
ANTS_bias_cmd : str, optional
location of N4BiasFieldCorrection binary
oname_root : str, optional
output filename prefix
weight_mask : str, optional
filename of optional weighting mask for ANTs N4BiasFieldCorrection (see ANTs documentation)
N4_shrinkFactor : int, optional
resolution reduction factor during N4 computations (default=3)
use_gaussian_prefilt : bool, optional
if True, do an initial crude bias field correction based on division by a Gaussian smoothed version of the image
gaussian_sigma : float, optional
if use_gaussian_prefilt = True: sigma for the gaussian smoothing stage (in voxels)
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: fname_bias : str
Bias corrected head
bias_field_vol : str
The bias field
See also
FSL,removal.Notes
T1-weighted head prior to bias correction
T1-weighted head after bias correction