niftkBiasFieldCorrection.py

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This script is for N3 or N4 bias field correction using Boyes et al. Neuroimage 2008 normalization process. 

Usage: niftkNormalization.py -in input_file -out output_file 

Mandatory Arguments:
 
  -in     : is the input file 
  -out      : is the output file 

Optional Arguments: 
  -mask     : is the mask atlas file
  -atlas    : is the atlas data file
  -n4     : runs N4 bias field correction method instead than N3, by default: N3
  -debug    : debug mode doesn't delete temporary intermediate images
  -same     : Always use the same temp directory for computing (this option is useful mixed with -debug)