Cancer Imaging Phenomics Toolkit (CaPTk)  1.8.1
Bias Correction (ITK filter)

This tool corrects an image, already loaded in CaPTk, for magnetic field inhomogeneities using a non-parametric method [1]. Users have the option to switch between N3 [1] and N4 [2] correction.

REQUIREMENTS:

  1. An image loaded in CaPTk.

USAGE:

  1. Load an image in CaPTk.
  2. Launch the tool using the 'Preprocessing' -> 'BiasCorrection' menu option.
  3. Specify the output filename.
  4. Click on 'Save'.
  5. The output image is saved in the specified folder and automatically loaded in CaPTk.
  6. This can also be used from the command line:
    ${CaPTk_InstallDir}/bin/Preprocessing.exe -i C:/test/image.nii.gz -o C:/test/image_biasCorr.nii.gz -n4
    

Reference:

  1. J.G.Sled, A.P.Zijdenbos, A.C.Evans. "A nonparametric method for automatic correction of intensity nonuniformity in MRI data", IEEE Trans Med Imaging. 17(1):87-97, 1998, DOI:10.1109/42.668698
  2. N.J.Tustison, B.B.Avants, P.A.Cook, Y.Zheng, A.Egan, P.A.Yushkevich, J.C.Gee. "N4ITK: improved N3 bias correction." IEEE Trans Med Imaging. 29(6): 1310-1320, 2010, DOI:10.1109/TMI.2010.2046908