Denoising tools

Noise generation

animaNoiseGenerator adds Gaussian or Rician noise to a scalar image at a user specified SNR (an external reference input image is necessary to compute the average reference signal value). The -n may be used to output multiple samples of noisy images from the input.

Example: this adds Gaussian noise (relative to the average signal computed from refSignalImage.nii.gz) to Image.nii.gz. It will provide as outputs 10 images named OutputImage_??.nii.gz

animaNoiseGenerator -i Image.nii.gz -o OutImage.nii.gz -G -n 10 -r refSignalImage.nii.gz

NL-Means denoising

NL-Means denoising is an implementation of the two papers from the team to denoise images corrupted by Gaussian [1] or Rician noise [2].

NL-Means for scalar images

animaNLMeans implements patch-based denoising for scalar images, considering it as a single image without a temporal dimension. It includes all parameters described in [1], including patch half size (real size being 2N+1), patch half search neighborhood, beta parameter for weighting, … One can choose between [1] and [2] with the -W option.

Example: this performs denoising of Image.nii.gz with the default parameters, a beta parameter of 0.5 and assuming Rician noise.

animaNLMeans -i Image.nii.gz -o OutImage.nii.gz -W 1 -b 0.5

NL-Means for images with a temporal dimension

animaNLMeansTemporal works in the same way as animaNLMeans except that it considers the last dimension of the input image as a temporal dimension and therefore processes each temporal volume independently (useful e.g. for DWI images).


  1. Pierrick Coupé, Pierre Yger, Sylvain Prima, Pierre Hellier, Charles Kervrann, Christian Barillot. An optimized blockwise nonlocal means denoising filter for 3-D magnetic resonance images. IEEE Transactions on Medical Imaging. 27(4): 425-441. 2008.
  2. Nicolas Wiest-Daesslé, Sylvain Prima, Pierrick Coupé, Sean Patrick Morrissey, Christian Barillot. Rician noise removal by non-Local Means filtering for low signal-to-noise ratio MRI: applications to DT-MRI. 11th International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, 5242 (Pt 2), pp.171-179, 2008.