Added bibliography reference for sct_denoising_onlm

[jcohenadad]

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Description

Currently, sct_denoise_onlm gives no indication about the algorithm(s) used for denoising. We should at least add the proper articles where the methods is implemented:

Function usage

julien-macbook:~/sct_testing_data/t2s $ sct_denoising_onlm 

--
Spinal Cord Toolbox (git-jca/3413-run-batch-session-c41958db922273a66764ef88239587f91af3adad)

sct_denoising_onlm 
--

usage: sct_denoising_onlm -i <file> [-h] [-p {Rician,Gaussian}] [-d <int>] [-std <float>] [-o <str>]
                          [-r {0,1}] [-v <int>]

Utility function to denoise images. (Return the denoised image and also the difference between the input and the output.)

MANDATORY ARGUMENTS:
  -i <file>             Input NIFTI image to be denoised. Example: image_input.nii.gz

OPTIONAL ARGUMENTS:
  -h, --help            Show this help message and exit
  -p {Rician,Gaussian}  Type of assumed noise distribution. Default is: Rician. (default: Rician)
  -d <int>              Threshold value for what to be considered as noise. The standard deviation
                        of the noise is calculated for values below this limit. Not relevant if -std
                        value is precised. Default is 80. (default: 80)
  -std <float>          Standard deviation of the noise. If not specified, it is calculated using a
                        background of point of values below the threshold value (parameter d).
  -o <str>              Name of the output NIFTI image.
  -r {0,1}              Remove temporary files. Specify 0 to get access to temporary files.
                        (default: 1)
  -v <int>              Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info
                        messages, 2: Debug mode (default: 1)

The appropriate reference is:

Pierrick Coupe, Jose Manjon, Montserrat Robles, Louis Collins. “Adaptive Multiresolution Non-Local Means Filter for 3D MR Image Denoising” IET Image Processing, Institution of Engineering and Technology, 2011

Linked issues

Fixes #3424

[joshuacwnewton]

Nice and quick fix! 😄