Denoise brick¶
Denoise image using Non-Local Means algorithm (NLMEANS)¶
The value of a pixel is replaced by an average of a set of other pixel values: the specific patches centered on the other pixels are contrasted to the patch centered on the pixel of interest, and the average only applies to pixels with patches close to the current patch.
Mandatory inputs parameters:
- in_file (a string representing an existing file)
Input file to denoise (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/func.nii'
Optional inputs with default value parameters:
- block_radius (an integer, optional, default value is 5)
The block size will be 2 x block_radius + 1.
ex. 5
- noise_model (rician or gaussian, optional, default value is rician)
Noise distribution model.
ex. rician
- out_prefix (a string, optional, default value is ‘denoise’)
Prefix of the output image.
ex. 'denoise_'
- patch_radius (an integer, optional, default value is 1)
The patch size will be 2 x patch_radius + 1.
ex. 1
Optional inputs parameters:
- in_mask (a string representing an existing file, optional)
Brain mask.
ex. '/home/username/data/derived_data/func_brain_mask.nii'
- noise_mask (a string representing an existing file, optional)
Mask in which the mean signal will be computed.
ex. '/home/username/data/derived_data/func_brain_mask.nii'
- signal_mask (a string representing an existing file, optional)
Mask in which the standard deviation of noise will be computed
ex. '/home/username/data/derived_data/func_brain_mask.nii'
- snr (a float, optional)
Set manually Signal to Noise Ratio. Default is Undefined (ie parameter not used).
ex. 260.0
Outputs parameters:
- out_file (a strings representing a file)
Out image (extensions: [.nii, .nii.gz]).
ex. '/home/username/data/derived_data/denoise_func.nii'
Usefull links: