Home

Documentation

GitHub

IntensityClip brick

Clip the intensity range as prescribed by the percentiles

Remove outliers at both ends of the intensity distribution and fit into a given dtype. To more robustly determine the clipping thresholds, data are removed of spikes with a median filter. Once the thresholds are calculated, the denoised data are thrown away and the thresholds are applied on the original image.

Adapted from niworkflows.


Mandatory inputs parameters:

  • in_file (a string representing an existing file)

    Input image which intensity will be clipped (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/T1w.nii'
    

Optional inputs with default value parameters:

  • dtype (one of int16, float32, uint8, optional, default value is int16)

    Output datatype.

    ex. int16
    
  • invert (a boolean, optional, default value is False)

    Finalize by inverting contrast.

    ex. False
    
  • nonnegative (a boolean, optional, default value is True)

    Whether input intensities must be positive.

    ex. True
    
  • p_max (a float, optional, default value is 99.9)

    Percentile for the upper bound.

    ex. 99.9
    
  • p_min (a float, optional, default value is 10.0)

    Percentile for the lower bound.

    ex. 10.0
    

Outputs parameters:

  • out_file (a strings representing a file)

    Path of the clipped image (xtensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/T1w_clipped.nii'
    

Useful links:

IntensityClip niworflow