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GradientThreshold brick

Computes a threshold from the histogram of the magnitude gradient image using a segmentation of the input image

Adapted from mriqc anatomical workflow.


Mandatory inputs parameters:

  • in_file (a string representing an existing file)

    Input image (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/T1w.nii'
    
  • seg_file (a string representing an existing file)

    Segmentation file (valid extensions: [.nii, .nii.gz]). For example, a tissue class map from the brick FastSegment (FSL).

    ex. 'home/username/data/derived_data/T1w_seg.nii'
    

Optional inputs with default value parameters:

  • prefix (a string, optional, default value is ‘’)

    Prefix of the output image.

    ex. ''
    
  • suffix (a string, optional, default value is ‘_grad’)

    Suffix of output image.

    ex. '_grad'
    

Outputs parameters:

  • out_file (a strings representing a file)

    Path of the thresholded scan (extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/T1w_grad.nii'
    

Useful links:

Gradient threshold mriqc