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Threshold brick

Makes a binary mask image at a given threshold

Mandatory inputs parameters:

• in_files (a list of items which are files)

  Path of the scans to be processed (valid extensions: [.nii, .nii.gz]).

  ex. ['/home/username/data/raw_data/c1Anat.nii',
       '/home/username/data/raw_data/c2Anat.nii',
       '/home/username/data/raw_data/c3Anat.nii',
       '/home/username/data/raw_data/c4Anat.nii',
       '/home/username/data/raw_data/c5Anat.nii']
  

Optional inputs with default value parameters:

• GM_filtering (a boolean, optional, default value is True)

  A boolean to indicate if the input images list (in_files input parameter) is filtered to retain only grey matter (based on the name of the image which must contain c1 in the first part, according to the SPM syntax).

  ex. True
  

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

  Prefix of the output image.

  ex. ''
  

• suffix (a string, optional, default value is ‘_002’)

  Suffix of the output image.

  ex. '_002'
  

• threshold (a float between 0 and 1, optional, default value is 0.3)

  Value of the rate defining the applied threshold (everything above becomes 1 and everything below becomes 0, as usual for a mask). The value of the actual threshold is thus the maximum value of the image multiplied by this rate.

  ex. 0.3
  

Outputs parameters:

• out_files

  Scan name after application of the threshold. The input files extension (in_files parameter) is kept.

  ex. '/home/username/data/derived_data/c1Anat_002.nii'