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ExtractROIbyLabel brick

Extract a specific ROI from a segmentation file using labels

Mandatory inputs parameters:

• in_file (a string representing an existing file)

  Input segmented image (valid extensions: [.nii, .nii.gz]). For example a binary brain mask or an image of tissues or structures segmentation (each region should be associated to an integer).

  ex. '/home/username/data/raw_data/native_structures_sub-001.nii'
  

Optional inputs with default value parameters:

• labels (a list of integer, default is [1])

  List of the labels of the ROI to extract.

  ex. ['47', '48']
  

• save_each_roi (a boolean, optional, default value is False)

  Save a each regions as a NIfTI file.

  ex. True
  

• save_concate_roi (a boolean, optional, default value is False)

  Save a concatenation of all the ROI extracted as a NIfTI file.

  ex. True
  

Outputs parameters:

• out_files (list of pathlike object or string representing a file)

  Extracted ROI files

  ex. ['/home/username/data/raw_data/native_structures_sub-001_47.nii',
       '/home/username/data/raw_data/native_structures_sub-001_48.nii'
    ]
  

• out_concate (a pathlike object or string representing a file)

  Image with all ROI

  ex. '/home/username/data/raw_data/native_structures_sub-001_concate_47_48.nii'