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EditingTrack brick

Perform various editing operations on track files

(mrtrix tckedit command)


Mandatory inputs parameters:

  • in_tracks (a list of items which are a pathlike object a string representing an existing file)

    Inputs track file(s)(valid extensions: [.tck]).

    ex. ['/home/username/data/raw_data/tracks.tck']
    

Optional inputs with default value parameters:

  • suffix (a string, default value is edited, optional)

    Output file suffix

    ex. 'edited'
    
  • inverse (a boolean, default value is False, optional)

    Output the inverse selection of streamlines based on the criteria provided; i.e. only those streamlines that fail at least one selection criterion, and/or vertices that are outside masks if provided, will be written to file

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

    Only test the ends of each streamline against the provided include/exclude ROIs.

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

    Get an output text scalar file containing streamline weights.

    ex. False
    

Optional inputs parameters:

  • roi_excl (string representing an existing file or a tuple of the form: (a float, a float, a float, a float), optional)

    Specify an exclusion region of interest, streamlines that enter ANY exclude region will be discarded.

    ex. '/home/username/data/derived_data/roi.mif'
    
  • roi_incl (string representing an existing file or a tuple of the form: (a float, a float, a float, a float), optional)

    Specify an inclusion region of interest, streamlines must traverse ALL inclusion regions to be accepted.

    ex. '/home/username/data/derived_data/roi.mif'
    
  • roi_incl_ordered (string representing an existing file or a tuple of the form: (a float, a float, a float, a float), optional)

    Specify an inclusion region of interest, streamlines must traverse ALL inclusion_ordered regions in the order they are specified in order to be accepted.

    ex. '/home/username/data/derived_data/roi.mif'
    
  • roi_mask (string representing an existing file or a tuple of the form: (a float, a float, a float, a float), optional)

    Specify a masking region of interest. If defined,streamlines exiting the mask will be truncated.

    ex. '/home/username/data/derived_data/DWI_brainmask.mif'
    
  • maxlength (a float, optional)

    The maximum length of any streamline in mm.

    ex. 26.0
    
  • minlength (a float, optional)

    The minimum length of any streamline in mm.

    ex. 2.0
    
  • number (an integer, optional)

    The desired number of selected streamlines to be propagated to the output file.

    ex. 20000
    
  • skip (an integer, optional)

    Omit this number of selected streamlines before commencing writing to the output file.

    ex. 500
    
  • maxweight (an integer, optional)

    The maximum weight of any streamline

    ex. 10
    
  • minweight (an integer, optional)

    The minimum weight of any streamline

    ex. 2
    
  • tck_weights_in (string representing an existing file, optional)

    Specify a text scalar file containing the streamline weights

    ex. '/home/username/data/derived_data/tck_weight.txt'
    

Outputs parameters:

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

    The output track file

    ex. '/home/username/data/derived_data/tracks_edited.tck'
    
  • tck_weights_out (a pathlike object or string representing a file, optional)

    Output text scalar file containing streamline weights

    ex. '/home/username/data/derived_data/tracks_tck_weight.txt'
    

Useful links:

mrtrix tckedit