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FilteringTrack brick

Filter tracking data

Filter a whole-brain fibre-tracking data set such that the streamline densities match the FOD lobe integrals

(mrtrix tcksift command)

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Mandatory inputs parameters:

• in_tracks (a pathlike object a string representing an existing file)

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

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

• in_fod (a pathlike object a string representing an existing file)

  Input image containing the spherical harmonics of the fibre orientation distributions

  ex. '/home/username/data/raw_data/wm_fod_norm.mif'
  

Optional inputs with default value parameters:

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

  Output file suffix

  ex. 'sift'
  

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

  Provide this option (in conjunction with -act) to heuristically downsize the fibre density estimates based on the presence of GM in the vox

  ex. False
  

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

  Do NOT dilate FOD lobe lookup tables; only map streamlines to FOD lobes if the precise tangent lies within the angular spread of that lobe

  ex. False
  

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

  Add an additional FOD lobe to each voxel, with zero integral, that covers all directions with zero / negative FOD amplitudes

  ex. False
  

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

  Remove FOD lobes that do not have any streamline density attributed to them

  ex. False
  

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

  Output statistics of execution per iteration to a .csv file

  ex. False
  

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

  Output statistics of execution per iteration to a .csv file

  ex. False
  

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

  Output a text file containing the binary selection of streamlines

  ex. False
  

Optional inputs parameters:

• proc_mask (string representing an existing file, optional)

  Provide an image containing the processing mask weights for the model.

  ex. '/home/username/data/derived_data/mask.mif'
  

• act_image (string representing an existing file, optional)

  Provide an ACT five-tissue-type segmented anatomical image to derive the processing mask

  ex. '/home/username/data/derived_data/5tt_coreg.mif'
  

• fd_thresh_value (an integer, optional)

  Fibre density threshold

  ex.
  

• term_ratio_value (an integer, optional)

  Termination ratio - defined as the ratio between reduction in cost function, and reduction in density of streamlines.

  ex.
  

• term_mu_value (an integer, optional)

  Terminate filtering once the SIFT proportionality coefficient reaches a given value

  ex.
  

Outputs parameters:

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

  The output filtered track file

  ex. '/home/username/data/derived_data/tracks_sift.tck'
  

• csv_file_out (a pathlike object or string representing a file, optional)

  A csv file with the output statistics of execution per iteration

  ex. '/home/username/data/derived_data/tracks_tcksift_stats.csv
  

• mu_file_out (a pathlike object or string representing a file, optional)

  The final value of SIFT proportionality coefficient mu in a text file

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

• selection_file_out (a pathlike object or string representing a file, optional)

  A text file containing the binary selection of streamlines

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

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Useful links:

mrtrix tcksift