nighres.brain.dots_segmentation(tensor_image, mask, atlas_dir, wm_atlas=1, max_iter=25, convergence_threshold=0.005, s_I=0.023809523809523808, c_O=0.5, max_angle=67.5, save_data=False, overwrite=False, output_dir=None, file_name=None)[source]

DOTS segmentation

Segment major white matter tracts in diffusion tensor images using Diffusion Oriented Tract Segmentation (DOTS) algorithm.

  • tensor_image (niimg) – Input image containing the diffusion tensor coefficients in the following order: volumes 0-5: D11, D22, D33, D12, D13, D23
  • mask (niimg) – Binary brain mask image which limits computation to the defined volume.
  • atlas_dir (str) – Path to directory where the DOTS atlas information is stored. The atlas information should be stored in a subdirectory called ‘DOTS_atlas’ as generated by
  • wm_atlas (int, optional) – Define which white matter atlas to use. Option 1 for 23 tracts [2] and option 2 for 39 tracts [1]. (default is 1)
  • max_iter (int, optional) – Maximum number of iterations in the conditional modes algorithm. (default is 20)
  • convergence_threshold (float, optional) – Threshold for when the iterated conditonal modes algorithm is considered to have converged. Defined as the fraction of labels that change during one step of the algorithm. (default is 0.002)
  • s_I (float, optional) – Parameter controlling how isotropic label energies propagate to their neighborhood. (default is 1/42)
  • c_O (float, optional) – Weight parameter for unclassified white matter atlas prior. (default is 1/2)
  • max_angle (float, optional) – Maximum angle (in degrees) between principal tensor directions before connectivity coefficient c becomes negative. Possible values between 0 and 90. (default is 67.5)
  • save_data (bool, optional) – Save output data to file. (default is False)
  • overwrite (bool, optional) – Overwrite existing results. (default is False)
  • output_dir (str, optional) – Path to desired output directory, will be created if it doesn’t exist.
  • file_name (str, optional) – Desired base name for output files without file extension, suffixes will be added.

Dictionary collecting outputs under the following keys (type of output files in brackets)

  • segmentation (array_like): Hard segmentation of white matter.
  • posterior (array_like): POsterior probabilities of tracts.

Return type:



Algorithm details can be found in the references below.


[1]Bazin, Pierre-Louis, et al. “Direct segmentation of the major white matter tracts in diffusion tensor images.” Neuroimage (2011) doi:
[2]Bazin, Pierre-Louis, et al. “Efficient MRF segmentation of DTI white matter tracts using an overlapping fiber model.” Proceedings of the International Workshop on Diffusion Modelling and Fiber Cup (2009)

Examples using nighres.brain.dots_segmentation