Welcome to UNRAVEL’s documentation!

Welcome to the documentation of UtiliziNg tRActography to uncoVEr muLti-fixel microstructure (UNRAVEL)!

The code is available at https://github.com/DelinteNicolas/UNRAVEL

To unravel has two meanings :

• to disentangle the fibers of

• to resolve the intricacy, complexity, or obscurity of

With the UNRAVEL framework, we utilize tractography to unravel the microstructure of multi-fixel models.

This repository contains the documentation of the code used to combine macroscopic tractography information with microscopic multi-fixel model estimates in order to improve the accuracy in the estimation of the microstructural properties of neural fibers in a specified tract.

Getting Started

• Tutorials
  • Fixel weight maps
  • Example
  • Adding color to streamline trajectory
  • Create GIFs from 3D volumes
  • Visualize relative contributions to a streamline segment
  • Visualize a streamline average trajectory
• API
  • Quick access
    • unravel
      • unravel.analysis
      • unravel.core
      • unravel.example
      • unravel.stream
      • unravel.utils
      • unravel.viz
  • unravel
    • analysis
      • connectivity_matrix()
      • get_metric_along_trajectory()
    • core
      • angle_difference()
      • angular_agreement()
      • angular_weighting()
      • closest_fixel_only()
      • compute_subsegments()
      • deltas_to_D()
      • fraction_weighting()
      • get_fixel_weight()
      • get_fixel_weight_DIAMOND()
      • get_fixel_weight_MF()
      • get_microstructure_map()
      • get_streamline_weights()
      • get_weighted_mean()
      • get_weighted_sums()
      • main_fixel_map()
      • peak_to_tensor()
      • plot_streamline_metrics()
      • plot_streamline_metrics_old()
      • relative_angular_weighting()
      • t6ToMFpeak()
      • tensor_to_peak()
      • total_segment_length()
      • tract_to_streamlines()
      • volumetric_agreement()
      • voxel_distance()
      • voxels_from_segment()
      • weighted_mean_dev()
    • stream
      • extract_nodes()
      • get_dist_from_median_trajectory()
      • get_roi_sections_from_nodes()
      • get_streamline_number_from_index()
      • remove_outlier_streamlines()
      • remove_streamlines()
      • smooth_streamlines()
    • utils
      • fuse_trk()
      • get_streamline_angle()
      • get_streamline_count()
      • get_streamline_density()
      • normalize_color()
      • peaks_to_RGB()
      • peaks_to_peak()
      • plot_streamline_trajectory()
      • spherical_to_xyz()
      • tensor_to_DTI()
      • tract_to_ROI()
      • xyz_to_spherical()
    • viz
      • compute_alpha_surface()
      • convert_to_gif()
      • export_alpha_surface()
      • grayscale_to_rgb()
      • overlap_volumes()
      • plot_alpha_surface_matplotlib()
      • plot_alpha_surface_pyvista()
      • plot_metric_along_trajectory()
      • plot_nodes_and_surfaces()
      • plot_roi_sections()
      • plot_trk()

Indices and tables

• Index

• Module Index

• Search Page