Documentation: [Tracts], [Tracts Cluster], and [Tracts Misc] Menus

This document provides a detailed overview of the [Tracts], [Tracts Cluster], and [Tracts Misc] menus, their features, functionalities, and associated commands based on the source code and UI definitions.

[Tracts] Menu

The [Tracts] menu provides comprehensive tools for managing, saving, and analyzing fiber tracts. It includes options for loading, saving, and processing tracts, as well as generating reports and analyzing connectivity.

Main Actions

Menu Item Command Description
Open Tract open_tract Load a tract file for visualization and analysis.
Open MNI Space Tracts open_mni_tracts Load tract files aligned with MNI space coordinates.
Load Built-In Atlas load_built_in_atlas Import tracts from a pre-defined atlas.
Save Tract As save_tract_as Save the currently selected tract to a file.
Save All Tracts As save_all_tracts_as Save all loaded tracts into a single file.
Save All Tracts As Multiple Files save_all_tracts_as_multiple_files Save each tract as an individual file.
Check All Tracts check_all_tracts Mark all tracts for processing or visualization.
Separate Deleted separate_deleted Separate deleted tracts into a different group.
Copy Track copy_track Duplicate the selected tract.
Merge All merge_all Merge all tracts into a single tract.
Delete Tract delete_tract Delete the selected tract.
Delete All Tracts delete_tract_all Delete all loaded tracts.
Tracts to Region tracts_to_region Convert selected tracts into a region of interest (ROI).
Endpoints to Region endpoints_to_region Convert tract endpoints into a region of interest (ROI).
Filter by ROI filter_by_roi Filter tracts based on their overlap with a region of interest (ROI).
Tract Analysis Report tract_analysis_report Generate a detailed analysis report for the selected tracts.
Connectivity Matrix connectivity_matrix Generate a connectivity matrix based on tracts.
Open Connectivity Matrix open_connectivity_matrix Load and visualize a saved connectivity matrix.
Statistics statistics Calculate statistical properties of the selected tracts.

Save Tracts (Misc)

This submenu provides advanced options for saving tracts and their associated data.

Menu Item Command Description
Save Tracts in Current Mapping save_tracts_in_current_mapping Save tracts in the current coordinate system.
Save Tracts in Template Space save_tracts_in_template_space Export tracts aligned with the template space.
Save Tracts in MNI Coordinates save_tract_in_mni_coordinates Save tracts transformed into MNI coordinates.
Save End Points As save_end_points_as Export tract endpoints as a separate file.
Save Endpoints in Current Mapping save_endpoints_in_current_mapping Save endpoints in the current mapping.
Save Endpoints in MNI Coordinates save_endpoints_in_mni_coordinates Save endpoint data in MNI space.
TDI Diffusion Space tdi_diffusion_space Generate tract density imaging (TDI) in diffusion space.
TDI Subvoxel Diffusion Space tdi_subvoxel_diffusion_space Create TDI in subvoxel resolution.

Save Along Tract Index

This submenu provides options for saving tracts categorized by specific indices.

Menu Item Command (Tooltip) Description
Save Along Tract Index save_along_tract_index Save tract data categorized by specific indices (e.g., FA, MD).

[Tracts Cluster] Menu

The [Tracts Cluster] menu provides tools for clustering and organizing tracts based on different criteria.

Actions

Menu Item Command Description
Open Tracts Name open_tracts_name Open a file containing tract names for display or modification.
Sort Tracts By Names sort_tracts_by_names Sort loaded tracts alphabetically by their names.
Assign Colors For Each assign_colors_for_each Automatically assign a unique color to each tract.
Set Cluster Color set_cluster_color Set a specific color for a selected cluster of tracts.
Open Cluster Colors open_cluster_colors Load a predefined color scheme for tract clusters.
Open Cluster Labels open_cluster_labels Load cluster labels from a file.
Open Cluster Values open_cluster_values Load cluster-specific values (e.g., statistical properties).
Save Cluster Colors save_cluster_colors Save the current cluster color scheme to a file.
Hierarchical Clustering hierarchical_clustering Perform hierarchical clustering to group tracts based on similarity.
K-Means Clustering k_means_clustering Use k-means clustering to partition tracts into k clusters.
EM Clustering em_clustering Apply expectation-maximization (EM) clustering for probabilistic grouping.

[Tracts Misc] Menu

The [Tracts Misc] menu provides additional tools for refining, modifying, and organizing tracts.

Actions

Menu Item Command Description
Trim Tracts trim_tracts Remove excess parts of tracts based on topology.
Cut Tracts cut_tracts Cut selected tracts using a defined plane or region.
Split Tracts split_tracts Divide a tract into smaller sub-tracts.
Merge Tracts merge_tracts Combine multiple tracts into a single bundle.
Negate Tracts negate_tracts Invert the selection of tracts.
Extract Subset extract_subset Extract a subset of tracts based on specific criteria.
Generate ROI from Tract generate_roi_from_tract Create a region of interest (ROI) from selected tracts.
Visualize Tract Density visualize_tract_density Generate a visual representation of tract density in a volume.

Notes