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[Tracts Misc] Menu
The [Tracts Misc] menu provides post-tracking tools to clean up bundles, bridge or resample streamlines, mirror coordinates, manage per-streamline colors and values, and match pathways against the built-in tractography atlas. For file I/O, interactive editing, and clustering, see the Tracts, Tract Edit, and Tracts Cluster menus.
Tract cleanup
| Menu item | Behavior |
|---|---|
| Combines all bundle rows—checked or unchecked—that share an identical name into the first matching row. Unlike [Tracts][Merge All], this groups strictly by bundle name and cannot be undone with [Tract Edit][Undo]. | |
Removes near-duplicate streamlines from all checked bundles within a specified voxel distance threshold (default 1.0 voxel; undoable with [Tract Edit][Undo]). Both streamlines in each matched pair are removed, so avoid routine use on sparse or whole-brain bundles. |
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Removes streamlines shorter than a physical millimeter (mm) cutoff (default 0.5 mm, or two or fewer points) from all checked bundles. Unlike Delete Repeated Tracks (which uses voxels), this filter uses mm and can be undone with [Tract Edit][Undo]. |
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| Prunes stray branches and prematurely stopping fibers from all checked bundles by keeping only streamlines that reach both main endpoint zones (undoable with [Tract Edit][Undo]). Use only on single two-endpoint pathways, never on fanning or whole-brain bundles. |
Tract geometry
| Menu item | Behavior |
|---|---|
Bridges broken segments in the highlighted bundle when endpoint separation (voxels, > 2.0) and alignment angle (degrees, > 0; default 4 30) meet your thresholds. Modifies streamlines in place without undo and can falsely join crossing fibers, so duplicate the bundle first. |
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Resamples streamline vertices across all checked bundles to a uniform voxel spacing (default 0.5 voxels) while preserving start and end points. Enter a strictly positive value (never 0.0); resampling overwrites geometry in place and cannot be undone. |
Move tracts
Mirrors the highlighted bundle in place when its row is also checked; repeat the same flip to restore original coordinates, as flipping is not undoable.
[Tracts Misc][Move Tracts]
| Menu item | Behavior |
|---|---|
| Mirrors all streamlines in the highlighted (and checked) bundle across the diffusion grid’s left–right (X) axis in place. | |
| Mirrors all streamlines in the highlighted (and checked) bundle across the diffusion grid’s anterior–posterior (Y) axis in place. | |
| Mirrors all streamlines in the highlighted (and checked) bundle across the diffusion grid’s inferior–superior (Z) axis in place. |
Tract colors and values
| Menu item | Behavior |
|---|---|
Loads per-streamline R G B colors (0–255 triplets in a .txt file) into the highlighted bundle row. Automatically switches Tract Color › Style in Options to Assigned to display the imported colors. |
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Loads one scalar value per visible streamline from a .txt file into the highlighted bundle row and sets Tract Color › Style to Loaded Value. The value count must match the bundle’s visible streamline count. |
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Saves the highlighted bundle’s assigned per-streamline R G B colors (0–255) to a .txt file, one triplet per line. Exports only stored painted or imported colors, not dynamic directional or metric colormaps. |
For per-bundle colors and scalar values across multiple checked rows, see the Tracts Cluster menu.
Tract recognition
| Menu item | Behavior |
|---|---|
Matches the highlighted bundle (or the first row if none is selected) against the built-in tractography atlas, running template registration if needed. Opens a summary of matched pathway percentages (with clipboard copy and .txt export) without altering the bundle. |
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| Classifies each checked bundle against the built-in tractography atlas (running template registration if needed) and renames each row to its highest-matching pathway without splitting or deleting streamlines. Use [Tracts Misc][Merge Tracts by Name] afterward to combine identically named rows. | |
| Splits the highlighted bundle by matching each streamline to the built-in tractography atlas, replacing the original row with separate colored rows per pathway. Unrecognized streamlines are discarded and splitting cannot be undone, so duplicate the bundle first to keep unmatched fibers. |
Atlas recognition reports the closest-matching reference pathway; always verify results against underlying anatomy, or use AutoTrack to reconstruct named pathways directly.