[Tracts Cluster] Menu

Docs › Menu reference

The [Tracts Cluster] menu renames, sorts, colors, and splits tract bundles in the Tracts list, including unsupervised geometric clustering into sub-bundles. Depending on the command, operations apply to the highlighted bundle row, all checked bundles, or the entire Tracts list.

Names and sorting

Menu item	Behavior
Open Tracts Name…	Loads whitespace-separated bundle names from a `.txt` file and renames rows from the bottom of the Tracts list upward so newly added clusters are named without overwriting earlier bundles. Join multi-word names with underscores instead of spaces (for example, `Arcuate_Fasciculus_L`).
Sort Tracts by Name	Reorders all rows in the Tracts list alphabetically by name while preserving visibility checkboxes and streamlines. Sorting is alphabetical rather than numeric, so `cluster10` appears before `cluster2` unless names are zero-padded.

Cluster colors

Menu item	Behavior
Color All Clusters	Assigns a distinct uniform RGB color to every bundle in the Tracts list (both checked and unchecked rows) and switches Tract Color › Style to Assigned.
Select Color to Current Cluster…	Opens a color picker to apply a uniform RGB color to the highlighted bundle row and switches Tract Color › Style to Assigned. Bundle colors store RGB only; adjust transparency via Tract Color › Opacity.

Cluster files

Menu item	Behavior
Open Cluster Colors…	Reads `R G B` integer triplets (`0–255`) from a `.txt` file, assigns each color in list order to the checked bundles (skipping unchecked rows), and switches Tract Color › Style to Assigned.
Open Cluster Labels…	Splits the highlighted bundle into checked `cluster0`, `cluster1`, … rows using one non-negative integer ID per visible streamline from a `.txt` file, then recolors all bundles. Replacing the selected row cannot be undone with [Tract Edit][Undo].
Open Cluster Values…	Loads one scalar per checked bundle from a `.txt` file (count must match checked rows) and sets Tract Color › Style to Loaded Value. Adjust Tract Color › Min Value and Max Value outside `0–1`; per-streamline values take precedence.
Save Cluster Colors…	Saves the RGB color (`0–255` per channel) of every checked bundle in list order to a `.txt` file (`R G B` per line), omitting unchecked rows.

Clustering

Clustering replaces the highlighted bundle row in place with checked cluster0, cluster1, … rows (largest first) in distinct colors; copy the bundle first with [Tracts][Copy Tracts], as this replacement cannot be undone.

Menu item	Behavior
Single-Linkage Clustering	Groups nearby streamlines in the highlighted bundle by endpoint and length proximity, prompting for max groups and clustering detail and placing leftovers in a hidden `others` row. Although labeled `mm`, detail is applied in voxels (divide desired mm by voxel size).
K-means Clustering	Partitions all streamlines in the highlighted bundle into k-means clusters by start/end endpoints, midpoints, and length, replacing the selected row with no `others` group. Prompts for the maximum group count and outputs up to `256` non-empty clusters.
EM Clustering	Partitions all streamlines in the highlighted bundle using Expectation-Maximization (Gaussian mixture) clustering by start/end endpoints, midpoints, and length, replacing the selected row with no `others` group. Prompts for the maximum group count and outputs up to `256` non-empty clusters.

Atlas recognition and bundle workflows

Unsupervised clustering groups streamlines purely by trajectory geometry; to classify, rename, or split bundles using DSI Studio’s anatomical tractography atlas (or load per-streamline colors and values), see the Tracts Misc menu. To filter clusters by regions or save checked clusters to .tt.gz or .trk files, see the Tract Edit menu and Tracts menu.