[Regions Misc] Menu

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The [Regions Misc] menu creates threshold, MNI-coordinate, and whole-brain seed masks, manages region colors and list sorting, exports voxel-level metrics, and refines subject-to-atlas alignment. For loading and saving masks, editing shapes, or constraining tractography, see the Regions menu, Region Edit menu, Region Move menu, and ROI-Based Fiber Tracking.

Create regions

Menu item	Behavior
New Region From Thresholding…	Creates a checked visualization-only (Type `...`) region on the active slice from an intensity threshold pre-filled with Otsu’s estimate (use a negative value to select lower intensities instead). Set Type to constrain tracking; canceling leaves an empty `New Region` row.
New Region From MNI Coordinate…	Creates a checked spherical region (Type `...`) on the active slice from `x y z radius`, computing subject-to-MNI registration automatically if needed. Note the mixed units: center `(x, y, z)` is in MNI mm, whereas `radius` is in active-slice voxels.

Region colors

Menu item	Behavior
Load Region Color…	Loads display colors (`0`–`255`) for all listed regions from a `.txt` file using positional `R G B` / `R G B A` lines or tab-separated `Name R G B A` rows. Mismatched counts, unknown or duplicate names, or invalid values abort the load unchanged.
Save Region Color…	Saves the assigned `R G B A` display color (`0`–`255`) of every listed region in row order to a `.txt` file, ready to reload with [Regions Misc][Load Region Color…].

Sort regions

Sorting reorders checked regions within their checked row slots while leaving unchecked rows in place; selecting the same sort again reverses ascending and descending order.

Menu item	Behavior
Sort By Name	Sorts checked regions alphabetically by Name, reversing between ascending and descending order when selected again.
Sort By Size	Sorts checked regions by physical volume in mm³ from smallest to largest, reversing to largest-first when selected again.
Sort By X	Sorts checked regions by center-of-mass X position in diffusion voxel space (reversing on repeat selection). Avoid sorting empty (`0`-voxel) checked regions, which lack a center of mass.
Sort By Y	Sorts checked regions by center-of-mass Y position in diffusion voxel space, reversing order when selected again.
Sort By Z	Sorts checked regions by center-of-mass Z position in diffusion voxel space, reversing order when selected again.

Seeding and voxel data

Menu item	Behavior
Whole Brain Seeding	Creates a checked `whole brain` region (Type `Seed`) on the active slice from primary anisotropy using the current Otsu Threshold in Tracking Parameters, letting you inspect, edit, or save the seed mask before tracking.
Save Voxel Data As…	Exports per-voxel data for the highlighted region row to a tab-delimited `.txt` table containing diffusion voxel coordinates, resolved fiber unit vectors, and values from all loaded diffusion metrics and slices. Large masks can produce very large text files.

Mapping and alignment

Menu item	Behavior
Move Slices To Current Region	Centers the 2D and 3D slice crosshairs on the highlighted region’s median voxel position across X, Y, and Z so outlier fragments do not pull the view off target. Has no effect if no non-empty region is highlighted.
Load MNI mapping…	Loads a precomputed nonlinear subject-to-template mapping file (`.mz`) matching the open FIB dataset and updates subsequent atlas parcellations and MNI region operations to use the loaded warp.
Manual Atlas Alignment…	Opens an interactive dialog to align the subject’s maps to the active template (unavailable for QSDR datasets already in template space). Accepting recomputes subject-to-MNI registration, replaces any cached `.mz` mapping on disk, and opens the atlas region dialog.