[Regions] Menu
The [Regions] menu creates, loads, saves, combines, and measures 3D regions of interest (ROIs) for slice overlays, 3D rendering, fiber tracking, and statistics. Right-clicking anywhere in the Assign Regions table opens the same menu.
Overview
The Assign Regions dock lists loaded regions with checkboxes (controlling 2D/3D visibility and inclusion in tracking or batch operations), tracking roles (ROI, ROA, End, Seed, Terminative, NotEnd, Limiting, or unassigned ...; see ROI-Based Fiber Tracking), color swatches, voxel grid dimensions, and toolbar shortcuts such as Atlas… and Segment…. Single-region commands act on the highlighted row, whereas multi-region commands and fiber tracking use all checked rows.
[Regions] Menu Actions
| Menu item | Behavior |
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| Shortcut: Ctrl+Shift+F1. Creates an empty checked region on the active slice’s voxel grid for manual 2D drawing. Select the target diffusion or registered structural slice beforehand so the region inherits that grid. | |
Shortcut: Ctrl+Shift+F2. Loads .nii, .nii.gz, .hdr, .mat, or .txt regions in diffusion or registered slice space, auto-warping mismatched NIfTIs with lowercase mni in the filename. Single masks load as one row; multi-label, .txt-labeled, and 4D NIfTIs split into separate checked rows. |
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Shortcut: Ctrl+Shift+F3. Loads MNI/template-space .nii, .nii.gz, .hdr, .mat, or .txt regions and nonlinearly warps them into subject diffusion space, running template registration first if needed. Caution: NIfTIs whose voxel dimensions already match a native-space FIB load directly without warping. |
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Shortcut: Ctrl+Shift+F5. Saves the highlighted region on its voxel grid as .nii.gz or .nii (binary mask preserving color and tracking role), .mat (3D mask), or .txt (0-based x y z voxel coordinates). Unrecognized file extensions default to .nii.gz. |
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Shortcut: Ctrl+Shift+F6. Combines checked regions onto the first checked region’s voxel grid as a 3D NIfTI parcellation with 1-based label IDs (1..N) and a <stem>.txt label file. Caution: later rows overwrite overlapping voxels; save a 4D NIfTI to preserve overlaps. |
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Shortcut: Ctrl+Shift+F7. Exports each checked region to a chosen folder on its own voxel grid as <region_name>.nii.gz (or .mat / .txt if set as the default ROI format). Give checked regions unique names beforehand to avoid overwriting duplicate filenames. |
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Shortcut: Ctrl+Shift+S. Stacks all checked regions onto the first checked region’s grid as a 4D NIfTI volume with a 0-based <stem>.txt label file, preserving overlapping voxels across volumes. Choose the menu item directly if Ctrl+Shift+S conflicts with [Region Edit][Smoothing]. |
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| Shortcut: Ctrl+Shift+A. Checks every region in the Assign Regions table, showing all regions in 2D/3D views and including them in fiber tracking and checked-region actions. | |
| Shortcut: Ctrl+Shift+U. Unchecks every region in the Assign Regions table, hiding all regions from 2D/3D views and excluding them from fiber tracking and checked-region actions. | |
| Shortcut: Ctrl+Shift+M. Combines two or more checked regions onto the first checked region’s voxel grid, replacing that first row with their union and deleting the other merged rows. Caution: Undo reverts the first row’s mask, but cannot restore deleted rows. | |
| Shortcut: Ctrl+Shift+Backspace. Permanently removes the highlighted region row from the Assign Regions table; row deletion cannot be undone with Undo. | |
| Removes every region row from the Assign Regions table and resets automatic region color cycling. | |
| Shortcut: Ctrl+Shift+V. Duplicates the highlighted region—including its mask, voxel grid, tracking role, and color—and inserts the checked copy directly below it. | |
| Shortcut: Ctrl+Shift+Z. Reverts the last voxel-mask edit (drawing, morphological or boolean edits, flips, or the merged first row’s mask) on the highlighted region. Does not undo row deletion, renaming, or role and color changes. | |
| Shortcut: Ctrl+Shift+Y. Reapplies the most recently undone voxel-mask edit on the currently highlighted region row. | |
Reports passing streamline counts, tract metrics, scalar means, and overlap volume (<stem>_<tract>_t2r.txt) between checked tract bundles and checked regions. Caution: compute streamline fraction from passing streamline counts rather than intersect ratio (voxel coverage); streamlines crossing multiple regions count in each. |
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Reports voxel count, volume (mm^3), diffusion-grid voxel bounds, MNI mm coordinates (once template mapping is active), and nonzero scalar metrics (<stem>_region_stat.txt) across all checked regions, including per-subject means for connectometry databases. |
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Intersects the highlighted region with a chosen built-in atlas and reports full statistics and MNI coordinates (<stem>_region_overlap_stat.txt) for every overlapping parcel without adding rows to Assign Regions. |
For the complete tract-to-region workflow, see Connectome (R2R / T2R).
File Formats and Coordinate Alignment
Multi-label and 4D NIfTI volumes resolve parcel names from companion <stem>.txt or <stem>.json files (or built-in FreeSurfer aparc/aseg tables), while .txt files store 0-based x y z voxel coordinates and .mat files store 3D masks. On native-space datasets, mismatched non-MNI NIfTIs require a matching structural slice loaded first via [Slices][Insert Other Images…]; on template-space datasets, NIfTI header transforms must match MNI space.
Built-In Atlas Parcels
Choose a template at the top of the Assign Regions dock and click Atlas… to search built-in atlases and warp selected parcels onto the active slice grid individually (Add) or as one combined region (Merge&Add). Inspect warped parcels on native-space slices before tracking, and refine inaccurate registrations with [Regions Misc][Manual Atlas Alignment…].
[Regions Misc] Additional Features
Additional region-creation tools live under the Regions Misc menu.
New Region From Thresholding
Creates a checked region on the active slice grid from an intensity threshold (positive values keep brighter voxels; negative values keep darker voxels).
New Region From MNI Coordinate
Creates a spherical region on the active slice grid from millimeter MNI coordinates and a radius in voxels (x y z radius).
Whole Brain Seeding
Creates a checked whole brain Seed region covering suprathreshold anisotropic tissue across the active slice grid.
Editing and moving regions
For morphological filtering, thresholding, boolean set operations, flips, voxel shifts, and 3D placement, see the Region Edit menu and Region Move menu.
Sorting, colors, and alignment
Region sorting, color-table import/export, per-voxel data export, crosshair centering, and atlas alignment tools are documented in the Regions Misc menu, while session step replay is covered in the Records menu.