TopSeg

Main file: surface.py

Skeleton analysis library: remove.c

C-Python interface: cutil/remove.py

Testing for skeleton analysis: testing.py

Operations & Shortcuts

File operations

• Upload target scan (Ctrl+Q): Opens prompt to select a .nii or .nii.gz file to use as the target scan for performing analysis
• Upload reference mesh (Ctrl+W): Opens prompt to select a .nii or .nii.gz file to use as a refernce scan for performing analysis (this can be switched with other uploaded references in the "View" tab)
• Save as (Ctrl+S): Save the current, updated target mesh as a .obj file

Edit operations

• Reset values (Ctrl+R): Resets the target mesh to its original state after it was uploaded
• Isolate CoW Region (Ctrl+E): Clips the mesh by a bounding box (select "Show isolation region" to see the bounding box)
• Show reference CoW (Ctrl+C): Reveals an overlay of an "ideal" CoW to reference during identification operations. This corresponds to the currently selected reference (see the "View" subsection for details)
• Undo (Ctrl+Z): Undoes the last operation (does not stack)
• Expand region on all/X/Y/Z (Ctrl+H/J/K/L): Sets the "Isolation box" slider to grow the isolation region on the specified axis
• Shift region on X/Y/Z (Ctrl+U/I/O): Sets the "Isolation box" slider to shift the isolation region on the specified axis

View operations

• Compute Hausdorff Distance (Ctrl+D): Computes the Hausdorff Distance between the target and reference meshes. The result is logged to the console
• Switch to ref x (Ctrl+<x>): Activates the uploaded reference mesh stored in slot x

Misc buttons

• Largest component: Opens a menu to take the largest n connected components from the target mesh
• Smooth: Performs Laplacian smoothing on the target mesh
• Align: Aligns the reference mesh with the target mesh via Laplacian deformation
• Remove furthest: Removes points on the target mesh greater than the distance specified by the "Identification distance" slider from the reference mesh
• Submit: Performs each of the described analysis operations in the following sequence: threshold, isolate region, take the largest connected component, align the meshes, remove furthest points from the reference mesh