Voxel Edit

The Voxel Edit mode in Freeview includes tools which can be used to remove, add or alter the value of voxels in volumes loaded into Freeview. You can create custom labels or an entire manual segmentation composed of many regions with custom names. The Voxel Edit tools can be used to make typical Freesurfer edits to correct surface topology and segmentation errors, but we recommend you use the Recon Edit mode instead which has all the tools listed below but with certain restrictions implemented to insure recon edits are recognized by recon-all. Please read the ReconEdit page for more details on the restrictions implemented to the tools described below.

Voxel edit mode is located just above the layer list and underneath the menu bar, or can be found under Action -> Voxel Edit in the menu bar. Alternatively, you can use the shortcut key Alt+E.

Selecting Voxel Edit mode will prompt the Voxel Edit pop-up window to appear, which will include the following button bar:

The freehand voxel edit tool allows you to erase and add voxels of a specified value. This is probably the most common voxel edit tool which you will use. Clicking on the Freehand tool button in the Voxel Edit pop-up window toolbar displays several options. Several relevant keyboard shortcuts are listed at the bottom of the Voxel Edit pop-up window as well. Below is a snapshot of the default Freehand tools options.

Brush size: Determines the size of the uniform brush stroke and the number of voxels which can be drawn/erased simultaneously. Examples of the first 5 brush sizes. Note the number of voxels each brush size covers.

Recon editing: Checking this box will change and lock the Brush value to 255, and the Eraser value to 1. It will also enable the voxel draw range limits, with Low set to 5 and high set to 250. This is useful for when making typical edits to Freesurfer recons, where any voxels added to the white matter mask (wm.mgz) should have a value of 255, and any erased voxels from the white matter mask or brainmask volumes should set to 1 so that Freesurfer can identify manual edits. The draw range limits prevent drawing over existing voxels in the white matter mask which have certain values which are useful to Freesurfer and for troubleshooting.

*** For extended editing involving the correction of surface topology and segmentation errors, we strongly suggest you use the Recon Edit mode instead ***

Brush value: Sets value of newly drawn voxels.

Eraser value: Sets value of erased voxels (typically 0 or 1).

Reference: Description N/A

Constrain drawings to...: Description N/A

Only draw on...: Designates the lowest and highest possible values of existing voxels which can be drawn over. Only voxels inside low and high settings can be edited.

Do not draw...: Designates the lowest and highest possible values of existing voxels which can not be drawn over regardless of brush value setting. Only voxels outside low and high settings can be edited.

Flood fill multiple...: Description N/A

The PolyLine voxel edit tool can be used to quickly create a rough trace of an area. With the PolyLine tool you can draw a series of points connected by straight lines. Any voxel which the series of straight lines cuts through will be set to the current brush value. Each new point in the series can be added with a left-click. To end the series, right-click anywhere in the main display window. After ending a PolyLine series, a line between the first and last points will be created completing the PolyLine series. The PolyLine tool can be useful for drawing ROI labels or segmenting sub-cortical structures. Note that addition of each point of the outline is considered to be independent of the others and can be undone in the reverse order they were created. After completing a PolyLine series, you can then easily fill it in by holding the crtl key and left-clicking inside the region outlined with the PolyLine tool.

Below is an example where a new label volume was created with Color map set to Lookup Table, and overlaid on top of a norm.mgz volume (1). The PolyLine tool was then used to outline the hippocampus with a brush value of 53 (2 & 3), and then the hippocampus outline was filled in with the flood fill tool (crtl+left-click) (4).

Similar to the PolyLine tool, the Livewire tool can be used to quickly create a rough trace of an area, but each segment of the outline you draw has some flexibility and will not necessarily be straight. Each new point in the series can be added with a left-click. To end the series, right-click anywhere in the main display window. Unlike the PolyLine tool, after ending a Livewire series, a line between the first and last points will not be created. Note that addition of each segment of the outline is considered to be independent of the others and can be undone in the reverse order they were created.

Below is an example where the Livewire tool has been used to draw a middle temporal gyrus label which could be converted to a surface label. The cortical label was drawn on a new label volume overlaid on top of the brainmask volume. The pial and white matter surfaces are displayed in first and last panel simply as a reference.

The Flood Fill tool allows you to fill-in or erase connected voxels which share an identical value or some degree of similarity determined by you before hand. It is worth knowing that at any time when using any of the other voxel edit tools, you can hold down crtl and you cursor will change to the Flood Fill tool. Holding down the crtl key and left clicking on a voxel will carry out the default Flood Fill operation. This will change the voxel you clicked on and any connected voxels with identical value to the current Brush value setting. With the Flood Fill tool selected in the Voxel Edit pop-up window, you can adjust a couple parameters. Most notably, the tolerance threshold and the eraser value, as well as imposing some additional limitations on the Flood Fill tool.

Brush value: Sets value of filled voxels.

Eraser value: Sets value of erased voxels (typically 0 or 1) selected with fill operation.

Reference: Description N/A

Tolerance: Extent to which (if any) neighboring voxels without identical values are included in the fill operation. At 0% only connected voxels equal to the value of the clicked voxel will be filled, with higher tolerance values leading to larger filled regions (less conservative).

Constrain drawings to...: Description N/A

Only draw on...: Designates the lowest and highest possible values of existing voxels which can be filled in. Only voxels inside low and high settings can be included in the filled-in region.

Do not draw...: Designates the lowest and highest possible values of existing voxels which can not be filled in regardless of brush value setting. Only voxels outside low and high settings can be included in the filled-in region.

Flood fill multiple...: Description N/A