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In most cases, the automatic surface reconstruction will be already quite good (of course depending on the original quality of the data as well as the preprocessing in BrainVoyager) but not perfect. So normally, one has to add more or less steps of manual correction to gain an improved result. We will describe the steps of manual correction in this part.

First of all, we have to load a VMR project that is resulting from the automatic segmentation procedure. The most important message is that we don’t correct the surface mesh, but the VMR created during the segmentation (representing the grey-white matter boundary) and create a new mesh afterwards.

If we have performed a bridge removal during automatic segmentation, we open the VMR file that ends with BL2 (BL stands for “bridgeless”).

To observe the correspondence between this segmentation result and the original VMR; we again use the “Load Secondary VMR” entry in the “File” menu and choose the Talairach VMR that was the starting point of the segmentation.

First, nothing seems to happen. From the Tab displaying the filename, we can already see there is more than meets the eye (two files are linked, but just one is visualized).
To visualize (blend) both files at the same time, we can use the “F9” button.


There are actually two modes of blending: one with filled and one with non-filled BL2 vmr. To cycle through the modes, we can repeatedly press the F9 button.


To be able to correct flaws in the segmentation result, we first have to find them. We can do this either by browsing the VMRs or by loading the surface reconstruction and to use the link between the surface mesh and the corresponding (original) VMR.

We load the surface reconstruction of the left hemisphere (Recosm_LH) and choose the “Tile” mode in the “Window” menu to show both mesh and VMR at the same time.



To get rid of the Open GL axis visualized in the surface, one can press the A button twice.

To switch to the VMR area that corresponds to a vertex of the surface mesh, we have to activate another mode of the surface tool, namely the “select vertex” mode.

After choosing this mode, the function of the mouse changes. A click on the surface reconstruction will now automatically transfer the crosshair in the VMR to the corresponding position.

Let’s assume we have just clicked on the wrongly selected cerebellar part of the surface reconstruction.
Now, the crosshair shows us where in the VMR this problem is located.

In this case, we could have also easily located the problem by just checking the cerebellum in the VMR right away, but there are more subtle problems in the surface reconstruction that can better be localized in the VMR by using the “select vertex” mode.

For correcting the erroneous segmentation, we need to activate the drawing mode of BrainVoyager. We can find it on the Segmentation tab of the 3D volume tools.

Depending on the size of the “to be corrected” area, we can adapt the mouse size. There is also an option to draw either in 2D or 3D mode. Personally, I prefer to draw what I can see, so I stay in 2D (in-plane) mode. But there may be cases where 3D drawing is just easier.

We open a visualisation of the dataset that makes drawing a little easier by zooming into the sagittal plane (CTRL + right-click).

Drawing comes in two modes: One can either mark new areas in the VMR or delete already selected areas. To do this, we have to hold down the CTRL button when clicking. To delete something, we have to hold down the “SHIFT” button while drawing.
In the screenshot below, we have deleted the cerebellum selection in the VMR. Of course, we have to repeat this procedure for all the slices that contain this problem.

To shift to the next slice, we use the arrow keys (left).

After deleting the problem on all of the slices, we have to do two things:
1. First of all, we have to click the button called “Prepare” to repair any problems we introduced in the line surrounding the (segmented) white matter.

2. Save the new (adjusted) VMR to keep the change. It is advised to save the corrected VMR with a new name to be able to switch back to the original just in case (or to compare to the original).

To create a new mesh out of the corrected Segmentation result, we have to perform three steps:

a) First of all, we click the F8 button to visualize only the corrected BL2.vmr file.

b) We hold down the “Shift” button and click the Create Mesh button in the surface tools on the right side of the screen:

In the “Create Mesh” dialog that pops up, we click the “Reconstruct” button.

This will create an unsmoothed strange looking surface reconstruction that correctly represents the current segmentation result. 

c) To obtain a more brain-like representation, we perform a smoothing operation. This can be started with a combination of the CTRL button and the “Morph Mesh” icon.

It can be easily seen that the most problems in the cerebellar domain have been solved. Of course more problems remain to be detected and corrected…

In the end, it is advised to save the corrected mesh with a new name, e.g. 

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