Brain Innovation

support portal


BrainVoyager Volume Space Creating Masks Grey Matter Mask ("quick and dirty")

Grey Matter Mask ("quick and dirty")

First, we have to load a VMR, in this case a talairachized dataset.


To get a quick grey matter selection without using the automatic segmentation, we peel the brain out of the head using the corresponding entry in the “Volumes” menu.



Notice that this procedure may not automatically work out in every dataset. The procedure relies on a proper data quality (esp. with respect to the distribution of intensities in the different matter types). The user can partially influence this when working with the contrast and brightness settings in BrainVoyager. We save the result as a new VMR.

The resulting VMR includes white as well as grey matter. To “get rid“ of the white matter, we have to mark it first, as is explained in this article.

To get rid of the white matter, we use the “Reload Non-Marked” button to get rid of the marked white matter.



We save the new dataset.

The resulting VMR is nicely stripped off the skull as well white matter. Now, we want to mark the grey matter to be able to finally create a mask out of it.

We adapt the Min and Max values to the grey matter, position the mouse inside the grey matter and click the Grow Region button.


We expand the selection by reducing the Min value and clicking the expand button.


In the current selection, the cerebellum is still included, so we may decide to just leave it into the dataset or to remove it manually. This can be done by holding down the Shift button while drawing with the mouse.
We open the “Options” of the Segmentation tab to save the grey matter just marked as a VOI.


Clicking the “Define VOI” button, we create a VOI.



Now, we have to turn the VOI into a mask file to be able to use it in the GLM procedure. We click the “Options” button in the VOI analysis window.
On the “VOI Functions” tab, we will find the corresponding option to create a mask from one or multiple VOIs.


We use the “Create MSK…” button to create a mask out of the loaded VOI. Please make sure that the proper VTC is linked when clicking this button to make sure the dimensions of the mask fit.


BrainVoyager will automatically color the mask and report the number of voxels included in the mask in the INFO tab of the global tools.

Using the “F8” button, we can switch back and forth between the VMR and the mask.

You are here: HomeBrainVoyagerVolume SpaceCreating Masks ≫ Grey Matter Mask ("quick and dirty")