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As soon as a proper segmentation has been created with a dataset (check this section), one can easily use the reconstructed surface to create a mask file. To do this, one usually loads the reconstructed and smoothed boundary representation between the grey and white matter (“Recosm”.srf). In this case, we load the result for the left hemisphere.


The option to create a mask on the basis of the surface reconstruction can be found in the “Meshes” menu


In the “create cortex based VTC mask” dialog, one can set different properties, e.g. the “sampling depth” of the mask. The default value is from -1 to +3mm.


Using this technique, one may also create a mask for the left and right hemisphere by adding both hemispheres to the surface module. The second mesh can be added by going to Meshes and clicking "Add Mesh".

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