One thing you can try:
If the selection can be represented as a sequence of 2d-vectors, you can think of it as a polygon. Allocate a new 1-channel image that will be your mask and fill it with 0. Then use
void cvFillPoly(CvArr* img, CvPoint** pts, int* npts, int contours, CvScalar color, int lineType=8, int shift=0)
documented on
http://opencv.willowgarage.com/documentation/drawing_functions.html
to draw a non-zero region on the mask image to represent the selected part of the image.
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