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I ended up doing split / merge on the GPU:

void percepUnit::applyAlpha() {

    int x,y,w,h;
    cv::gpu::GpuMat tmpImage, tmpMask, tmpAlphaImage;
    std::vector<cv::gpu::GpuMat> channels;

    tmpImage.upload(this->image);
    tmpMask.upload(this->mask);

    cv::gpu::split(tmpImage,channels); // break image into channels
    channels.push_back(tmpMask); // append alpha channel
    cv::gpu::merge(channels,tmpAlphaImage); // combine channels

    tmpAlphaImage.download(this->alphaImage);

    tmpAlphaImage.release();
    tmpImage.release();
    tmpMask.release();

    channels[0].release();
    channels[1].release();
    channels[2].release();
}

I ended up doing split / merge on the GPU:

void percepUnit::applyAlpha() {

    int x,y,w,h;
    cv::gpu::GpuMat tmpImage, tmpMask, tmpAlphaImage;
    std::vector<cv::gpu::GpuMat> channels;

    tmpImage.upload(this->image);
    tmpMask.upload(this->mask);

    cv::gpu::split(tmpImage,channels); // break image into channels
    channels.push_back(tmpMask); // append alpha channel
    cv::gpu::merge(channels,tmpAlphaImage); // combine channels

    tmpAlphaImage.download(this->alphaImage);

    tmpAlphaImage.release();
    tmpImage.release();
    tmpMask.release();

    channels[0].release();
    channels[1].release();
    channels[2].release();
}