I found Imagick::clipPathImage and Imagic::clipImage did not work as I had expected. I thought they would just clip the path and throw away the extra data and you are done. Not the case.
Here is how I was able to use a clipping path:
$img = new Imagick("/Path/To/Test/Image.psd");
$geometry = $img->getImageGeometry();
$draw = new ImagickDraw();
$composite = new Imagick($path);
$composite->newImage( $geometry['width'], $geometry['height'], new ImagickPixel("white"), 'png');
$composite->compositeImage($img, imagick::COMPOSITE_COPY, 0, 0);
Then doing any resizing or creating thumbnails from the resulting image disregarded all the previous commands so I "saved" it and started with a new Imagick object
$clipped = new Imagick();
I'm sure there is a simpler way, but this took me awhile to get right and there were some hurdles to cross so I hope it is able to help someone on the way.
This is all the convert equivalent of:
$ convert Test.psd -fill white -colorspace rgb -draw "color 0 0 reset" -clip -colorspace rgb -draw "Image Copy 0,0 0,0 'Test.psd'" OutputFile.png