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The bag_to_pcd file will use the topic that you choose as input, and turn each sensor_msgs/PointCloud2 message on that topic into it's own PCD file.

If you want a single PCD file, you need to use a tool like the point_cloud_assembler (http://wiki.ros.org/laser_assembler) to concatenate all of the clouds together into a single cloud. You can then use the bag_to_pcd tool to save that new single cloud.

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