BE, Clonezilla allows that (,no cost, imaging to a file, copying only the used areas of the disk, rather than free space.) When you are starting it, choose the "Device to Image" option, rather than the "Device to Device" mode. Edit -> The only thing I've never really looked at closely is how large the image created is - I'd be shocked if it isn't roughly the size of the used space, because I'm sure I would have noticed otherwise - but it's never been an important factor when I've needed device to image mode.
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