This is a long-standing problem with radiology.
For lungs, you simply ask the patient to hold their breath for 10 seconds or so. This usually accomplishes the task of fixating the lungs.
For the heart, you hook up some electrodes to the patient which measures the rhythm of the heart. Then you synch those electrodes to the CT/MRI. So the machine knows where the heart is in time, and then when you reconstruct the image, you pick only the images taken at the same phase of the rhythm.
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