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Rachel often gets really bad headaches. She is afraid of having a brain tumor. I know that she does not have other symptoms, which are common in brain tumor so I do not think it is likely that she has a brain tumor. But I would like to reassure her completely. I would like to say to her, that a brain tumor can be excluded/ruled out by a brain MRI. Which is more understandable for her?

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In your exact phrasing, it would be more natural to say, "ruled out." However, one could say any of the following:

A brain tumor could be ruled out by an MRI.

An MRI can exclude the possibility of a brain tumor.

The MRI allowed for us to eliminate a brain tumor as a potential explanation for your symptoms.