Having worked in hospitals for nearly 40 years, I can tell you there is a style of writing that transcends normal rules of punctuation.
If there remains a strong clinical concern for mass in the chest, then follow up will be obtained or alternatively a CT scan of the chest will be performed.
In a medical setting, not using a comma after the "or" would be quite routine particularly as "alternatively" sets the next section apart. Otherwise, use a comma - it will be ignored anyway since doctors have to read quickly!!
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