First of all, Ct thorax generally doesn't cover whole part of neck and axilla. If pathology is suspected in neck portion, special advise should be given to radiologist to include neck portion also in scan.
Second thing lymphadenopathy absent in CT doesn't mean it was completely absent, as sensitivity and specificity of test is not 100% i.e, false positive and false negative pictures both can occurs.
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clinical assessment oxygen saturation and symptoms of patients are also important here.