A wide range of conditions are characterised by focal neurological symptoms, yet the pathophysiolgy often remains poorly understood. This thesis has focussed on applying functional neuroimaging in clinical groups. Migraines with aura are amongst the most common conditions posing a significant burden to sufferers. Elevated connectivity was detected in the visual cortex of migraine with aura patients, potentially complementing one of the leading proposed mechanisms for attacks. Minor strokes patients are also affected by focal symptoms after events which in some cases can be prolonged. Altered connectivity was observed in a number of regions reflecting previous findings for acute stroke. A group of transient ischaemic attack patients were also analysed, revealing subtle differences necessitating further study. Lastly disorders of consciousness pose acute challenges for treatment and ongoing care. Task based imaging was applied to form a more accurate picture of residual cognition. Additionally the correlation between measures derived from resting state data and cerebral glucose consumption was explored.