Basal ganglia and thalamus signal abnormalities occur in a wide variety of conditions. Ischemia/hypoxia, metabolic disorders and toxins, particularly those that affect the respiratory chain, have a predilection for affecting the basal ganglia as they are highly metabolically active.
They can be thought of in terms of the specific signal abnormality or according to the underlying disease processes.
Signal intensity changes
Although there is significant overlap between some of these lists they are discussed separately.
increased T2 signal in the basal ganglia (usually also results in decreased T1 signal)
Pathological processes
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infection/inflammatory
viruses (e.g. flavivirus encephalitis)
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ischemia/hypoxia/hypoglycemia
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neurodegenerative/metabolic
autoimmune encephalitis (e.g. anti-D2 dopamine antibodies)
neurodegeneration with brain iron accumulation (NBIA) (e.g. PKAN)
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toxins
alcohol: e.g. Wernicke encephalopathy
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respiratory chain toxins
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tumors