Dear Bharti,
T1 weighted sequences are typically optimized for a good contrast between cortical white and grey matter. However, the consistence of subcortical structures differs from that of cortical grey matter (no layers, more axons - note that cortical grey matter also includes axons, otherwise the cell bodies would be useless ;), which influences the physical properties relevant for MRI. Thus the contrast of the acquired data is often quite poor. If you adjust the sequence you might still have some problems if the templates / tissue probability maps have a low contrast and/or a relatively high smoothing kernel (good for cortex, but too large for small structures).
Hope this helps,
Helmut
|