if it's consistently in the same part of the pallidum you could manually correct some set of subjects (10 or so) and try building your own atlas and relabeling.

cheers Bruce On Mon, 30 Apr 2012, Julius Juurmaa wrote:

Hello!

This is probably a novice question, but here goes. We are using FreeSurfer to reconstruct the brains of a number of patients, some of whom have a bilateral T1 signal hyperintensity in globus pallidus due to manganese exposure. Problem is, this hyperintensity seems to confuse FreeSurfer and the subcortical segmentation goes a bit off -- parts of the pallidum is considered cerebral white instead (see attachment; globus pallidus is violet, putamen is pink). Is there any way this could be mitigated?

Thank you in advance :)