Hi Josh

catastrophic subcortical failures are pretty rare. What kind do you mean? You will need to diagnose the cause before figuring out how to fix it. I'm happy to take a look if you upload it

cheers Bruce

On Tue, 5 Feb 2013, Joshua Lee wrote:

Hi All,

I'm just wondering what kind of protocol people are using to address the situation when Freesurfer has a catastrophic failure in accurately segmenting the sub-cortical structures. While manual editing is an option, are there upstream changes that might improve the subcortical segmentation is re-run (e.g. wm control points?). Drop them? If conducting an analysis of Freesurfer subcortical segmentation in some population, how have people handled these cases?

Thanks,

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