Dear all,

I am trying to improve talairach registration and I noticed the following suggestion in the freesurfer wiki:

"If you suspect that the bad transform is the result of a bright neck region, edit the volume to erase the neck and run mritotal on the edited volume. This can be accomplished through simple volume editing: set all the regions to zero where y is greater than a certain value (around 170). This generally works better than using the brain volume. Check your transform using tkmedit"

I would like to try this, but I don't know which command to use. Could someone please fill me in?

Also, after fixing the talairach registration, is it necessary to re-run -autorecon2? Or is it sufficient to over-write the header files and talairach.xfm?

Thanks, Sasha

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