Hi Krista
1. it's hard to answer 1 as it depends on the magnitude of the error, how accurate the fix would make the surfaces and what you are going to use the surfaces for. Allison or Louis or someone can correct me but in general I think we only edit a small % of the surface.
2. If the skull isn't included in the aseg or the pial surface you don't have to worry about it.
3. this should be fine
cheers Bruce
On Mon, 9 Sep 2013, krista kelly wrote:
Just wanted to resend these questions to see if anyone has any answers. Thanks! I am doing cortical thickness and surface area analyses and had a few questions regarding editing the borders.
- Is it reasonable to edit every (big and small) error that I find? Basically, how much a difference
would it make in terms of the surface area and cortical thickness values if I did not edit the smaller errors?
- If the skull hasn't been completely stripped, but is not designated as either white or gray matter,
do I need to adjust the thresholding for extracting the brain and re-extract? The only situation in which I feel this would be a problem is when doing whole brain analyses.
- Would it make a difference to the data if I initially ran recon-all using freesurfer version 5.0
and then, after editing the segmentations/labels/skullstripping, reran autorecon 2,or 3 using freesurfer version 5.1?
If anyone could answer any or all of these questions that would be great! Krista