better to do it from inside recon-all so as to get it's bookkeeping. Run with -finalsurfs

doug

Brian T. Quinn wrote:

hi Lars-

perhaps you need to delete more voxels. make sure you're editting the brain volume, and you can just run make_final_surfaces if you only want to regenerate a new pial surface (takes [a lot] less time).

thanks, brian

On Mon, 12 Sep 2005, Lars Tjelta Westlye wrote:

...

Dear all,

I am trying to edit the pial surface by editing/deleting voxels in the brain volume within the pial surface ('labeled' as a part of cortex), but clearly are parts of dura when manually inspected. When I rerun the last automatic procedures (fix, make_final, morph), and check the pial surface, nothing has appeared to have changed. The voxels I deleted are gone, though the pial surface still looks the same.

How can I fix this without having to regenerate/reconstruct all my subjects? (I have approx. 100). Any tip?

I am by the way using the Freesurfer version from june (?) 2005, and due to time restrictions I am not considering changing to the latest version for this project.

Thanks a lot!

Best wishes,

Lars Tjelta Westlye University of Oslo

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