Hi Alex,

I've looked into your problem and I do see what you mean. Here's a brief run-down on the different flags.

-autorecon2-cp begins with -normalization2, using your control points. Problem is it WILL write over the brain volume, creating a new one. It then finishes the stream from here, using -keepwmedits when running the -segmentation step to preserve any editing you've done to the wm volume.

-autorecon2-wm begins with a newly edited wm volume and first runs -fill generating a new filled.mgz volume and then completes the stream from here.

-autorecon2-pial simply reruns -makefinalsurfs and -cortribbon to remake the final surfaces, reflecting any editing that was done to the brain volume.

We are currently working on a new flag to combat this problem, but until then - here are my suggestions for you now.

1. If your brain editing is necessary for achieving an accurate wm volume:

a. set your control points and run recon-all -normalization2 -usecontrolpoints to fix the intensity. b. make your edits to the brain.mgz volume c. run recon-all -segmentation -keepwmedits to generate a new wm, reflecting your changes to the brain volume and keeping any previous wm edits. d. you will then still need to complete the rest of the stream. You can do this using this command: recon-all -autorecon2 -nosubcortseg -nonormalization2 -nosegmentation.

2. If your brain editing is only necessary for obtaining an accurate pial surface:

a. set your control points and run recon-all -autorecon2-cp (you can add in -nofinalsurfs and -nocortribbon if you are sure that your control points won't fix your pial surfaces without edits. This will save a little processing time, but those steps don't take a tremendous amount of time) b. make your brain volume edits (if the problem wasn't fixed with the control points) c. run recon-all -autorecon2-pial to regenerate your final surfaces.

hope this helps! Jenni

On Tue, 18 Oct 2005, Fornito, Alexander wrote:

Hi, Is there any way to run autorecon2-cp with an edited brain volume so that it concurrently adjusts the pial surface. Everytime I try to run it, it seems to erase my edits to the brain volume. Howeever, running autorecon2-wm or -pial, uses the brain edits. Some help on this would be much appreciated as it would save me a lot of re-processing time! Thanks, Alex

Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au

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