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
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Jenni Pacheco, M.A.
Massachusetts General Hospital
Athinoula A. Martinos Center for Biomedical Imaging
Bldg. 149, 13th Street, CNY 2301
Charlestown, MA 02129
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